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DNA Res. 2014;21(2):103-14. doi: 10.1093/dnares/dst041. Epub 2013 Oct 1.

Next-generation survey sequencing and the molecular organization of wheat chromosome 6B.

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1
1Bioinformatics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.

Abstract

Common wheat (Triticum aestivum L.) is one of the most important cereals in the world. To improve wheat quality and productivity, the genomic sequence of wheat must be determined. The large genome size (∼17 Gb/1 C) and the hexaploid status of wheat have hampered the genome sequencing of wheat. However, flow sorting of individual chromosomes has allowed us to purify and separately shotgun-sequence a pair of telocentric chromosomes. Here, we describe a result from the survey sequencing of wheat chromosome 6B (914 Mb/1 C) using massively parallel 454 pyrosequencing. From the 4.94 and 5.51 Gb shotgun sequence data from the two chromosome arms of 6BS and 6BL, 235 and 273 Mb sequences were assembled to cover ∼55.6 and 54.9% of the total genomic regions, respectively. Repetitive sequences composed 77 and 86% of the assembled sequences on 6BS and 6BL, respectively. Within the assembled sequences, we predicted a total of 4798 non-repetitive gene loci with the evidence of expression from the wheat transcriptome data. The numbers and chromosomal distribution patterns of the genes for tRNAs and microRNAs in wheat 6B were investigated, and the results suggested a significant involvement of DNA transposon diffusion in the evolution of these non-protein-coding RNA genes. A comparative analysis of the genomic sequences of wheat 6B and monocot plants clearly indicated the evolutionary conservation of gene contents.

KEYWORDS:

chromosome 6B; genome sequencing; next-generation sequencing; wheat

PMID:
24086083
PMCID:
PMC3989483
DOI:
10.1093/dnares/dst041
[Indexed for MEDLINE]
Free PMC Article
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