Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1.

PloS One
Silvia FluchTamas Lelley

Abstract

The purpose of the study is to elucidate the sequence composition of the short arm of rye chromosome 1 (Secale cereale) with special focus on its gene content, because this portion of the rye genome is an integrated part of several hundreds of bread wheat varieties worldwide. Multiple Displacement Amplification of 1RS DNA, obtained from flow sorted 1RS chromosomes, using 1RS ditelosomic wheat-rye addition line, and subsequent Roche 454FLX sequencing of this DNA yielded 195,313,589 bp sequence information. This quantity of sequence information resulted in 0.43× sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%. A detailed analysis revealed that more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions. Repetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3%) being the most abundant. More than four thousand simple sequence repeat (SSR) sites mostly located in gene related sequence reads were identified for possible marker development. The existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads. ...Continue Reading

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Datasets Mentioned

BETA
SRA012605

Methods Mentioned

BETA
flow cytometry
454 sequencing
PCR
MDA

Software Mentioned

SciRoKo
BLAST
SQL Server
RepeatMasker
C t analysis
BLASTClust
MySQL
WU
Secale
Perl scripts

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