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Hoekom is dit moeiliker om plantgenome te volgorde as dieregenome?

Hoekom is dit moeiliker om plantgenome te volgorde as dieregenome?


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Plante blyk minder komplekse organismes as diere te wees, maar ten spyte daarvan is daar minder plantgenome in volgorde. Is dit omdat plantgenome meer kompleks is, byvoorbeeld in terme van regulatoriese streke en transposons wat volgordebepaling moeiliker maak, of is daar ander redes waarom die aantal opeenvolgende plantgenome kleiner is as diere?


Die skrywers van hierdie 2012-oorsigartikel som die probleem goed op in hul inleiding:

In teenstelling met die geweldige vordering in deurset, bly die samestelling van volgordebepaling-lesings 'n aansienlike poging, veel groter as wat die volgorde-pogings alleen sou voorstel [22-24]. Groot komplekse plantgenome bly 'n besonder moeilike uitdaging vir de novo-samestelling om 'n verskeidenheid biologiese, berekenings- en biomolekulêre redes. Plantgenome kan byna 100 keer groter [25] wees as die voëlgenome [26], vis [27] of soogdiergenome [28]. Daarbenewens kan hulle baie hoër ploïdie hê, wat na raming in tot 80% van alle plantspesies voorkom [29], en hoër koerse van heterosigositeit en herhalings [30] as hul eweknieë in ander koninkryke. Verder kan die geeninhoud in plante baie kompleks wees, soos getoon deur die teenwoordigheid van groot geenfamilies en oorvloedige pseudogene met byna identiese volgordes afgelei van onlangse heelgenoomdupliseringsgebeure en transposonaktiwiteit [13]. Plante is geneig om hoë kopie-chloroplaste en mitochondria-organelle te hê, wat die samestelling van hul oorblyfsels in die kerngenoom bemoeilik en skewe bedekkingsvlakke [12]. Ten slotte is dit dikwels baie moeilik om groot hoeveelhede hoë-gehalte DNA uit plantmateriaal te onttrek, wat dit moeilik maak om behoorlike biblioteke vir volgordebepaling voor te berei.

Van: Schatz, Witkowski en McCombie. "Huidige uitdagings in de novo plantgenoomvolgordebepaling en samestelling". Genome Biology (2012). 13:243

Soos u kan sien, is al die belangrikste redes aangeraak deur die verskillende mense wat onder u vraag kommentaar gelewer het.


3. Uitdagende kenmerke van plantgenome

3.1. Monsterneming

3.2. Genoomgrootte en kompleksiteit

3.3. Oordraagbare elemente

3.4. Heterosigositeit

3.5. Poliploïdie

3.6. Gene-inhoud en genefamilies

270 kbp van die mitochondriale genoom ingevoeg in Chromosoom 2 van Arabidopsis [62]. Maar geenduplisering word beskou as 'n groot krag in die ontstaan ​​van nuwe gene en genetiese funksies. By wyse van voorbeeld, die voorkoms van C4-fotosintese het uit die C3-baan ontwikkel en het onafhanklik by ten minste 50 geleenthede tydens plant-evolusie verskyn [63]. Ander voorbeelde van geenduplisering is die opvallende toename in die aantal stysel-geassosieerde gene in papaja (39) met betrekking tot Arabidopsis (20), of die uitgebreide aantal kinase familielede, sitochrome P450 en die ensieme wat betrokke is by plant sekondêre metabolisme [ 64]. Onlangse vergelykings van Arabidopsis-, populier-, wingerd-, papaja- en rysgenome het egter geskat dat die angiosperm-voorouer tussen 12 000 en 14 000 gene moet bevat [15]. As gevolg hiervan is meer as die helfte van plantgene werklik 'n geenfamilie, 45% van hulle met dieselfde funksie maar verskillende uitdrukkingspatrone [65]. Spesifieke strategieë word vereis om allele van paraloë te onderskei wanneer natuurlike heterosigotiese isolate opeenvolgend gemaak word, hoewel dit nie na verwagting in die nabye toekoms 'n baie belowende sukses sal hê nie [59]. Verder, die teenwoordigheid van uit-paraloë wat deur duplisering geproduseer word voor die divergensie van twee lyne en in-paraloë wat in elke lyn geproduseer word, tesame met die veelvuldige rondes van poliploïdie in plantlyne, beklemtoon hierdie probleme aangesien divergensie tussen paraloë teen verskillende tempo's voorkom.

3.7. Nie-koderende RNA's

3.8. Wyd verspreide herhalende reekse (lae kompleksiteit reekse)

250 tandem duplisering elk van

10 kbp op Chromosoom 2 van Arabidopsis) en tussen chromosome (bv.

4 Mbp lang streke tussen Chromosome 2 en 4, of 700 Mbp lang streke tussen Chromosome 1 en 2 in Arabidopsis

3 Mbp by die termini van die kort arms van Chromosome 11 en 12 in rys, asook Chromosome 5 en 8 in sorghum) [62,74].


Wetenskap sê: Waarom wetenskaplikes plant- en dieregenome prys

Hierdie Dinsdag, 12 Februarie 2019-foto wys manlike muskiete by die Vosshall-laboratorium by die Rockefeller-universiteit in New York. In 2018 het navorsers by die laboratorium 'n baie verbeterde beskrywing van die DNS-kode vir 'n besonder gevaarlike spesie muskiet gepubliseer: Aedes aegypti, wat berug is vir die verspreiding van Zika, dengue en geelkoors. Associated Press

Op hierdie Dinsdag, 12 Februarie 2019-foto, praat navorser Ben Matthews in 'n kamer wat muskiete in die Vosshall-laboratorium by die Rockefeller-universiteit in New York huisves. Om die DNS-volgorde te ken, laat wetenskaplikes dit met geenredigeringstegnieke manipuleer, sê Matthews, wat deel was van die internasionale span wat die verfynde beskrywing van die muskietgenoom in November 2018 gepubliseer het. Associated Press

Op hierdie Dinsdag 12 Februarie 2019-foto paar PhD-student Krithika Venkataraman muskiete deur mannetjies in 'n houer te blaas wat wyfies by die Vosshall-laboratorium van die Rockefeller-universiteit in New York huisves. Navorsers het die bekende grootte van 'n familie gene wat muskiete help om inligting uit hul omgewing, soos die reuk van mense, byna te verdubbel. Dit was "heeltemal, verbasend, onverwags," sê Leslie Vosshall. Associated Press

Op hierdie Dinsdag, 12 Februarie 2019-foto, sorteer navorsingsassistent Anjali Pandey muskietlarwes met bewerkte DNS in die Vosshall-laboratorium by die Rockefeller-universiteit in New York. Hul oë het rooi of blou onder haar mikroskoop gegloei om aan te dui dat hulle genetiese modifikasies dra. Associated Press

Hierdie ongedateerde mikroskoopbeeld verskaf deur navorser Ben Matthews van Rockefeller Universiteit in Februarie 2019 wys muskietlarwes wat by die Vosshall-laboratorium in New York bestudeer is. In November 2018 het navorsers by die laboratorium 'n baie verbeterde beskrywing van die DNS-kode vir 'n besonder gevaarlike spesie muskiet gepubliseer: Aedes aegypti, wat berug is vir die verspreiding van Zika, dengue en geelkoors. (Ben Matthews/Rockefeller Universiteit via AP) Associated Press

NEW YORK -- Sowat elke week, blyk dit, publiseer wetenskaplikes die unieke DNS-kode van een of ander wese of plant. Net in Februarie het hulle die genoom vir die aarbei, die papiermoerbeiboom, die grootwithaai en die Antarktiese swartvin-ysvis ​​gepubliseer.

Hulle het ook aangekondig dat hulle, danksy 'n skarefinansieringsveldtog, die genoom van Lil BUB, 'n vroulike kat met 'n groot internetaanhang, geproduseer het.

Dit het gevolg op 'n noemenswaardige vooruitgang in Januarie: 'n verbeterde genoom vir die axolotl, 'n salamander wat bekend is vir die hergroei van afgesnyde ledemate en ander liggaamsdele.

Wetenskaplikes het genome vir 'n geruime tyd ontbloot. Die eerste van 'n dier - 'n wurm - het in 1998 gekom. Nou het die tegnologie ver genoeg gevorder dat wetenskaplikes verlede jaar 'n projek aangekondig het om die genome te produseer vir alle lewensvorme op Aarde behalwe bakterieë en eensellige organismes wat archaea genoem word. Hulle het dit 'n "maanskoot vir biologie" genoem.

