title: An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.).
abstract: Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Sabiha
authors.initials: S
authors.lastname: Parween
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Kashif
authors.initials: K
authors.lastname: Nawaz
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Riti
authors.initials: R
authors.lastname: Roy
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Anil K
authors.initials: AK
authors.lastname: Pole
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: B
authors.initials: B
authors.lastname: Venkata Suresh
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Gopal
authors.initials: G
authors.lastname: Misra
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Mukesh
authors.initials: M
authors.lastname: Jain
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Gitanjali
authors.initials: G
authors.lastname: Yadav
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Sabhyata
authors.initials: S
authors.lastname: Bhatia
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Debasis
authors.initials: D
authors.lastname: Chattopadhyay
mesh_terms: D002874:Chromosome Mapping; D029863:Cicer / Q000235:genetics*; D018745:Genome, Plant; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*