RRC ID 12002
Author Sato K, Motoi Y, Yamaji N, Yoshida H.
Title 454 sequencing of pooled BAC clones on chromosome 3H of barley.
Journal BMC Genomics
Abstract BACKGROUND:Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000 Mbp). Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H.
RESULTS:We sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1.
CONCLUSIONS:We demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1.
Volume 12
Pages 246
Published 2011-5-19
DOI 10.1186/1471-2164-12-246
PII 1471-2164-12-246
PMID 21592415
PMC PMC3224129
MeSH Alleles Chromosome Mapping Chromosomes, Artificial, Bacterial / genetics* Chromosomes, Plant / genetics* Cloning, Molecular Expressed Sequence Tags Gene Library Genes, Plant / genetics Genetic Variation Genomics Haplotypes Hordeum / genetics* Oryza / genetics Sequence Analysis, DNA / methods* Sequence Homology, Nucleic Acid
IF 3.501
Times Cited 9
WOS Category BIOTECHNOLOGY & APPLIED MICROBIOLOGY GENETICS & HEREDITY
Resource
Barley BAC clones