Maar wat is die punt daarvan om nuwe genome te ontbloot?

Vir wetenskaplikes bied 'n gedetailleerde blik onder die kap van hul gunsteling organisme 'n vastrapplek om die diepste geheime van hul voorwerpe van aandag te leer, dit lei tot ontdekkings oor hoe die lewe werk, en moontlik hoe om siektes te voorkom.

Neem die muskiet. Laat verlede jaar het navorsers 'n baie verbeterde beskrywing van die DNS-kode vir 'n besonder gevaarlike muskietspesie gepubliseer: Aedes aegypti, wat berug is vir die verspreiding van Zika, dengue en geelkoors.

Dié prestasie kom uit die ontleding van die DNS van 80 muskietbroers. Hulle is in Leslie Vosshall se laboratorium by die Rockefeller-universiteit in New York gebore, waar duisende muskiete onlangs in hokke geswerm het toe Krithika Venkataraman nog probeer maak het.

Sy het 'n buis wat soos 'n strooitjie by haar mond uitgesteek het in 'n deursigtige kubus gevul met muskietemannetjies gesteek. Toe het sy herhaaldelik sowat 30 mannetjies op 'n slag in die buis gesuig. Sy het hulle getel en toe in 'n ander kubus geblaas wat wyfies gehuisves het. Kort voor lank het die twee geslagte gepaar.

Jy kan aan 'n genoom dink as 'n instruksieboek vir die bou van 'n lewende wese. Die taal daarvan is 'n vierletter-alfabet, wat staan ​​vir die vier verbindings wat die binnekant van die DNA-molekule uitmaak. Die volgorde van daardie verbindings langs die molekule is die kode wat dit "woorde" skep wat ons gene noem.

Die muskietgenoom, byvoorbeeld, is ongeveer 1,28 miljard letters lank, 'n bietjie minder as die helfte van die lengte van die menslike weergawe. Om die DNS-volgorde te ken, laat wetenskaplikes dit met geenredigeringstegnieke manipuleer, het Ben Matthews van die Vosshall-laboratorium gesê, wat deel was van die internasionale span wat die verfynde beskrywing van die muskietgenoom verlede November gepubliseer het.

En sodra navorsers daardie weergawe van die DNS-kode begin ontleed het, het ontdekkings begin verskyn.

- Hulle het die bekende grootte van 'n familie gene wat muskiete help om inligting uit hul omgewing, soos die reuk van mense, byna te verdubbel. Dit was "heeltemal, verbasend, onverwags," het Vosshall gesê. (Vosshall se salaris word betaal deur die Howard Hughes Medical Institute, wat ook die Associated Press Health & Science Department ondersteun.)

Verdere studie kan verrassings openbaar oor waaraan muskiete aandag gee, het Vosshall gesê. En dit kan lei tot beter lokmiddels vir muskietvalle, sowel as beter afweermiddels. Miskien kan wetenskaplikes iets "10 000 keer meer walglik" vir 'n muskiet vind as die ou bystand, DEET, het sy gesê.

- Hulle het nuwe besonderhede gevind oor gene wat sommige muskiete toelaat om sekere insekdoders te weerstaan. Dit is 'n moontlike stap om te voorspel watter insekdoders nutteloos sal wees om sekere bevolkings te beveg, sowel as 'n potensiële leidraad om met nuwe chemiese wapens teen die insek vorendag te kom.

- Hulle het voorheen onbekende teikens vir 'n groot klas insekdoders gevind. Dit kan die deur oopmaak vir die ontwerp van nuwe weergawes wat muskiete teiken terwyl voordelige insekte gespaar word en minder risiko vir mense inhou.

– Hulle het die soektog na genetiese variante verklein wat verhoed dat sommige Aedes aegypti-muskiete mense met dengue besmet, ’n ernstige griepagtige siekte wat miljoene jaarliks ​​siek maak. As daardie variante geïdentifiseer kan word, kan wetenskaplikes genetiese ingenieurswese gebruik om hulle in sommige muskiete te reproduseer, wat dan vrygestel kan word om die variante deur wilde bevolkings te versprei, het Vosshall gesê. Hierdie variante, of ander, kan ook werk om dreigemente van verspreiding van Zika en geelkoors te verminder, het Vosshall en Matthews gesê.

- 'n Soortgelyke strategie kan gebruik word om muskietbevolkings mannetjies te laat oorproduseer. Dit sal muskietbyte op kort termyn verminder - net wyfies byt - en die deur oopmaak vir krimpende wilde bevolkings deur genetiese manipulasie. Die nuwe genoom het besonderhede aan die lig gebring van die DNA-strek wat muskiete as mans laat ontwikkel, wat Matthews "stap een" genoem het in die nastrewing van die maak-meer-mannetjies-strategie.

Die salamander-genoom wat in Januarie gepubliseer is, het voortgebou op 'n vorige publikasie deur Europese wetenskaplikes verlede jaar. Alhoewel sy genoom ongeveer 10 keer die grootte van die menslike een is, wat die ontleding moeiliker maak, is die axolotl se regenererende vermoëns 'n ooglopende lokmiddel.

Axolotls kan "amper enigiets wat jy van hulle kan afsny, vervang, solank jy nie hul koppe afsny nie," sê Jeramiah Smith van die Universiteit van Kentucky in Lexington, 'n skrywer van die meer onlangse genoomvraestel.

Maar Smith wys op 'n ander truuk wat dalk gouer vrugte afwerp vir menslike medisyne: Die salamander kan ook groot wonde genees sonder om littekens te kry.

Wat betref die leer hoe om mense 'n afgesnyde arm te laat groei, reken hy dit is ver weg.

"Dit sal waarskynlik nie vir my nuttig wees nie," het Smith, wat 42 is, geskerts. "Ek sal dood wees, so ek sal nie nodig hê om my arm terug te laat groei nie."

En Lil BUB? Sy is die grootte van 'n katjie al is sy 8 jaar oud, en het 'n aantal ander vreemde eienskappe. Wetenskaplikes het na genetiese mutasies gesoek, en veranderde gene gevind wat blykbaar verantwoordelik is vir haar ekstra tone en vir 'n seldsame beensiekte.

Volg Malcolm Ritter by @MalcolmRitter.

Die Associated Press Health & Science Department ontvang ondersteuning van die Howard Hughes Medical Institute se Departement van Wetenskap Onderwys. Die AP is alleen verantwoordelik vir alle inhoud.


Funksionele genomika

Satoshi Tabata (Kazusa DNA-navorsingsentrum, Japan) gepraat oor hul ontledings van Lotus japonicus. Hulle het 'n SAGE-benadering gebruik om die wortel-na-nodule-oorgang te bestudeer, en stadiumspesifieke volgordes te identifiseer, waarvan verskeie deur RT-PCR geverifieer is. Die volgordes word vergelyk met hul EST hulpbronne om gene te identifiseer, waar geen passing verkry word nie, gebruik hulle 3' RACE om langer fragmente te verkry. Hulle beplan nou om hierdie benadering op ander weefsels toe te pas. Hulle het 'n EST-biblioteek vanaf saadpunte gegenereer en is besig om 3'UTR's van hul klone te volgorde. Boonop gebruik hulle gene van ander peulgewasse om genomiese biblioteke te PCR-sifter, en klone wat geïdentifiseer is, word in volgorde gerangskik vir geenvoorspelling. Hulle het TAC- en BAC-biblioteke van die genoom en is eindvolgordebepaling van 640 klone. Gebaseer op die 914 gene wat tot dusver geïdentifiseer is, is die gemiddelde L. japonicus geen is 2,7 kb lank, 76% van gene het introne, die gemiddelde intronlengte is 380 bp en die gemiddelde ekson is 276 bp lank. Ander werk sluit in die soek van klone vir SSR's en die gebruik van PCR-toetsing vir polimorfisme in die ouers van die karteringpopulasie. Hulle soek ook SNP's. Vir meer inligting oor die projek, besoek: http://www.kazusa.or.jp/lotus/.

