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Analysis of genome organization, composition and microsynteny using 500 kb BAC sequences in chickpea

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Abstract

The small genome size (740 Mb), short life cycle (3 months) and high economic importance as a food crop legume make chickpea (Cicer arietinum L.) an important system for genomics research. Although several genetic linkage maps using various markers and genomic tools have become available, sequencing efforts and their use are limited in chickpea genomic research. In this study, we explored the genome organization of chickpea by sequencing approximately 500 kb from 11 BAC clones (three representing ascochyta blight resistance QTL1 (ABR-QTL1) and eight randomly selected BAC clones). Our analysis revealed that these sequenced chickpea genomic regions have a gene density of one per 9.2 kb, an average gene length of 2,500 bp, an average of 4.7 exons per gene, with an average exon and intron size of 401 and 316 bp, respectively, and approximately 8.6% repetitive elements. Other features analyzed included exon and intron length, number of exons per gene, protein length and %GC content. Although there are reports on high synteny among legume genomes, the microsynteny between the 500 kb chickpea and available Medicago truncatula genomic sequences varied depending on the region analyzed. The GBrowse-based annotation of these BACs is available at http://www.genome.ou.edu/plants_totals.html. We believe that our work provides significant information that supports a chickpea genome sequencing effort in the future.

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Acknowledgments

PNR wishes to thank McKnight Foundation, USA, for the financial support. MB wishes to thank National Science Foundation, USA, for supporting genome sequencing research. We thank Hongshing Lai and Steve Kenton of bioinformatics group at OU for implementing the Genome Browser for the Chickpea BACs and for their help and advice during their analysis.

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Authors and Affiliations

  1. USDA-ARS and Crop and Soil Sciences, Washington State University, 303 Johnson Hall, Pullman, WA, 99164-6434, USA

    P. N. Rajesh & Fred J. Muehlbauer

  2. Advanced Center for Genome Technology (ACGT), Department of Chemistry and Biochemistry Stephenson Research and Technology Center (SRTC), University of Oklahoma, 101 David L. Boren Blvd, Rm 2107, Norman, OK, 73019-0370, USA

    Majesta O’Bleness & Bruce A. Roe

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  1. P. N. Rajesh
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  2. Majesta O’Bleness
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  3. Bruce A. Roe
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  4. Fred J. Muehlbauer
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Correspondence to P. N. Rajesh.

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Communicated by D. A. Hoisington.

P. N. Rajesh and M. O’Bleness have contributed equally.

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Rajesh, P.N., O’Bleness, M., Roe, B.A. et al. Analysis of genome organization, composition and microsynteny using 500 kb BAC sequences in chickpea. Theor Appl Genet 117, 449–458 (2008). https://doi.org/10.1007/s00122-008-0789-0

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  • DOI: https://doi.org/10.1007/s00122-008-0789-0

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