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Common Wheat Chromosome 5B Composition Analysis Using Low-Coverage 454 Sequencing
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SYSNO ASEP 0433557 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Common Wheat Chromosome 5B Composition Analysis Using Low-Coverage 454 Sequencing Author(s) Sergeeva, E.M. (RU)
Afonnikov, D. A. (RU)
Koltunova, M. K. (RU)
Gusev, V.D. (RU)
Miroshnichenko, L. A. (RU)
Vrána, Jan (UEB-Q) RID, ORCID
Kubaláková, Marie (UEB-Q) RID
Poncet, C. (FR)
Sourdille, P. (FR)
Feuillet, C. (US)
Doležel, Jaroslav (UEB-Q) RID, ORCID
Salina, E.A. (CU)Source Title Plant Genome. - : Wiley
Roč. 7, č. 2 (2014)Number of pages 16 s. Language eng - English Country US - United States Keywords GENOME SHOTGUN SEQUENCES ; IN-SITU HYBRIDIZATION ; HEXAPLOID WHEAT Subject RIV EB - Genetics ; Molecular Biology R&D Projects GBP501/12/G090 GA ČR - Czech Science Foundation (CSF) LO1204 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Institutional support UEB-Q - RVO:61389030 UT WOS 000338834700002 DOI 10.3835/plantgenome2013.10.0031 Annotation The sequencing of individual chromosomes of common wheat is in progress. The molecular size of wheat chromosome 5B is nearly 870 Mb (5BL = 580 Mb and 5BS = 290 Mb). We produced the first low coverage 454-sequencing of the long and short arms of wheat chromosome 5B (110,793 and 39,695 reads, which compose 8 and 6% of total 5BL and 5BS length, respectively) and calculated the ratios of the different families of repetitive sequences, including transposable elements (TEs), satellite repeats (Afa, pSc119.2, 5S rDNA and 45S rDNA), and microsatellites, as well as direct and inverted repeat motifs. The TEs accounted for 70% of the total analyzed nucleotide sequences. The content of the Cereba retrotransposon family differed between the two arms of chromosome 5B. Comparing the reads of chromosome 5B with the data from chromosome 5A, we found the retrotransposons Fatima and Sakura and DNA transposon Jorge were prevalent in 5B. The hypothetical coding sequences accounted for 2.0% of the short arm and 2.07% of the long arm. Using in silico mapping, we identified the regions of synteny with rice and Brachypodium chromosomes (1,073,526 and 1,767,298 bp aligned, respectively), and the result was consistent with the data from the expressed sequence tag (EST) mapping of wheat 5B chromosome to the genomes of these grasses. Thus, these results show that low coverage survey sequencing can provide useful information about the composition and evolution of wheat chromosome 5B. Workplace Institute of Experimental Botany Contact David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Year of Publishing 2015
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