Khalid Meksem (Suidelike Illinois Universiteit, VSA) het oor sy werk in die integrasie van fisiese kaarte en genetiese merkers in 'n reeks plante. Sy groep ontwikkel BAC biblioteke en fisiese kaarte vir plante insluitend sojabone, Arabidopsis, Lotus en mos en vir swamme insluitend Ustilago en Fusarium (http://hbz.tamu.edu). Hiervoor gebruik hulle 'n eie PAGE-vingerafdrukmetode en ensiemstel. Die sojaboon fisiese kaart het 95 322 vingerafdruk BAC's wat 11.8X sojaboon haploïede genome dek. Hierdie kaart is geïntegreer met 256 genetiese merkers op 20 skakelgroepe en 313 mikrosatelliete sal binnekort hierby gevoeg word. Hulle gebruik multiplekshibridisasiemetodes om EST's in groepe van 512 te integreer om die kaart te bevestig. Die kaart is gebruik om nuwe genetiese merkers (mikrosatelliete, InDels en SNPs) te ontwikkel in streke van die genoom wat nie konvensionele genetiese merkers het nie. Hulle maak ook 'n vergelykende kaart van 'n wilde ras, hulle het 'n homoloog van 'n gevind Glysien maks geen van belang, maar dit was omring deur verskillende gene. In hul twee streke van belang het hulle 1,5 gene/10kb gesien en dat slegs 50% van gene deur die EST-hulpbron gedek is, wat 'n behoefte aan meer EST's aandui.

Don Langmore (Rubicon Genomics) hul aangebied OmniPlex-tegnologie en sy toepassings in funksionele genomika. Hierdie direkte genomiese volgordebepaling (wat geen kloning vereis nie) kan gebruik word vir volgordebepaling van transgeenaansluitings, invoegingsmutagenese-aansluitings en geenstreke (gebaseer op EST-data) in 'n reeks bakterieë en eukariote.

Lynn Jablonski gedemonstreer die gebruik van gereedskap van Integrated Genomics Inc. vir vergelykende analise en funksionele rekonstruksie. Sy het hoofsaaklik gepraat oor ERGO, 'n databasis wat publieke en eiendomsreeksdata insluit, wat ontwerp is vir gebruik om interaksies binne die sel te ontdek. Die databasis brei uit op die PUMA- en WIT-databasisse vir metaboliese rekonstruksie.

Michael Udvardi (Max Planck Instituut, Golm, Duitsland) werk aangebied deur gebruik te maak transkriptoom- en proteoomanalise vir die begrip van orgaandifferensiasie. Hy het die huidige kennis van plantseldifferensiasie tydens knoppiesvorming in peulplante uiteengesit en die rol van transkriptomiese, proteomiese en metabolomiese ontledings in sy groep se mees onlangse ontdekkings beklemtoon (sien Trevaskis et al., hierdie saak).

Bradley Till (FHCRC, VSA) aangebied TILLING (Teiken geïnduseerde plaaslike letsels IN genome). Hierdie metode gebruik EMS-puntmutagenese, gevolg deur selfkruising en dan produksie van 'n parallelle saadbank en DNA-hulpbron vir PCR vir mutasie-opsporing. Die mutasie-opsporingstap maak staat op CEL1, 'n nuwe plant-endonuklease wat by voorkeur wanpassings in heteroduplekse tussen wilde tipe en mutant klief. Dit word gebruik om die produkte van geenspesifieke PCR-amplifikasie van DNA vanaf mutante te verteer, deur gebruik te maak van verskillend gemerkte primers. Die produkte van die vertering is twee fragmente (waarvan die lengtes behoort op te tel tot die volle grootte van die verwagte PKR-produk), wat by verskillende golflengtes fluoresserend. Dit laat die opsporing van enige mutante op 'n jel toe, waarop agt monsters per baan saamgevoeg kan word. In 'n proef van die stelsel het hulle ook 'n natuurlike variasie in een van die verskafde ekotipes opgespoor en het voortgegaan om te wys dat dit gebruik kan word om toetredings vir SNP's te tik. Hulle het PARSESNP ontwikkel om inligting oor die mutasies te stoor, soos watter nukleïensuurverandering betrokke is, en die effek. Gesteun deur NSF-befondsing, het die groep begin met 'n Arabidopsis TILLING-program (http://blocks.fhcrc.org/˜steveh/Welcome_to_ATP.html) waarin hulle ∼12 000 monsters/dag/1kb-streek kan skerm. Hulle het ook 'n instrument, genaamd CODDLE, ontwikkel wat die beste streek vir TILLING binne 'n geen van belang sal voorstel. TILLING word nou op 'n wye reeks organismes toegepas.

D.B. Goodenowe gepraat oor die metaboliese profilering benadering van fenomeenontdekkings Inc. Hulle volg 'n nie-geteikende benadering, die opsporing van net daardie metaboliete in die monsters, eerder as om te probeer om alle metaboliete op te spoor. Hulle voeg monsters direk in 'n ioonsiklotron-massaspektrometer, en vertrou op sy vermoë om baie hoë massa-akkuraatheid te gee om hulle in staat te stel om te aanvaar dat hulle korrekte empiriese formules uit die data kan onttrek.

Peter Gresshoff (Universiteit van Queensland, Australië) oor syne gepraat het noduleverwante geenontdekking en uitdrukkingsprofielvorming werk. Sy groep stel belang in wortelontwikkeling en die vestiging van nodules. Daar is 'n paar gene wat by hierdie proses betrokke is, soos dié in die NOD-faktor seintransduksie-weg, maar nie al die gene is bekend nie en die regulatoriese meganismes is ook nie heeltemal bekend nie. Hulle het 'n invoeging promotor vang benadering gevolg, met behulp van 'n promotor-lose GUS verslaggewer geen. Dit gee inligting oor geenuitdrukkingpatrone en regulering van gene. Hulle het 'n vroeë geen gevind, wat 'n rol in vaskulatuur het, dit het mutante met net een nodule gegee. Hulle het ook 'n laterale wortel- en nodule-spesifieke invoeging geïdentifiseer en werk tans uit watter geen se promotor die patroon veroorsaak. In 'n ander benadering het sy groep 'n mikroskikking gemaak, met 4000 unieke EST's en ander gene verteenwoordig. Deur dit te gebruik, het hulle 10 differensieel uitgedrukte gene geïdentifiseer wat hulle geverifieer het deur intydse RT-PCR en Northern-analise te gebruik. In die meeste gevalle het die resultate goed ooreengestem, die plot van die korrelasie van die skikking met qRT-PCR het 'n baie goeie korrelasietelling van r 2 ~1 gegee met lineariteit oor 6 logs.


Advertensie

En sodra navorsers daardie weergawe van die DNS-kode begin ontleed het, het ontdekkings begin verskyn.

- Hulle het die bekende grootte van 'n familie gene wat muskiete help om inligting uit hul omgewing, soos die reuk van mense, byna te verdubbel. Dit was "heeltemal, verbysterend, onverwags," het Vosshall gesê. (Vosshall se salaris word betaal deur die Howard Hughes Medical Institute, wat ook die Associated Press Health & Science Department ondersteun.)

Verdere studie kan verrassings openbaar oor waaraan muskiete aandag gee, het Vosshall gesê. En dit kan lei tot beter lokmiddels vir muskietvalle, sowel as beter afweermiddels. Miskien kan wetenskaplikes iets "10 000 keer meer walglik" vir 'n muskiet vind as die ou bystand, DEET, het sy gesê.

- Hulle het nuwe besonderhede gevind oor gene wat sommige muskiete toelaat om sekere insekdoders te weerstaan. Dit is 'n moontlike stap om te voorspel watter insekdoders nutteloos sal wees om sekere bevolkings te bestry, sowel as 'n moontlike leidraad om met nuwe chemiese wapens teen die insek vorendag te kom.

- Hulle het voorheen onbekende teikens vir 'n groot klas insekdoders gevind. Dit kan die deur oopmaak vir die ontwerp van nuwe weergawes wat muskiete teiken terwyl voordelige insekte gespaar word en minder risiko vir mense inhou.

- Hulle het die soektog na genetiese variante verklein wat verhoed dat sommige Aedes aegypti-muskiete mense met dengue besmet, 'n ernstige griepagtige siekte wat miljoene jaarliks ​​siek maak. As daardie variante geïdentifiseer kan word, kan wetenskaplikes genetiese ingenieurswese gebruik om hulle in sommige muskiete te reproduseer, wat dan vrygestel kan word om die variante deur wilde bevolkings te versprei, het Vosshall gesê. Hierdie variante, of ander, kan ook werk om dreigemente van verspreiding van Zika en geelkoors te verminder, het Vosshall en Matthews gesê.


