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The Plant Genome Abstract - Original Research

Common Wheat Chromosome 5B Composition Analysis Using Low-Coverage 454 Sequencing

 

This article in TPG

  1. Vol. 7 No. 2
    unlockOPEN ACCESS
     
    Received: Oct 08, 2013
    Published: December 1, 2014


    * Corresponding author(s): sergeeva@bionet.nsc.ru
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doi:10.3835/plantgenome2013.10.0031
  1. E. M. Sergeeva *a,
  2. D. A. Afonnikova,
  3. M. K. Koltunovaa,
  4. V. D. Gusevb,
  5. L. A. Miroshnichenkob,
  6. J. Vránac,
  7. M. Kubalákovác,
  8. C. Poncetd,
  9. P. Sourdilled,
  10. C. Feuillete,
  11. J. Doleželc and
  12. E. A. Salinaa
  1. a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentieva Ave. 10, 630090, Novosibirsk, Russia
    b Sobolev Institute of Mathematics, Siberian Branch of Russian Academy of Sciences, Koptyug Ave. 4, 630090, Novosibirsk, Russia
    c Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, ŠlechtitelŮ 31, CZ-78371, Olomouc, Czech Republic
    d UMR INRA-UBP Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 630390 Clermont–Ferrand, Cedex 2, France
    e Bayer Crop Science, 3500 Paramount Pkwy., Morrisville, NC 27560

Abstract

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.

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