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

Result code in 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>

Result on the web

<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>

Result language

angličtina

Original language name

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

Original language description

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

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

EB - Genetics and molecular biology

OECD FORD branch

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Project

<a href="/en/project/GAP501%2F12%2F2554" target="_blank" >GAP501/12/2554: Physical map of wheat chromosome arm 7DS and its use to clone a Russian wheat aphid resistance gene</a><br>

Continuities

Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year

2013

Confidentiality

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

Name of the periodical

B M C Genomics

ISSN

1471-2164

e-ISSN

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Volume of the periodical

14

Issue of the periodical within the volume

APR 4 2013

Country of publishing house

GB - UNITED KINGDOM

Number of pages

11

Pages from-to

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UT code for WoS article

000317415500001

EID of the result in the Scopus database

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