Resultate

Ons het 'n inligting-herwinning-gebaseerde metode ontwikkel om alle lang identiese multispesie-elemente (LIME's) te identifiseer wat deur twee of meer genome gedeel word, gegewe die element se minimale lengte (Materiale en Metodes). Die metode is belyningsvry, wat ons in staat stel om beide sinteniese en nie-sinteniese rye op te spoor. Ons het hierdie metode gebruik om volgordes van uiterste bewarings wat gedeel word tussen 'n stel diergenome en 'n stel plantgenome te identifiseer en te vergelyk (Fig. 1 en SI Aanhangsel, Fig. S1–S5). Spesifiek, ons het eers 'n omvattende stel LIME's van 100 bp of langer vir ses diere-genome verkry: hond (Canis familiaris Cf), hoender (Gallus gallus Gg), mens (Homo sapiens Hs), muis (Muskulus Ma), makaak (Macaca mulatta Mam), en rot (Rattus norvegicus Rn). Ons het ook alle LIME's van 100 bp of langer onder die ses publiek beskikbare groot (>100 Mbp) plantgenome verkry: Arabidopsis (Arabidopsis thaliana At), sojaboon (Glysien maks Gm), rys (Oryza sativa Os), katoenhout (Populus trichocarpa Pt), sorghum (Sorghum tweekleurig Sb), en druiwe (Vitis vinifera Vv).

Strukturele taksonomie van plant- en dierekalk. Die plantgenoomstel bestaan ​​uit Arabidopsis, sojaboon, rys, katoenhout, sorghum en druiwe. Die diergenoomstel is hond, hoender, mens, muis, makaak en rot. LIME's (≥100 bp) word vir elke paar plantgenome en elke paar diergenome geïdentifiseer en gekategoriseer. 'n Sirkelgrafiek toon die persentasie bydrae van elke LIME-kategorie wat met die sirkelgrafiek verband hou. Weens die gebrek aan die aantekening vir alle betrokke spesies, sluit die laaste klassifikasievlak, Oorsprongklas, die persentasies vir Arabidopsis LIME's in plante (*) en die persentasies vir die dier LIME's in mens, muis, rot en hoender (**) word die absolute getalle gegee in SI Aanhangsel, Tabel S5. Ons het telomere herhalings as sintenies gedefinieer vir duidelikheid. LYNE, lang afgewisselde elemente SINES, kort afgewisselde elemente.

Die vergelykende ontleding van blomplante en diere LIMEs het sleutelooreenkomste en verskille tussen die twee groepe aan die lig gebring (Fig. 1). Albei groepe sluit herhalende LIME's in, wat bestaan ​​uit veelvuldige kopieë van een of twee herhaalde motiewe, sowel as nie-herhalende, of komplekse, LIME's. Verder het elke groep LIME's wat in veelvuldige kopieë in 'n genoom voorkom en dikwels oor veelvuldige chromosome versprei is. Laastens, dier- en plant-LIME's sal waarskynlik hul oorsprong aan verskeie meganismes te danke hê, insluitend die suiwering van seleksie, die oordrag van genetiese materiaal van organellêre na kerngenome, en de novo-volgorde-vervaardiging van sommige van hierdie meganismes kan uniek aan plante wees.

KALKE in dieregenome.

Ons het eers die komplekse LIME's wat gedeel word tussen die mens-, muis- en rotgenome (2004-bou) wat deur ons algoritme gevind word, vergelyk met die UCE's verkry deur Bejerano et al. (3). Ons het gevind dat benewens die identifisering van al 481 voorheen gerapporteerde UCE's, ons metode 12 voorheen onbeskryfde elemente van 200 bp of langer geïdentifiseer het (meer besonderhede word verskaf in Materiale en Metodes en SI Aanhangsel, Tabel S1). Onverwags was 4 van daardie 12 elemente nie-sintenies (SI Aanhangsel, Tabel S2), insluitend twee LIME's wat afkomstig is van retrotransposisiegebeure (SI Aanhangsel, afdelings S1 en S2). In die geheel was daar 1 572 580 unieke komplekse elemente van ten minste 100 bp in die dierestel van ses genome: 19% (297 329) het veelvuldige kopieë in 'n enkele genoom gehad, en 10% (157 723) het veelvuldige kopieë in veelvuldige genome gehad, insluitend 95 met veelvuldige kopieë in ten minste vier genome. Hierdie 95 is saamgevoeg in net 12 "supervolgorde" gebaseer op oorvleuelings in hul genomiese liggings. 'N BLAST-soektog van hierdie elemente teen die nie-oortollige (NR) nukleotieddatabasis by die Nasionale Sentrum vir Biotegnologie-inligting (NCBI) (24) het presiese ooreenkomste met snRNA's getoon, soos menslike 7SL, RNU1-6, RNU1-9 en RNU6-1 , sowel as heterogene nukleêre ribonukleoproteïen A1 van perd (meer besonderhede word verskaf in SI Aanhangsel, afdeling S1). SI Aanhangsel, Fig. S6 toon die verspreiding van multikopie komplekse en herhalende LIMEs. Die meeste van die komplekse LIME's is gedeel tussen mens en makaak (SI Aanhangsel, afdeling S3), terwyl muis die meeste van die herhalende LIME's gehad het. Komplekse elemente was dikwels naby mekaar en het soms oorvleuel. Byvoorbeeld, in die mens, 92% (7,384,943 van 7,960,078) van die komplekse elemente oorvleuel as gevolg daarvan, kan hulle in net 668 trosse gegroepeer word (2 elemente word aan dieselfde groep toegewys as hulle binne 60,000 bp is). Daar was slegs 11 enkel-element trosse, terwyl die grootste groep 295 876 ​​elemente bevat het.

Daar was 241 afsonderlike motiewe wat die herhalende LIME's in diere uitgemaak het (SI Aanhangsel, Tabel S3), en hulle het gewissel van 2 tot 30 bp, met 'n gemiddelde lengte van 8.2 bp (SD = 4.7 bp). Daar was 127 motiewe wat deur drie spesies gedeel is, 74 gedeel deur vier, 48 gedeel deur vyf, en 28 gedeel deur al ses spesies. Alhoewel die meeste herhalende elemente oorvleuel het, was dit nie universeel die geval nie. Daar was byvoorbeeld 8 331 nie-oorvleuelende herhalende elemente in diere wat oor 90% (142 van 157) van die chromosome versprei was, behalwe vir 15 chromosome in hoender.

Van die komplekse LIMES wat deur ten minste twee diere-genome gedeel is (Fig. 1), was daar 1 120 (gemiddelde lengte = 136.55 bp, SD = 41.60 bp) wat deur al ses genome gedeel is, met 76 LIME's van langer as 200 bp. Van daardie 76 LIME's was 33 nie-genies in die mens, 43 was genies, en nie een het meer as 50% volgorde-identiteit met hoender gedeel wanneer die omliggende genomiese streke in ag geneem word (±40 000 bp). Trouens, 3 van die 76 LIME's het slegs 2–3% volgorde-identiteit met hoender gehad ('n voorbeeld word verskaf in SI Aanhangsel, Fig. S7). Dit kontrasteer skerp met die resultate wat voorheen in diere gerapporteer is, waar UCE's almal uit hoogs soortgelyke genomiese streke was. Trouens, die term "ultraskonserveer" is waarskynlik nie van toepassing in hierdie gevalle nie.

KALKE in plantgenome.

