Rajeev K Varshney1,2,*, Chi Song3, Rachit K Saxena1, Sarwar Azam1, Sheng Yu3, Andrew G Sharpe4, Steven Cannon5, Jongmin Baek6, Benjamin D Rosen6, Bunyamin Tar'an7, Teresa Millan8, Xudong Zhang3, Larissa D Ramsay4, Aiko Iwata9, Ying Wang3, William Nelson10,
Andrew D Farmer11, Pooran M Gaur1, Carol Soderlund10,
R Varma Penmetsa6, Chunyan Xu3, Arvind K Bharti11, Weiming He3, Peter Winter12, Shancen Zhao3, James K Hane13,
Noelia Carrasquilla-Garcia6, Janet A Condie4, Hari D Upadhyaya1, Mingcheng Luo6, Mahendar Thudi1, CLL Gowda1, Narendra P Singh14,
Judith Lichtenzveig15, Krishna K Gali4, Josefa Rubio8, N Nadarajan16, Jaroslav Dolezel17, Kailash C Bansal18, Xun Xu3, David Edwards19, Gengyun Zhang3, Guenter Kahl20, Juan Gil8, Karam B Singh13,21,
Swapan K Datta22, Scott A Jackson9, Jun Wang3,23,*, Douglas R Cook6,*
1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
2CGIAR Generation Challenge Programme, Mexico
3Beijing Genomics Institute (BGI) - Shenzhen, China
4National Research Council Canada (NRC-CNRC), Canada
5USDA-ARS, Iowa State University, Ames, USA
6Department of Plant Pathology, University of California-Davis, Davis, California, USA
7Crop Development Centre, Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
8Departamento de Genetica, University of Cordoba, Cordoba, Spain
9Centers for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA
10University of Arizona, Tucson, Arizona, USA
11National Center for Genome Resources (NCGR), Santa Fe, New Mexico, USA
12GenXPro GmbH, Frankfurt Main, Germany
13Commonwealth Scientific and Industrial Research Organization (CSIRO), Australia
14All India Coordinated Research Project on Chickpea (AICRP), Indian Council of Agricultural Research (ICAR), New Delhi, India
15Environment and Agriculture, Curtin University, Bentley, Australia
16Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, India
17Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
18National Bureau of Plant Genetic Resources (NBPGR), Indian Council of Agricultural Research (ICAR), New Delhi, India
19ACPFG and The University of Queensland, St. Lucia, Queensland, Australia
20Johann Wolfgang Goethe - University, Frankfurt am Main, Germany
21The University of Western Australia Institute of Agriculture, The University of Western Australia, Crawley, Australia
22Division of Crop Sciences, Indian Council of Agricultural Research (ICAR), New Delhi, India
23Department of Biology, University of Copenhagen, Copenhagen, Denmark
*Correspondence should be addressed to Rajeev K Varshney (r.k.varshney@cgiar.org),
Jun Wang (wangj@genomics.org.cn), or Douglas R Cook (drcook@ucdavis.edu).
Abstract
Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen and playing a crucial role in food security in developing countries. We report the draft genome sequence of the ~738 Mb chickpea genome from CDC Frontier, a kabuli variety, which contains an estimated 28,269 genes. Re-sequencing and analysis of 90 cultivated and wild genotypes from 10 different countries identifies both targets of breeding-associated genetic sweeps and targets of breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main classes of cultivated chickpea- desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding, and provide insights into both genome diversity and domestication.
Click here to download the full research article published in Nature Biotechnology(AOP 27 Jan 2013)
Click here to download "Assembly and annotation data" for Chickpea genome
Supplementary material
Supplementary Table 1 Details on 90 Cicer accessions used for re-sequencing (29 cultivars) and RAD genotyping (61 accessions including cultivars/breeding lines, landraces and wild relatives)
Supplementary Table 2 Construction of libraries, generation and filtering of sequencing data used for genome assembly
Supplementary Table 3 Statistics of the raw and final genome assembly
Supplementary Table 4 Estimation of chickpea genome size based on K-mer statistics
Supplementary Table 5 Genome sequence assembly organized by chromosome-level pseudomolecules
Supplementary Table 6 Details on the repeat regions and masking
Supplementary Table 7 Prediction of protein-coding genes in chickpea
Supplementary Table 8 Functional annotation of predicted
genes of chickpea
Supplementary Table 9Summary of non-coding RNA genes in the
chickpea genome
Supplementary Table 10 Assessment of gene space captured in genome assembly (CaGA V1.0), using the 454 reads with length more than 500 bp from CDC Frontier
Supplementary Table 11 Evaluation of completeness of the genome assembly using core eukaryotic gene mapping approach (CEGMA)
Supplementary Table 12 The statistics of aligned genes between chickpea and A. thaliana, chickpea and M. truncatula, chickpea and G. max, chickpea and C. cajan, chickpea and L. japonicus. The BLASTP with the 1e-5 was used to do the alignment
Supplementary Table 13 Synteny blocks of the chickpea genome conserved with genomes of four legume (Medicago truncatula, Lotus japonicus, soybean, and pigeonpea) and two non-legume dicot (Arabidopsis thailiana and grape) genomes
Supplementary Table 14 Gene family analysis of predicted chickpea genes in comparison to six other dicot genomes
Supplementary Table 15 Summary of orthologous and paralogous genes in chickpea relative to four legume (Medicago truncatula, Lotus japonicus, pigeonpea, and soybean) and two non-legume dicot (Arabidopsis thaliana and grape) genomes
Supplementary Table 16 Identification of simple sequence repeats: their distribution and primer design for chickpea genetics and breeding applications
Supplementary Table 17 Primer sequences for SSR markers
Supplementary Table 18 Identification of SNPs as compared to CDC Frontier
Supplementary Table 19 Diversity levels in elite chickpea varieties
Supplementary Table 20 Identification and distribution of molecular variation (SNPs and INDELs) among 8 pseudomolecules Ca1 to Ca8 and unanchored genome sequence as Ca0
Supplementary Figure 1 CDC Frontier kabuli chickpea
Supplementary Figure 2 K-mer (17-mer) analysis for estimating the chickpea genome
Supplementary Figure 3 FISH (fluorescence in situ hybridization) image of 100 bp tandem repeat (green) and 74 bp tandem repeat (red)
Supplementary Figure 4 An overview on orthologs and paralogs
genes in chickpea
Supplementary Figure 5 Maximum likelihood phylogram comparing NBS domains of the non-TIR resistance gene homologs from chickpea (Ca) with Medicago (Mt)
Supplementary Figure 6 Maximum likelihood phylogram comparing NBS domains of the TIR resistance gene homologs from chickpea (Ca) with Medicago truncatula (Mt)
Supplementary Figure 7 Identification of single nucleotide polymorphisms (SNPs) in five genotypes
Supplementary Figure 8 Seeds of some representative wild species, landraces and breeding lines/ released varieties showing the diversity in the germplasm lines used for re-sequencing
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