Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F13%3A00396781" target="_blank" >RIV/61389030:_____/13:00396781 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1186/1471-2164-14-222" target="_blank" >http://dx.doi.org/10.1186/1471-2164-14-222</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/1471-2164-14-222" target="_blank" >10.1186/1471-2164-14-222</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat

Popis výsledku v původním jazyce

Background: The assembly of the bread wheat genome sequence is challenging due to allohexaploidy and extreme repeat content (>80%). Isolation of single chromosome arms by flow sorting can be used to overcome the polyploidy problem, but the repeat contentcause extreme assembly fragmentation even at a single chromosome level. Long jump paired sequencing data (mate pairs) can help reduce assembly fragmentation by joining multiple contigs into single scaffolds. The aim of this work was to assess how mate pair data generated from multiple displacement amplified DNA of flow-sorted chromosomes affect assembly fragmentation of shotgun assemblies of the wheat chromosomes. Results: Three mate pair (MP) libraries (2 Kb, 3 Kb, and 5 Kb) were sequenced to a totalcoverage of 89x and 64x for the short and long arm of chromosome 7B, respectively. Scaffolding using SSPACE improved the 7B assembly contiguity and decreased gene space fragmentation, but the degree of improvement was greatly affected by

Název v anglickém jazyce

Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat

Popis výsledku anglicky

Background: The assembly of the bread wheat genome sequence is challenging due to allohexaploidy and extreme repeat content (>80%). Isolation of single chromosome arms by flow sorting can be used to overcome the polyploidy problem, but the repeat contentcause extreme assembly fragmentation even at a single chromosome level. Long jump paired sequencing data (mate pairs) can help reduce assembly fragmentation by joining multiple contigs into single scaffolds. The aim of this work was to assess how mate pair data generated from multiple displacement amplified DNA of flow-sorted chromosomes affect assembly fragmentation of shotgun assemblies of the wheat chromosomes. Results: Three mate pair (MP) libraries (2 Kb, 3 Kb, and 5 Kb) were sequenced to a totalcoverage of 89x and 64x for the short and long arm of chromosome 7B, respectively. Scaffolding using SSPACE improved the 7B assembly contiguity and decreased gene space fragmentation, but the degree of improvement was greatly affected by

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

EB - Genetika a molekulární biologie

OECD FORD obor

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Projekt

<a href="/cs/project/GAP501%2F12%2F2554" target="_blank" >GAP501/12/2554: Fyzická mapa krátkého ramene chromozómu 7D pšenice a její využití pro klonování genu pro rezistenci k mšici zhoubné</a><br>

Návaznosti

Z - Vyzkumny zamer (s odkazem do CEZ)

Rok uplatnění

2013

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

B M C Genomics

ISSN

1471-2164

e-ISSN

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Svazek periodika

14

Číslo periodika v rámci svazku

APR 4 2013

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

11

Strana od-do

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Kód UT WoS článku

000317415500001

EID výsledku v databázi Scopus

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