Met behulp van metodes wat identies is aan dié wat vir diere-genome gebruik word, het ons die omvattende stel LIME's bepaal wat tussen ses plantspesies gedeel word (Fig. 1). Omdat uiterste bewaring tussen drie of meer plantspesies nog nooit vantevore aangespreek is nie, het ons gefokus op die karakterisering van plant LIME's in hierdie werk, die bepaling van hul moontlike oorsprong en vergelyk dit met die dier LIME's. Anders as dieregenome, was herhalende LIME's algemeen in al ses plantgenome (Fig. 2)A). 'n Gemiddelde plant herhalende KALK was 143 bp lank, wat korter is as 'n gemiddelde komplekse KALK (175 bp Fig. 3)A). Die relatiewe verhoudings van herhalende LIMEs tot komplekse LIMEs was soortgelyk oor die plantgenome wat oorweeg is (Fig. 3)B) die Arabidopsis genoom was tipies in sy besit en verspreiding van herhalende en komplekse LIME's. Ons het 214 unieke komplekse LIME's opgespoor wat deur Arabidopsis en ten minste een van die oorblywende vyf genome (Fig. 2 B en C), insluitend 91 unieke komplekse elemente wat tussen gedeel word Arabidopsis en rys, 3,64 keer meer as wat voorheen geïdentifiseer is (23). In Arabidopsis, 35 van die 91 komplekse LIMES is nie-oorvleuelend en (wanneer veelvuldige kopieë oorweeg word) 81 oorvleuel met ander komplekse elemente (SI Aanhangsel, afdeling S4), terwyl 69 van die 91 komplekse LIMES in rys nie oorvleuel nie en 72 oorvleuel met ander komplekse elemente. Die herhalende elemente het die meerderheid van Arabidopsis LIME's [1 685 afsonderlike LIME's (~88.7%)], maar die repertorium van herhaalde motiewe was verbasend klein, ons het gevind dat 'n herhalende LIME kopieë bevat van óf een óf twee motiewe uit 'n totale stel van ses motiewe van 2–7 bp, met elk kom tot 323 keer in tandem voor. Die meerderheid van Arabidopsis LIME's was nie-genies van 26,367 unieke liggings van herhalende LIME's, 4,015 het ooreengestem met geniese volgordes en 22,352 met nie-geniese volgordes van die 305 liggings van komplekse LIME's, 169 was genies en 136 was nie-genies. Gebruik die Arabidopsis inligting hulpbron annotasie raamwerk TAIR (25), ons het ook gekategoriseer alle genetiese LIME's as eksonies, gedeeltelik eksonies, of moontlik intronies, gebaseer op hul oorvleueling met geannoteerde geenmodelle. Ons het 3 251 eksoniese, 713 gedeeltelik eksoniese en 220 moontlik introniese liggings van beide herhalende en komplekse LIME's gevind.

Plantkalk is merkwaardig uiteenlopend in hul struktuur en funksie. (A) Filogenetiese bome van die ses dier- en ses plantspesies vir komplekse en herhalende KALKE. Mamma stem ooreen met Macaca mulatta, en Mamma stem ooreen met Muskulus. 'n Nodusnommer (vetgedruk) is die aantal elemente wat algemeen is vir elke spesie in 'n subboom hieronder. Alle LIME's ≥100 bp word vir elke subboom oorweeg. By, Arabidopsis thaliana GM, Glysien maks (sojaboon) Hs, Homo sapiens (mens) Mamma, Macaca mulatta (makak) Mamma, Muskulus (muis) Os, Oryza sativa (rys) Pt, Populus trichocarpa (katoenhout) Rn, Rattus norvegicus (rat) Sb, Sorghum tweekleurig (sorghum) Vv, Vitis vinifera (druif). (B) LIME's in die Arabidopsis (At) genoom, uitgebeeld as gekleurde bosluise met komplekse LIME's bo en herhalende LIME's onder elke chromosoom (chr) volgorde. Bosluiskleur stem ooreen met die aantal genome, insluitend die At-genoom, wat 'n LIME deel: rooi vir drie genome, oranje vir vier, ligblou vir vyf en donkerblou vir ses. Wanneer twee LIME's 45 kbp of minder uitmekaar is, word hulle in dieselfde boks gegroepeer. Sodra daar meer as 20 LIME's in so 'n boks is, is die boksgrootte onveranderd, maar korrekte proporsies van LIME's wat deur drie, vier, vyf en ses genome gedeel word, word uitgebeeld deur die relatiewe dikte van die gekleurde dele. Oranje nommers spesifiseer die totale aantal LIME's per boks, en blou stem ooreen met die motief-ID vir een of meer herhalende LIME's. Geïdentifiseerde sentromeerposisies word as grys blokkies getoon. (C) Gedetailleerde voorstelling van 'n chromosoom 3-streek wat 2 LIME's insluit wat deur al ses genome gedeel word, en die naaste gene.

Elke geïdentifiseerde plant KALK kan in een van twee basiese strukturele klasse geklassifiseer word: herhalende en komplekse KALKE. (A) Verspreiding van LIME-lengtes in vier groepe elemente: enkelkopie-kompleks, enkelkopie-herhalend, meervoudig-kopie-kompleks en meervoudige-kopie-herhalend. (B) Verspreiding van herhalende en komplekse LIME's oor ses genome (as persentasie van totaal). By, Arabidopsis thaliana GM, Glysien maks (sojaboon) Os, Oryza sativa (rys) Pt, Populus trichocarpa (katoenhout) Sb, Sorghum tweekleurig (sorghum) Vv, Vitis vinifera (druif). (C) Basiese tipes volgordemotiewe wat deur herhalende LIME's gebruik word. In totaal is daar 12 unieke motiewe 2–7 bp lank.

Taksonomie van plantkalk gebaseer op hul moontlike oorsprong.

Sinteniese analise met behulp van die Vergelykende Genomiese platform CoGe (26) het aan die lig gebring dat komplekse plant LIMEs nie-sintenies is (Fig. 1). Hierdie bevinding kontrasteer onverwags met die sinteniese aard van die soogdier-UCE's (3). Die gebrek aan sintensie ondersteun verder ons bewering dat sommige plant LIME's nie vertikaal geërf word nie. Inderdaad, ons stel voor dat daar drie moontlike oorspronge is vir die identiese volgordes wat in ons stel plantgenome gevind word: vertikale oorerwing, horisontale oordrag en de novo-vervaardiging. Although vertical inheritance of nuclear material is straightforward, detecting it can be confounded by extensive genome rearrangements. For instance, to determine whether the four overlapping LIMEs from Table 1 are conserved in species other than the six plants considered above, we used the shortest one (107 bp) in a BLAST search against the NR nucleotide database at the NCBI (24) and found exact copies of this LIME in the mature coding sequence of 18S (cytoplasmic), 26S (organellar), and 28S (cytoplasmic) rRNA genes of 76 eukaryotic organisms, including plants, animals, and fungi (more details are provided in SI Aanhangsel, section S5).

Four LIMEs common to all six species and papaya

Horizontally Inherited LIMEs.

The sequences of proposed horizontal inheritance detected by our algorithm could be of natural origin or artifactual. Some of the identified elements are likely the products of sequence assembly errors and/or bacterial sequence insertions (bacterial sequences were exclusively from Escherichia coli). On the other hand, we found several Arabidopsis repetitive elements associated with a transposon. A copy of a repetitive element containing the motif “GAGA” was found within an Arabidopsis gene annotated as “hAT-like transposase family” (TAIR gene ID AT5G28673) two other copies of this element were identified in genes annotated as “probable serine/threonine-protein kinase” (TAIR gene ID AT3G59410) and “unknown protein” (TAIR gene ID AT1G01725). Another copy of the same repetitive element, located on chromosome 2 of Arabidopsis, is classified as nongenic. SI Aanhangsel, Fig. S8 shows the mapping of mitochondrial to nuclear genomes in Arabidopsis, rice, and sorghum. Arabidopsis has nine exonic LIMEs (SI Aanhangsel, Table S4) that were derived from mitochondrial insertions. The cross-species genomic-to-genomic and mitochondrial-to-mitochondrial comparisons of these LIMEs revealed that the surrounding mitochondrial and nuclear sequences had rearranged and/or diverged, although still retaining these few elements throughout evolution (more details are provided in SI Aanhangsel, section S6).

De Novo Sequence Manufacturing.

A process we refer to as “de novo sequence manufacturing” could be another possible source of identical cross-species sequences in plants. For example, telomeric repeats are manufactured by a known enzymatic mechanism (27), and these repeats certainly populate our collection of LIMEs. Strand slippage during DNA synthesis is another likely explanation for some of the repetitive elements identified. Likewise, gene conversion may underlie the LIMEs found among the rDNA genes. Similar to the previous description of Arabidopsis, although there were 25,066 unique repetitive LIMEs among the six genomes, these LIMEs were remarkably limited in the repeats they used. Thus, a repetitive LIME consisted of 1 or 2 short motifs the set of all motifs used in LIMEs encompassed only 12 of the 1,699 possible 2- to 7-bp motifs (Fig. 3C). Moreover, only sorghum contained repetitive LIMEs of all 12 motifs, whereas other genomes used subsets of 5–11 motifs (Tables 2 and 3). On average, a repertoire of ∼7.8 unique motifs was used by repetitive LIMEs from one genome. Many repeats appeared to be microsatellites, consisting of motifs 2–6 bp long (28). The exceptions were the TTTAGGG (LIME label 1 in Fig. 2B) and GAGA, which are telomeric (29) and GAGA-binding (30) protein, respectively, and possibly two other motifs, ATACAT and ATTAT (Fig. 3C en SI Aanhangsel, section S7).

