eprintid: 111
rev_number: 22
eprint_status: archive
userid: 6
dir: disk0/00/00/01/11
datestamp: 2011-07-25 11:47:49
lastmod: 2011-07-25 11:49:42
status_changed: 2011-07-25 11:47:49
type: article
metadata_visibility: show
contact_email: Library-ICRISAT@CGIAR.ORG
item_issues_count: 0
creators_name: Dubey, A
creators_name: Farmer, A
creators_name: Schlueter, J
creators_name: Cannon, S B
creators_name: Abernathy, B
creators_name: Tuteja, R
creators_name: Woodward, J
creators_name: Shah, T
creators_name: Mulasmanovic, B
creators_name: Kudapa, H
creators_name: Raju, N L
creators_name: Gothalwal, R
creators_name: Pande, S
creators_name: Xiao, Y
creators_name: Town, C D
creators_name: Singh, N K
creators_name: May, G D
creators_name: Jackson, S
creators_name: Varshney, R K
icrisatcreators_name: Dubey, A
icrisatcreators_name: Tuteja, R
icrisatcreators_name: Shah, T
icrisatcreators_name: Kudapa, H
icrisatcreators_name: Raju, N L
icrisatcreators_name: Pande, S
icrisatcreators_name: Varshney, R K
affiliation: ICRISAT(Patancheru)
affiliation: Barkatullah University(Bhopal)
affiliation: National Centre for Genome Resources(Santa Fe)
affiliation: University of North Carolina(Charlotte)
affiliation: USDA-ARS(Ames)
affiliation: Purdue University(West Lafayette)
affiliation: J. Craig Venter Institute(Rockville)
affiliation: National Research Centre on Plant Biotechnology(New Delhi)
affiliation: CGIAR Generation Challenge Programme(Mexico)
country: India
country: USA
country: Mexico
title: Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.)
ispublished: pub
subjects: s1.2
full_text_status: public
keywords: Cajanus cajan L.; next generation sequencing; transcriptome assembly; molecular markers; gene discovery
agrotags: <b>Agrotags</b>     - genes | genomes | genotypes | proteins | group communication | genetics | gene expression | dna | planting | crops <br><b>Fishtags</b>    - NOT-AVAILABLE<br><b>Geopoliticaltags</b> - india | centre | act | mexico
note: The authors are thankful to
Dr Pawan Kulwal, Dr Punjabrao Deshmukh Krishi
Vishwavidalaya, Akola (India), for providing the seeds
of some genotypes used in this study.
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.
date: 2011
date_type: published
publication: DNA Research
volume: 18
number: 3
publisher: Oxfor University Press
pagerange: 153-164
refereed: TRUE
issn: 1340-2838, 1756-1663
official_url: http://dx.doi.org/doi:10.1093/dnares/dsr007
funders: Generation Challenge Programme
funders: Indian Council of Agricultural Research
citation:   Dubey, A and Farmer, A and Schlueter, J and Cannon, S B and Abernathy, B and Tuteja, R and Woodward, J and Shah, T and Mulasmanovic, B and Kudapa, H and Raju, N L and Gothalwal, R and Pande, S and Xiao, Y and Town, C D and Singh, N K and May, G D and Jackson, S and Varshney, R K  (2011) Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.).  DNA Research, 18 (3).  pp. 153-164.  ISSN 1340-2838, 1756-1663     
document_url: http://oar.icrisat.org/111/1/DNAResearch18_153-164_2011.pdf