Belova, T., Zhan, B., Wright, J., Caccamo, M., Asp, T., Šimková, H., Kent, M., Bendixen, C., Panitz, F., Lien, S., Doležel, J., Olsen, O.-A., Sandve, S.R.
BMC GENOMICS
14:
222,
2013
Klíčová slova:
Wheat, Assembly, Scaffold, Mate-pair, MDA, Improvement
Abstrakt:
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 ~7 fold, while at the
highest stringency N50 was only increased by ~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 ~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.
Fulltext: kontaktujte autory z ÚEB
Autoři z ÚEB: Jaroslav Doležel,
Hana Šimková
Čeština
English