Repeat motifs of repetitive LIMEs in plant genomes

Distinct repeat motifs with a length of 2–7 bp shared between pairs of genomes that are found to contribute to the repetitive LIMEs

Colocalization of LIMEs: Clusters and Superclusters in Plants.

Whether to consider elements individually or in groups depends on the question being asked. For instance, when studying sequence function, it is often beneficial to view elements individually, whereas when studying evolution, as we do now, it is beneficial to group nearby elements into a cluster that serves as a coselected functional unit. The animal UCEs, including the nonexonic elements, are often clustered in the genomes near transcription factors and genes associated with development (3) however, little is known about the colocalization of plant LIMEs. Although this property is expected for repetitive plant LIMEs, where one tandem repeat sequence could be a source of many repetitive LIMEs, we also found more overlapping than nonoverlapping complex LIMEs in four of the six plant genomes, with the exceptions being rice and sorghum (Fig. 4A en SI Aanhangsel, section S8). The soybean genome, for example, contained 5,451 copies of 336 unique complex elements that could be grouped into just 47 clusters, where adjacent/overlapping elements were ≤60,000 bp apart. In Arabidopsis, the cluster of such neighboring LIMEs containing the 4 LIMEs shared by all six genomes was located in close proximity to the centromere of chromosome 3. On the other hand, the cluster in rice (chromosome 2) containing the same LIMEs was not located near the centromere or the telomere (SI Aanhangsel, Fig. S1). Colocalization of LIMEs had its extremes: Soybean chromosome 13 (SI Aanhangsel, Fig. S2B) contained the largest group of 3,062 neighboring LIMEs (the average distance between the starting nucleotides of 2 neighboring LIMEs for the first 3,061 LIMEs was only 291 bp). This number was surprisingly high, surpassing the number of neighboring LIMEs in the remaining five genomes by at least an order of magnitude the rest of the soybean genome had 43 clusters with an average of 3.325 elements per cluster. Determining the origins of these abundant complex LIMEs in the region of the chromosome that is known for its unique association with the nucleolus organizer region (NOR) (31) could provide insights into differences between the soybean NOR and NORs of other species. For all six species, there were 631 complex clusters in total, with an average of ∼14 LIMEs per cluster (96.6%) and 306 complex LIMEs occurring alone (Fig. 4B). Also, there were 3,601 repetitive clusters (99.99%), with ∼1,007 LIMEs per cluster on average and 193 repetitive LIMEs occurring alone. A possible explanation for this clustering of LIMEs is horizontal gene/genome transfer events from organelle genomes.

Plant LIMEs are often found overlapping or in close proximity to each other. (A) Numbers of complex LIMEs that (i) overlap with at least one complex LIME and (ii) do not overlap. Shown in the last column is the total number of complex LIME clusters, where each element in the cluster either overlaps with another element or is located within 60 kbp of another complex LIME. At, Arabidopsis thaliana Gm, Glysien maks (soybean) Os, Oryza sativa (rice) Pt, Populus trichocarpa (cottonwood) Sb, Sorghum tweekleurig (sorghum) Vv, Vitis vinifera (grape). (B) Distribution of cluster sizes among clusters containing repetitive and complex LIMEs.

We next studied the relationship between the propensity of LIMEs to localize within the same cluster and to occur in multiple copies within the same genome and across multiple genomes. When constructing a network of clustered complex LIMEs, where two clusters were connected if they shared at least one common LIME, we found that the clusters were naturally grouped into 170 “superclusters,” where no 2 superclusters shared a single LIME (Fig. 5 and SI Aanhangsel, section S9 and Fig. S9). When analyzing connectivity within superclusters, we found that LIMEs that belonged to the same cluster in one species were dispersed into multiple clusters in another species. For instance, in a supercluster that included a single complex LIME from Arabidopsis (LIME ID 1516), the average number of interspecies connections for one cluster was ∼3.4 (red edges in Fig. 5). Similarly, the intraspecies copies of a multicopy LIME often did not colocalize in the same cluster (dark green edges in Fig. 5 and SI Aanhangsel, Fig. S10).

“Supercluster” of complex LIMEs that includes a single element from Arabidopsis (LIME ID 1516) and 24 clusters from four other genomes: soybean, rice, sorghum, and grape. The network of complex LIMEs from Arabidopsis (At maroon node), soybean (Gm gray nodes), rice (Os gold nodes), sorghum (Sb green nodes), and grape (Vv blue nodes) is shown. All elements in one cluster are connected to a selected representative with the edges of the same color as the nodes. Clusters of LIMEs within one species are connected through the representative nodes with dark green edges if they share one or more multiple-copy complex LIMEs. Clusters sharing LIMEs across multiple species are connected through their representatives with red edges.

LIMEs in Plants vs. Animals.

Individual elements are defined as the longest common subsequence between two larger sequences. Our algorithm finds all such matching subsequences (≥100 bp) between genomes. The simplest way to quantify the elements is to count them individually. However, this leads to “double counting,” because many overlap (Materiale en Metodes). The structural taxonomy shown in Fig. 1 can be used to quantify them differently. It breaks down cross-species elements into two initial categories: repeated motifs and complex sequences. SI Aanhangsel, Table S3 lists the 241 repeated motifs in the animal set and the 12 motifs in the plant set. To determine whether any of the repeated sequences were contained within mobile elements, we used the Repeat Masker server (32, 33), scanning the entire set of repetitive LIMEs. Among our LIMEs, we found homology only to several long interspersed elements (LINEs) and LTRs in mammals (1 LINE and 2 LTRs in human, 2 LINEs and 8 LTRs in rat as well as in mouse, and 1 LINE in dog) no homologous repeats for the chicken or plant LIMEs were found. Interestingly, nine repetitive LIMEs are shared between plants and animals. However, the LIME distribution is quite different between the two groups: Only a small minority of plant LIMEs have complex sequences [1,110 (4%)]. On the other hand, most of the elements in the animal set have complex sequences [1,572,580 (85%)]. If we count not the existence of an element but the total number of copies of it in each genome, these figures change to 0.24% and 60% for plants and animals, respectively. The number of copies of repetitive and complex elements also differs: 16,029 (64%) of repeated motif elements in plants and 151,091 (54%) in animals have multiple copies in at least one genome. For complex elements, the numbers are 435 (39%) and 455,052 (29%), respectively. In the plant set, there were 1,110 unique complex sequences of LIMEs shared by two genomes, 234 shared by three genomes, 144 shared by four genomes, 54 shared by five genomes, and 4 shared by all six genomes (Fig. 1 and SI Aanhangsel, Fig. S1–S5). Exact copies of the shortest of the last four LIMEs were also found in 76 different organisms, including species from plants, animals, and fungi.


Science Says: Why scientists prize plant, animal genomes

NEW YORK (AP) " Just about every week, it seems, scientists publish the unique DNA code of some creature or plant. Just in February, they published the genome for the strawberry, the paper mulberry tree, the great white shark and the Antarctic blackfin icefish.

They also announced that, thanks to a crowdfunding campaign, they'd produced the genome of Lil BUB, a female cat with a large internet following.

That followed a notable advance in January: an improved genome for the axolotl, a salamander renowned for regrowing severed limbs and other body parts.

Scientists have been uncovering genomes for quite a while. The first from an animal " a worm " came in 1998. Now, the technology has advanced far enough that scientists last year announced a project to produce the genomes for all life forms on Earth other than bacteria and single-celled organisms called archaea. They called it a "moonshot for biology."

But what's the point of uncovering new genomes?

For scientists, a detailed look under the hood of their favorite organism provides a foothold for learning the deepest secrets of their objects of attention, it leads to discoveries about how life works, and possibly how to prevent disease.

