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Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1.
PLoS One. 2012; 7(2):e30784.Plos

Abstract

BACKGROUND

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.

METHODOLOGY/PRINCIPAL FINDINGS

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. 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.

CONCLUSIONS

The 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.

Authors+Show Affiliations

Health and Environment Department, Bioresources, Austrian Institute of Technology, Tulln, Austria.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

22328922

Citation

Fluch, Silvia, et al. "Sequence Composition and Gene Content of the Short Arm of Rye (Secale Cereale) Chromosome 1." PloS One, vol. 7, no. 2, 2012, pp. e30784.
Fluch S, Kopecky D, Burg K, et al. Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1. PLoS One. 2012;7(2):e30784.
Fluch, S., Kopecky, D., Burg, K., Šimková, H., Taudien, S., Petzold, A., Kubaláková, M., Platzer, M., Berenyi, M., Krainer, S., Doležel, J., & Lelley, T. (2012). Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1. PloS One, 7(2), e30784. https://doi.org/10.1371/journal.pone.0030784
Fluch S, et al. Sequence Composition and Gene Content of the Short Arm of Rye (Secale Cereale) Chromosome 1. PLoS One. 2012;7(2):e30784. PubMed PMID: 22328922.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1. AU - Fluch,Silvia, AU - Kopecky,Dieter, AU - Burg,Kornel, AU - Šimková,Hana, AU - Taudien,Stefan, AU - Petzold,Andreas, AU - Kubaláková,Marie, AU - Platzer,Matthias, AU - Berenyi,Maria, AU - Krainer,Siegfried, AU - Doležel,Jaroslav, AU - Lelley,Tamas, Y1 - 2012/02/06/ PY - 2011/06/14/received PY - 2011/12/26/accepted PY - 2012/2/14/entrez PY - 2012/2/14/pubmed PY - 2012/6/12/medline SP - e30784 EP - e30784 JF - PloS one JO - PLoS One VL - 7 IS - 2 N2 - BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. 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. CONCLUSIONS: The 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. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/22328922/Sequence_composition_and_gene_content_of_the_short_arm_of_rye__Secale_cereale__chromosome_1_ L2 - https://dx.plos.org/10.1371/journal.pone.0030784 DB - PRIME DP - Unbound Medicine ER -