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Plant Cell. 2013 Oct;25(10):3685-98. doi: 10.1105/tpc.113.114553. Epub 2013 Oct 8.

Reticulate evolution of the rye genome.

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  • 1Helmholtz Center Munich, German Research Centre for Environmental Health, Munich Information Center for Protein Sequences/IBIS, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany.

Abstract

Rye (Secale cereale) is closely related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to its large genome (~8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes. This was achieved by high-throughput transcript mapping, chromosome survey sequencing, and integration of conserved synteny information of three sequenced model grass genomes (Brachypodium distachyon, rice [Oryza sativa], and sorghum [Sorghum bicolor]). This enabled a genome-wide high-density comparative analysis of rye/barley/model grass genome synteny. Seventeen conserved syntenic linkage blocks making up the rye and barley genomes were defined in comparison to model grass genomes. Six major translocations shaped the modern rye genome in comparison to a putative Triticeae ancestral genome. Strikingly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks. This indicates that introgressive hybridizations (diploid or polyploidy hybrid speciation) and/or a series of whole-genome or chromosome duplications played a role in rye speciation and genome evolution.

PMID:
24104565
PMCID:
PMC3877785
DOI:
10.1105/tpc.113.114553
[PubMed - indexed for MEDLINE]
Free PMC Article
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