Take the mosquito. Late last year, researchers published a much-improved description of the DNA code for a particularly dangerous species of mosquito: Aedes aegypti, notorious for spreading Zika, dengue and yellow fever.

That achievement came from analyzing the DNA of 80 mosquito brothers. They were born in Leslie Vosshall's lab at Rockefeller University in New York, where thousands of mosquitoes swarmed in cages recently as Krithika Venkataraman was trying to make some more.

She stuck a tube that protruded from her mouth like a straw into a transparent cube filled with male mosquitoes. Then she repeatedly sucked about 30 males at a time into the tube. She counted them, and then blew them into another cube that housed females. Before long, the two sexes were mating.

You can think of a genome as an instruction book for building a living thing. Its language is a four-letter alphabet, which stand for the four compounds that make up the innards of the DNA molecule. The order of those compounds along the molecule is the code it creates "words" that we call genes.

The mosquito genome, for example, is about 1.28 billion letters long, a bit less than half the length of the human version. Knowing the DNA sequence lets scientists manipulate it with gene editing techniques, said Ben Matthews of the Vosshall lab, who was part of the international team that published the refined description of the mosquito genome last November.

And once researchers started analyzing that version of the DNA code, discoveries began to pop out.

" They nearly doubled the known size of a family of genes that help mosquitoes sense information from their environment, such as the odor of humans. That was "totally, mind-blowingly, unexpected," Vosshall said. (Vosshall's salary is paid by the Howard Hughes Medical Institute, which also supports The Associated Press Health & Science Department.)

Further study may reveal surprises about what mosquitoes pay attention to, Vosshall said. And that could lead to better lures for mosquito traps, as well as better repellents. Maybe scientists can find something "10,000 times more disgusting" to a mosquito than the old standby, DEET, she said.

" They found new details about genes that let some mosquitoes resist certain insecticides. That's a possible step toward predicting what insecticides would be useless for fighting certain populations, as well as a potential lead for coming up with new chemical weapons against the insect.

" They found previously unknown targets for a major class of insecticides. That could open the door to designing new versions that target mosquitoes while sparing beneficial insects and posing less risk to people.

" They narrowed the search for genetic variants that prevent some Aedes aegypti mosquitoes from infecting people with dengue, a severe flu-like illness that sickens millions every year. If those variants can be identified, scientists might use genetic engineering to reproduce them in some mosquitoes, which could then be released to spread the variants though wild populations, Vosshall said. Those variants, or others, might also work for reducing threats of spreading Zika and yellow fever, Vosshall and Matthews said.

" A similar strategy might be used to make mosquito populations overproduce males. That would reduce mosquito bites in the short term " only females bite " and open the door to shrinking wild populations through genetic engineering. The new genome revealed details of the DNA stretch that makes mosquitoes develop as males, which Matthews called "step one" in pursuing the make-more-males strategy.

The salamander genome published in January built on a previous publication by European scientists last year. Although its genome is about 10 times the size of the human one, which makes the analysis harder, the axolotl's regenerating capabilities are an obvious lure.

Axolotls can replace "almost anything you can cut off of them, as long as you don't cut off their heads," says Jeramiah Smith of the University of Kentucky in Lexington, an author of the more recent genome paper.

But Smith points to another trick that might pay off sooner for human medicine: The salamander can also heal large wounds without scarring.

As for learning how to let people grow back a severed arm, he figures that's a long way off.

"That probably won't be useful for me," joked Smith, who's 42. "I'll be dead, so I won't need to grow my arm back."

And Lil BUB ? She's the size of a kitten even though she's 8 years old, and has a number of other odd traits. Scientists looked for genetic mutations, and found altered genes that appear to be responsible for her extra toes and for a rare bone disease.

Follow Malcolm Ritter at @MalcolmRitter.

The Associated Press Health & Science Department receives support from the Howard Hughes Medical Institute's Department of Science Education. The AP is solely responsible for all content.


Annelida

Only one complete annelid mtDNA sequence has been determined, that of the oligochaete Lumbricus terrestris ( 97) small portions have been published of two other annelids, Platynereis en Helobdella, and of the related taxa Galatheolinum (phylum Pogonophora) and Urechis (phylum Echiura) ( 31) ( Fig. 4B). Unlike most studied mtDNAs, all Lumbricus mitochondrial genes are encoded on the same strand. One speculates that there could be a ‘ratchet’ effect to such a set of rearrangements. That is, if rearrangements were to place all genes on one strand, it would be expected that transcription of the other strand would soon cease, since presumably selection would not maintain the necessary signaling elements and the futile transcription would be an energetic burden. This would then constitute an effective barrier to further inversions which would place a gene on the non-transcribed strand unless that inversion also carried with it the necessary sequence elements to resume its expression.

In several respects Lumbricus mtDNA is quite conventional: only ATG is used as an initiation codon, whereas most mtDNAs use a variety of alternatives ( 18) the tRNAs have uncommonly uniform potential secondary structures nucleotide composition is more balanced than for most mtDNAs and non-coding nucleotides are very few. One unusual feature, however, is that A8 en A6 are separated by ∼2700 nt. In nearly all animal mtDNAs A8 en A6 are adjacent, often overlapping in alternate reading frames. In mammals, A8 en A6 are translated from a bicistronic transcript, with translation initiating alternatively at the 5′ end of the mRNA for A8 or at an internal start codon for A6 ( 98). It is unknown whether this is also the mode of translation of these two genes in other organisms, although, if so, it could explain their nearly universal juxtaposition. Other than A8 being missing from the mtDNAs of nematodes (see below), all exceptions to this are members of phyla assigned to the group ‘Eutrochozoa’ ( 99). A8 is missing from the mtDNA of Mitilus (Mollusca) ( 12) and these two genes are separated in the mtDNAs of Lumbricus (Annelida), Helobdella en Platynereis (Annelida unpublished) three pulmonate snails (Mollusca) ( 90), Dentalium en Nautilus (Mollusca unpublished) Urechis (Echiura unpublished), Galatheolinum (Pogonophora unpublished) Phascolopsis (Sipuncula unpublished) and Terebratalia (Brachiopoda unpublished). It may be that loss of co-translation of this bicistron is a derived feature of the Eutrochozoa this could be studied in members that retain A8 adjacent to A6, such as the polyplacophoran mollusk Katharina ( 95).


Science Says: Why scientists prize plant, animal genomes

This Tuesday, Feb. 12, 2019 photo shows male mosquitos at the the Vosshall Laboratory at Rockefeller University in New York. In 2018, researchers at the lab published a much-improved description of the DNA code for a particularly dangerous species of mosquito: Aedes aegypti, notorious for spreading Zika, dengue and yellow fever. (AP Photo/Mary Altaffer)

NEW YORK (AP) — Just about every week, it seems, scientists publish the unique DNA code of some creature or plant. Just in February, they published the genome for the strawberry, the paper mulberry tree, the great white shark and the Antarctic blackfin icefish.

They also announced that, thanks to a crowdfunding campaign, they'd produced the genome of Lil BUB, a female cat with a large internet following.

That followed a notable advance in January: an improved genome for the axolotl, a salamander renowned for regrowing severed limbs and other body parts.

Scientists have been uncovering genomes for quite a while. The first from an animal — a worm — came in 1998. Now, the technology has advanced far enough that scientists last year announced a project to produce the genomes for all life forms on Earth other than bacteria and single-celled organisms called archaea. They called it a "moonshot for biology."

But what's the point of uncovering new genomes?

For scientists, a detailed look under the hood of their favorite organism provides a foothold for learning the deepest secrets of their objects of attention, it leads to discoveries about how life works, and possibly how to prevent disease.

Take the mosquito. Late last year, researchers published a much-improved description of the DNA code for a particularly dangerous species of mosquito: Aedes aegypti, notorious for spreading Zika, dengue and yellow fever.

That achievement came from analyzing the DNA of 80 mosquito brothers. They were born in Leslie Vosshall's lab at Rockefeller University in New York, where thousands of mosquitoes swarmed in cages recently as Krithika Venkataraman was trying to make some more.

She stuck a tube that protruded from her mouth like a straw into a transparent cube filled with male mosquitoes. Then she repeatedly sucked about 30 males at a time into the tube. She counted them, and then blew them into another cube that housed females. Before long, the two sexes were mating.

