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Title

Analysis of expressed sequence tags (ESTs) from cocoa (Theobroma cacao L) upon infection with Phytophthora megakarya

 

Authors

Sudalaimuthu Asari Naganeeswaran 1, Elain Apshara Subbian 2 & Manimekalai Ramaswamy 3*

 

Affiliation

1Senior Research Fellow, DIT- Agribioinformatics Promotion centre, Central Plantation Crops Research Institute, P. O. Kudlu, Kasaragod-671124, Kerala, India; 2Senior Scientist, Crop Improvement Division, Central Plantation Crops Research Institute, Regional station, Vittal-574 243, Karnataka, India; 3Senior Scientist, Molecular biology and Biotechnology, Crop Improvement Division, Central Plantation Crops Research Institute, P. O. Kudlu, Kasaragod-671124, Kerala, India.

 

Email

rmanimekalai@rediffmail.com; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received December 22, 2011; Accepted December 28, 2011; Published January 20, 2012

 

Abstract

Phytophthora megakarya, the causative agent of cacao black pod disease in West African countries causes an extensive loss of yield. In this study we have analyzed 4 libraries of ESTs derived from Phytophthora megakarya infected cocoa leaf and pod tissues. Totally 6379 redundant sequences were retrieved from ESTtik database and EST processing was performed using seqclean tool. Clustering and assembling using CAP3 generated 3333 non-redundant (907 contigs and 2426 singletons) sequences. The primary sequence analysis of 3333 non-redundant sequences showed that the GC percentage was 42.7 and the sequence length ranged from 101 2576 nucleotides. Further, functional analysis (Blast, Interproscan, Gene ontology and KEGG search) were executed and 1230 orthologous genes were annotated. Totally 272 enzymes corresponding to 114 metabolic pathways were identified. Functional annotation revealed that most of the sequences are related to molecular function, stress response and biological processes. The annotated enzymes are aldehyde dehydrogenase (E.C: 1.2.1.3), catalase (E.C: 1.11.1.6), acetyl-CoA C-acetyltransferase (E.C: 2.3.1.9), threonine ammonia-lyase (E.C: 4.3.1.19), acetolactate synthase (E.C: 2.2.1.6), O-methyltransferase (E.C: 2.1.1.68) which play an important role in amino acid biosynthesis and phenyl propanoid biosynthesis. All this information was stored in MySQL database management system to be used in future for reconstruction of biotic stress response pathway in cocoa.

 

Keywords

cocoa, EST, annotation, cDNA

 

Citation

Naganeeswaran et al. Bioinformation 8(2): 065-069 (2012)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.