title: Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.).
abstract: This study reports generation of large-scale genomic resources for pigeonpea, a so-called 'orphan crop species' of the semi-arid tropic regions. FLX/454 sequencing carried out on a normalized cDNA pool prepared from 31 tissues produced 494 353 short transcript reads (STRs). Cluster analysis of these STRs, together with 10 817 Sanger ESTs, resulted in a pigeonpea trancriptome assembly (CcTA) comprising of 127 754 tentative unique sequences (TUSs). Functional analysis of these TUSs highlights several active pathways and processes in the sampled tissues. Comparison of the CcTA with the soybean genome showed similarity to 10 857 and 16 367 soybean gene models (depending on alignment methods). Additionally, Illumina 1G sequencing was performed on Fusarium wilt (FW)- and sterility mosaic disease (SMD)-challenged root tissues of 10 resistant and susceptible genotypes. More than 160 million sequence tags were used to identify FW- and SMD-responsive genes. Sequence analysis of CcTA and the Illumina tags identified a large new set of markers for use in genetics and breeding, including 8137 simple sequence repeats, 12 141 single-nucleotide polymorphisms and 5845 intron-spanning regions. Genomic resources developed in this study should be useful for basic and applied research, not only for pigeonpea improvement but also for other related, agronomically important legumes.
authors.affiliation: Centre of Excellence in Genomics (CEG), Building #300, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Greater Hyderabad, India.
authors.forename: Anuja
authors.initials: A
authors.lastname: Dubey
authors.forename: Andrew
authors.initials: A
authors.lastname: Farmer
authors.forename: Jessica
authors.initials: J
authors.lastname: Schlueter
authors.forename: Steven B
authors.initials: SB
authors.lastname: Cannon
authors.forename: Brian
authors.initials: B
authors.lastname: Abernathy
authors.forename: Reetu
authors.initials: R
authors.lastname: Tuteja
authors.forename: Jimmy
authors.initials: J
authors.lastname: Woodward
authors.forename: Trushar
authors.initials: T
authors.lastname: Shah
authors.forename: Benjamin
authors.initials: B
authors.lastname: Mulasmanovic
authors.forename: Himabindu
authors.initials: H
authors.lastname: Kudapa
authors.forename: Nikku L
authors.initials: NL
authors.lastname: Raju
authors.forename: Ragini
authors.initials: R
authors.lastname: Gothalwal
authors.forename: Suresh
authors.initials: S
authors.lastname: Pande
authors.forename: Yongli
authors.initials: Y
authors.lastname: Xiao
authors.forename: Chris D
authors.initials: CD
authors.lastname: Town
authors.forename: Nagendra K
authors.initials: NK
authors.lastname: Singh
authors.forename: Gregory D
authors.initials: GD
authors.lastname: May
authors.forename: Scott
authors.initials: S
authors.lastname: Jackson
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D036561:Cajanus / Q000235:genetics*; D020869:Gene Expression Profiling; D005819:Genetic Markers; D018745:Genome, Plant; D007438:Introns; D018895:Microsatellite Repeats; D005810:Multigene Family; D020641:Polymorphism, Single Nucleotide; D014158:Transcription, Genetic
chemical_list: D005819:Genetic Markers