Abstract - A legume genomics resource: The Chickpea Root Expressed Sequence Tag Database

A legume genomics resource: The Chickpea Root Expressed Sequence Tag Database

Jayashree B.
Bioinformatics and Computational Biology Unit
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)
Patancheru, Andhra Pradesh 502 324, India
Tel: 91 40 23296161
Fax: 91 40 23241239
E-mail: b.jayashree@cgiar.org

Hutokshi K. Buhariwalla
MS Swaminathan Applied Genomics Lab
International Crops Research Institute for the Semi- Arid Tropics (ICRISAT)
Patancheru, Andhra Pradesh 502 324, India
Tel: 91 40 23296161
Fax: 91 40 23241239
E-mail: h.k.buhariwalla@cgiar.org

Sanjeev Shinde
Bioinformatics and Computational Biology Unit
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)
Patancheru, Andhra Pradesh 502 324, India
Tel: 91 40 23296161
Fax: 91 40 23241239
E-mail: s.shinde@cgiar.org

Jonathan H. Crouch*
M.S. Swaminathan Applied Genomics Lab
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)
Patancheru, Andhra Pradesh 502 324, India
Tel:91 40 23296161
Fax:91 40 23241239
E-mail: j.crouch@cgiar.org

*Corresponding author

Financial support: Earmarked unrestricted grants from the governments of UK, Japan, European Union and the Generation Challenge Program.

Keywords: cloning, data mining, drought avoidance, drought tolerance, EST database, root traits, stress.

Abbreviations:

ASP: active server page;
BLAST: Basic Local Alignment Search Tool;
dbEST ID: database for expressed sequence tags- Identity;
EST: expressed sequence tag;
GO: Genome ontology;
NCBI: National Centre for Biotechnology Information;
NSH: no significant homology;
RPS-BLAST: Reversed Position Specific BLAST;
SSH: subtractive suppressive hybridization;
SSR: simple sequence repeats;
TIGR: The Institute for Genomic Research;

Chickpea, a lesser-studied grain legume, is being investigated due to its taxonomic proximity with the model legume genome Medicago truncatula and its ability to endure and grow in relatively low soil water contents making it a model legume crop for the study of agronomic response to drought stress. Public databases currently contain very few sequences from chickpea associated with expression in root tissues. However, root traits are likely to be one of the most important components of drought tolerance in chickpea. Thus, we have generated a set of over 2800 chickpea expressed sequence tags (ESTs) from a library constructed after subtractive suppressive hybridization (SSH) of root tissue from two closely related chickpea genotypes possessing different sources of drought avoidance and tolerance (ICC4958 and Annigeri respectively). This database provides researchers in legume genomics with a major new resource for data mining associated with root traits and drought tolerance. This report describes the development and utilization of the database and provides the tools we have developed to facilitate the bioinformatics pipeline used for analysis of the ESTs in this database. We also discuss applications that have already been achieved using this resource.