Počet záznamů: 1
Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat
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SYSNO ASEP 0396781 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat Tvůrce(i) Belova, T. (NO)
Zhan, B.J. (NO)
Wright, J. (GB)
Caccamo, M. (GB)
Asp, T. (DK)
Šimková, Hana (UEB-Q) RID, ORCID
Kent, M. (NO)
Bendixen, C. (DK)
Panitz, F. (DK)
Lien, S. (NO)
Doležel, Jaroslav (UEB-Q) RID, ORCID
Olsen, O.A. (NO)
Sandve, S.R. (NO)Zdroj.dok. BMC Genomics. - : BioMed Central - ISSN 1471-2164
Roč. 14, APR 4 2013 (2013)Poč.str. 11 s. Jazyk dok. eng - angličtina Země vyd. GB - Velká Británie Klíč. slova Scaffold ; Assembly ; Wheat Vědní obor RIV EB - Genetika a molekulární biologie CEP GAP501/12/2554 GA ČR - Grantová agentura ČR CEZ AV0Z50380511 - UEB-Q (2005-2011) UT WOS 000317415500001 DOI 10.1186/1471-2164-14-222 Anotace 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 content cause 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 total coverage 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 scaffolding stringency applied. At the lowest stringency the assembly N50 increased by similar to 7 fold, while at the highest stringency N50 was only increased by similar to 1.5 fold. Furthermore, a strong positive correlation between estimated scaffold reliability and scaffold assembly stringency was observed. A 7BS scaffold assembly with reduced MP coverage proved that assembly contiguity was affected only to a small degree down to similar to 50% of the original coverage. Conclusion: The effect of MP data integration into pair end shotgun assemblies of wheat chromosome was moderate; possibly due to poor contig assembly contiguity, the extreme repeat content of wheat, and the use of amplified chromosomal DNA for MP library construction. Pracoviště Ústav experimentální botaniky Kontakt David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Rok sběru 2014
Počet záznamů: 1