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.

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

“…For checking the completeness of the assembly, a transcriptome assembly comprising 21,434 unigenes, referred to as transcriptome assembly contigs (TACs) and defined based on 10,817 Sanger ESTs, 2.19 million 454/FLX transcript reads 34 and 128.91 million Illumina transcript reads 34 was used for mapping the TACs to the assembly genome with the help of BLAT software. Analysis was done at different criteria of percent sequence homology and percent coverage (Supplementary Table 5).…”

“…The genome assembly was also used to align 128.9 million Illumina transcript reads from 12 different pigeonpea genotypes that are parents of 6 mapping populations for identification of SNPs 34 . By aligning the transcript reads for a given parental combination onto the pigeonpea genome assembly, we identified sequence variants that differ between the parental combinations.…”

An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants

“…The emergence of next-generation sequencing has facilitated the identification of transcribed genes in a number of nonmodel species. For many species, nextgeneration sequencing technology has allowed the development of a transcriptome sequence prior to the sequencing of the genome, as in alfalfa (Medicago sativa; Yang et al, 2011), lentil (Lens culinaris; Kaur et al, 2011), pea (Pisum sativum; Franssen et al, 2011), pigeon pea (Cajanus cajan; Dubey et al, 2011), sweet potato (Ipomoea batatas; Wang et al, 2010b), eucalyptus (Eucalyptus spp. ; Mizrachi et al, 2010), carrot (Daucus carota; Iorizzo et al, 2011), watermelon (Citrullis vulgaris; Guo et al, 2011), rubber tree (Hevea brasiliensis; Xia et al, 2011), pitcher plant (Sarracenia spp.…”

Functional genomics to study stress responses in crop legumes: progress and prospects

“…The application of NGS technology has led to the production of transcriptome assemblies for chickpea (Hiremath et al 2011;Garg et al 2011a), pigeonpea (Dubey et al 2011;Kudapa et al 2012), peanut , pea (Franssen et al 2011) and lupin (Parra-González et al 2012). In addition, the combination of reads generated by NGS platforms and Sanger ESTs has improved transcriptome assemblies, particularly in the context of contig length (Hiremath et al 2011).…”

“…This report identified 250 transcripts with root-, and 217 transcripts with shoot-specific expression. In the case of pigeonpea, significant differential expression was observed for 6673 to 11 518 TUSs for specific parental combinations (tolerant/ sensitive for FW and SMD) (Dubey et al 2011), and candidate FW-and SMD-responsive genes identified, which represent starting points to analyse biotic stress.…”