title: The first draft of the pigeonpea genome sequence.
abstract: Pigeonpea (Cajanus cajan) is an important grain legume of the Indian subcontinent, South-East Asia and East Africa. More than eighty five percent of the world pigeonpea is produced and consumed in India where it is a key crop for food and nutritional security of the people. Here we present the first draft of the genome sequence of a popular pigeonpea variety 'Asha'. The genome was assembled using long sequence reads of 454 GS-FLX sequencing chemistry with mean read lengths of >550 bp and >10-fold genome coverage, resulting in 510,809,477 bp of high quality sequence. Total 47,004 protein coding genes and 12,511 transposable elements related genes were predicted. We identified 1,213 disease resistance/defense response genes and 152 abiotic stress tolerance genes in the pigeonpea genome that make it a hardy crop. In comparison to soybean, pigeonpea has relatively fewer number of genes for lipid biosynthesis and larger number of genes for cellulose synthesis. The sequence contigs were arranged in to 59,681 scaffolds, which were anchored to eleven chromosomes of pigeonpea with 347 genic-SNP markers of an intra-species reference genetic map. Eleven pigeonpea chromosomes showed low but significant synteny with the twenty chromosomes of soybean. The genome sequence was used to identify large number of hypervariable 'Arhar' simple sequence repeat (HASSR) markers, 437 of which were experimentally validated for PCR amplification and high rate of polymorphism among pigeonpea varieties. These markers will be useful for fingerprinting and diversity analysis of pigeonpea germplasm and molecular breeding applications. This is the first plant genome sequence completed entirely through a network of Indian institutions led by the Indian Council of Agricultural Research and provides a valuable resource for the pigeonpea variety improvement.
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Nagendra K
authors.initials: NK
authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Deepak K
authors.initials: DK
authors.lastname: Gupta
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Pawan K
authors.initials: PK
authors.lastname: Jayaswal
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Ajay K
authors.initials: AK
authors.lastname: Mahato
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Sutapa
authors.initials: S
authors.lastname: Dutta
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Sangeeta
authors.initials: S
authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Shefali
authors.initials: S
authors.lastname: Bhutani
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Vivek
authors.initials: V
authors.lastname: Dogra
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Bikram P
authors.initials: BP
authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Giriraj
authors.initials: G
authors.lastname: Kumawat
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Jitendra K
authors.initials: JK
authors.lastname: Pal
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Awadhesh
authors.initials: A
authors.lastname: Pandit
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Archana
authors.initials: A
authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Hukum
authors.initials: H
authors.lastname: Rawal
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Kumar
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: G
authors.initials: G
authors.lastname: Rama Prashat
authors.affiliation: Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012 India.
authors.forename: Ambika
authors.initials: A
authors.lastname: Khare
authors.affiliation: Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012 India.
authors.forename: Rekha
authors.initials: R
authors.lastname: Yadav
authors.affiliation: Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012 India.
authors.forename: Ranjit S
authors.initials: RS
authors.lastname: Raje
authors.affiliation: Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, UP 221005 India.
authors.forename: Mahendra N
authors.initials: MN
authors.lastname: Singh
authors.affiliation: Indian Institute of Pulses Research, Kanpur, UP 208024 India.
authors.forename: Subhojit
authors.initials: S
authors.lastname: Datta
authors.affiliation: University of Agricultural Sciences, Dharwad, Karnataka 580005 India.
authors.forename: Bashasab
authors.initials: B
authors.lastname: Fakrudin
authors.affiliation: Panjabrao Deshmukh Krishi Vidyapeeth, Krishinagar, Akola, Maharasthra 444 104 India.
authors.forename: Keshav B
authors.initials: KB
authors.lastname: Wanjari
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Rekha
authors.initials: R
authors.lastname: Kansal
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Prasanta K
authors.initials: PK
authors.lastname: Dash
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Pradeep K
authors.initials: PK
authors.lastname: Jain
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Ramcharan
authors.initials: R
authors.lastname: Bhattacharya
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Kishor
authors.initials: K
authors.lastname: Gaikwad
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Trilochan
authors.initials: T
authors.lastname: Mohapatra
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: R
authors.initials: R
authors.lastname: Srinivasan
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012 India.
authors.forename: Tilak R
authors.initials: TR
authors.lastname: Sharma
keywords: Disease resistance; Genome sequence; Legumes; Pigeonpea; SSR markers