title: Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement.
abstract: Cicer reticulatum L. is the wild progenitor of the fourth most important legume crop chickpea (C. arietinum L.). We assembled short-read sequences into 416 Mb draft genome of C. reticulatum and anchored 78% (327 Mb) of this assembly to eight linkage groups. Genome annotation predicted 25,680 protein-coding genes covering more than 90% of predicted gene space. The genome assembly shared a substantial synteny and conservation of gene orders with the genome of the model legume Medicago truncatula. Resistance gene homologs of wild and domesticated chickpeas showed high sequence homology and conserved synteny. Comparison of gene sequences and nucleotide diversity using 66 wild and domesticated chickpea accessions suggested that the desi type chickpea was genetically closer to the wild species than the kabuli type. Comparative analyses predicted gene flow between the wild and the cultivated species during domestication. Molecular diversity and population genetic structure determination using 15,096 genome-wide single nucleotide polymorphisms revealed an admixed domestication pattern among cultivated (desi and kabuli) and wild chickpea accessions belonging to three population groups reflecting significant influence of parentage or geographical origin for their cultivar-specific population classification. The assembly and the polymorphic sequence resources presented here would facilitate the study of chickpea domestication and targeted use of wild Cicer germplasms for agronomic trait improvement in chickpea.
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
authors: Sonal
authors: S
authors: Gupta
authors: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
authors: Kashif
authors: K
authors: Nawaz
authors: Sabiha
authors: S
authors: Parween
authors: Riti
authors: R
authors: Roy
authors: Kamlesh
authors: K
authors: Sahu
authors: Anil
authors: A
authors: Kumar Pole
authors: Hitaishi
authors: H
authors: Khandal
authors: Rishi
authors: R
authors: Srivastava
authors: Swarup
authors: S
authors: Kumar Parida
authors: Debasis
authors: D
authors: Chattopadhyay
mesh_terms: D029863:Cicer / Q000235:genetics*; D018745:Genome, Plant; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012987:Soil
chemical_list: D012987:Soil
keywords: Cicer reticulatum L. PI489777; annotation; diversity; genome sequence; wild chickpea