You can think of a genome as an instruction book for building a living thing. Its language is a four-letter alphabet, which stand for the four compounds that make up the innards of the DNA molecule. The order of those compounds along the molecule is the code it creates "words" that we call genes.

The mosquito genome, for example, is about 1.28 billion letters long, a bit less than half the length of the human version. Knowing the DNA sequence lets scientists manipulate it with gene editing techniques, said Ben Matthews of the Vosshall lab, who was part of the international team that published the refined description of the mosquito genome last November.

And once researchers started analyzing that version of the DNA code, discoveries began to pop out.

— They nearly doubled the known size of a family of genes that help mosquitoes sense information from their environment, such as the odor of humans. That was "totally, mind-blowingly, unexpected," Vosshall said. (Vosshall's salary is paid by the Howard Hughes Medical Institute, which also supports The Associated Press Health & Science Department.)

Further study may reveal surprises about what mosquitoes pay attention to, Vosshall said. And that could lead to better lures for mosquito traps, as well as better repellents. Maybe scientists can find something "10,000 times more disgusting" to a mosquito than the old standby, DEET, she said.

— They found new details about genes that let some mosquitoes resist certain insecticides. That's a possible step toward predicting what insecticides would be useless for fighting certain populations, as well as a potential lead for coming up with new chemical weapons against the insect.

— They found previously unknown targets for a major class of insecticides. That could open the door to designing new versions that target mosquitoes while sparing beneficial insects and posing less risk to people.

— They narrowed the search for genetic variants that prevent some Aedes aegypti mosquitoes from infecting people with dengue, a severe flu-like illness that sickens millions every year. If those variants can be identified, scientists might use genetic engineering to reproduce them in some mosquitoes, which could then be released to spread the variants though wild populations, Vosshall said. Those variants, or others, might also work for reducing threats of spreading Zika and yellow fever, Vosshall and Matthews said.

— A similar strategy might be used to make mosquito populations overproduce males. That would reduce mosquito bites in the short term — only females bite — and open the door to shrinking wild populations through genetic engineering. The new genome revealed details of the DNA stretch that makes mosquitoes develop as males, which Matthews called "step one" in pursuing the make-more-males strategy.

The salamander genome published in January built on a previous publication by European scientists last year. Although its genome is about 10 times the size of the human one, which makes the analysis harder, the axolotl's regenerating capabilities are an obvious lure.

Axolotls can replace "almost anything you can cut off of them, as long as you don't cut off their heads," says Jeramiah Smith of the University of Kentucky in Lexington, an author of the more recent genome paper.

But Smith points to another trick that might pay off sooner for human medicine: The salamander can also heal large wounds without scarring.

As for learning how to let people grow back a severed arm, he figures that's a long way off.

"That probably won't be useful for me," joked Smith, who's 42. "I'll be dead, so I won't need to grow my arm back."

And Lil BUB ? She's the size of a kitten even though she's 8 years old, and has a number of other odd traits. Scientists looked for genetic mutations, and found altered genes that appear to be responsible for her extra toes and for a rare bone disease.

Follow Malcolm Ritter at @MalcolmRitter.

The Associated Press Health & Science Department receives support from the Howard Hughes Medical Institute's Department of Science Education. The AP is solely responsible for all content.


Science Says: Why scientists prize plant, animal genomes

In this Tuesday, Feb. 12, 2019 photo, PhD student Krithika Venkataraman mates mosquitos by blowing males into a container housing females at the the Vosshall Laboratory of Rockefeller University in New York. Researchers nearly doubled the known size of a family of genes that help mosquitoes sense information from their environment, such as the odor of humans. That was "totally, mind-blowingly, unexpected," Leslie Vosshall says. (AP Photo/Mary Altaffer)

NEW YORK -- Just about every week, it seems, scientists publish the unique DNA code of some creature or plant. Just in February, they published the genome for the strawberry, the paper mulberry tree, the great white shark and the Antarctic blackfin icefish.

They also announced that, thanks to a crowdfunding campaign, they'd produced the genome of Lil BUB, a female cat with a large internet following.

That followed a notable advance in January: an improved genome for the axolotl, a salamander renowned for regrowing severed limbs and other body parts.

Scientists have been uncovering genomes for quite a while. The first from an animal -- a worm -- came in 1998. Now, the technology has advanced far enough that scientists last year announced a project to produce the genomes for all life forms on Earth other than bacteria and single-celled organisms called archaea. They called it a "moonshot for biology."

But what's the point of uncovering new genomes?

For scientists, a detailed look under the hood of their favorite organism provides a foothold for learning the deepest secrets of their objects of attention, it leads to discoveries about how life works, and possibly how to prevent disease.

Take the mosquito. Late last year, researchers published a much-improved description of the DNA code for a particularly dangerous species of mosquito: Aedes aegypti, notorious for spreading Zika, dengue and yellow fever.

That achievement came from analyzing the DNA of 80 mosquito brothers. They were born in Leslie Vosshall's lab at Rockefeller University in New York, where thousands of mosquitoes swarmed in cages recently as Krithika Venkataraman was trying to make some more.

She stuck a tube that protruded from her mouth like a straw into a transparent cube filled with male mosquitoes. Then she repeatedly sucked about 30 males at a time into the tube. She counted them, and then blew them into another cube that housed females. Before long, the two sexes were mating.

You can think of a genome as an instruction book for building a living thing. Its language is a four-letter alphabet, which stand for the four compounds that make up the innards of the DNA molecule. The order of those compounds along the molecule is the code it creates "words" that we call genes.

The mosquito genome, for example, is about 1.28 billion letters long, a bit less than half the length of the human version. Knowing the DNA sequence lets scientists manipulate it with gene editing techniques, said Ben Matthews of the Vosshall lab, who was part of the international team that published the refined description of the mosquito genome last November.

And once researchers started analyzing that version of the DNA code, discoveries began to pop out.

-- They nearly doubled the known size of a family of genes that help mosquitoes sense information from their environment, such as the odor of humans. That was "totally, mind-blowingly, unexpected," Vosshall said. (Vosshall's salary is paid by the Howard Hughes Medical Institute, which also supports The Associated Press Health & Science Department.)

Further study may reveal surprises about what mosquitoes pay attention to, Vosshall said. And that could lead to better lures for mosquito traps, as well as better repellents. Maybe scientists can find something "10,000 times more disgusting" to a mosquito than the old standby, DEET, she said.

-- They found new details about genes that let some mosquitoes resist certain insecticides. That's a possible step toward predicting what insecticides would be useless for fighting certain populations, as well as a potential lead for coming up with new chemical weapons against the insect.

-- They found previously unknown targets for a major class of insecticides. That could open the door to designing new versions that target mosquitoes while sparing beneficial insects and posing less risk to people.

-- They narrowed the search for genetic variants that prevent some Aedes aegypti mosquitoes from infecting people with dengue, a severe flu-like illness that sickens millions every year. If those variants can be identified, scientists might use genetic engineering to reproduce them in some mosquitoes, which could then be released to spread the variants though wild populations, Vosshall said. Those variants, or others, might also work for reducing threats of spreading Zika and yellow fever, Vosshall and Matthews said.

-- A similar strategy might be used to make mosquito populations overproduce males. That would reduce mosquito bites in the short term -- only females bite -- and open the door to shrinking wild populations through genetic engineering. The new genome revealed details of the DNA stretch that makes mosquitoes develop as males, which Matthews called "step one" in pursuing the make-more-males strategy.

The salamander genome published in January built on a previous publication by European scientists last year. Although its genome is about 10 times the size of the human one, which makes the analysis harder, the axolotl's regenerating capabilities are an obvious lure.

Axolotls can replace "almost anything you can cut off of them, as long as you don't cut off their heads," says Jeramiah Smith of the University of Kentucky in Lexington, an author of the more recent genome paper.

But Smith points to another trick that might pay off sooner for human medicine: The salamander can also heal large wounds without scarring.

As for learning how to let people grow back a severed arm, he figures that's a long way off.

"That probably won't be useful for me," joked Smith, who's 42. "I'll be dead, so I won't need to grow my arm back."

And Lil BUB? She's the size of a kitten even though she's 8 years old, and has a number of other odd traits. Scientists looked for genetic mutations, and found altered genes that appear to be responsible for her extra toes and for a rare bone disease.

Print Headline: Science Says: Why scientists prize plant, animal genomes


Kyk die video: Encyclopedia of Plant Genome Using Tutorial (September 2022).