ArticlePloS one2012
Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi-omics approach.The plant genome · 2022Article
- Review
- Article
- The Diversity of Sequence and Chromosomal Distribution of New Transposable Element-Related Segments in the Rye Genome Revealed by FISH and Lineage Annotation.Frontiers in plant science · 2017Article
- The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements.BMC genomics · 2016Article
- Characterization of Stripe Rust Resistance Genes in the Wheat Cultivar Chuanmai45.International journal of molecular sciences · 2016Article
- DArT Markers Effectively Target Gene Space in the Rye Genome.Frontiers in plant science · 2016Article
- Genomics approaches for crop improvement against abiotic stress.TheScientificWorldJournal · 2013Review
- Chromosomes in the flow to simplify genome analysis.Functional & integrative genomics · 2012Review
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Authors and funding
12 authors.
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Abstract
backgroundThe 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. METHODOLOGY/PRINCIPAL
findingsMultiple 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. Synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of Brachypodium distachyon chromosome 2. Comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice.
conclusionsThe present study revealed the gene content and potential gene functions on this chromosome arm and demonstrated numerous sequence elements like SSRs and gene-related sequences, which can be utilised for future research as well as in breeding of wheat and rye.
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