EST-database search of plant defensins - An example using sugarcane, a large and complex genome

L. C. Belarmino, P. V S Z Capriles, S. Crovella, L. E. Dardenne, A. M. Benko-Iseppon

Research output: Contribution to journalArticlepeer-review

Abstract

EST (Expressed Sequence Tags) databases are increasing in number and size, especially regarding cultivated plants. Sugarcane is one of the most important tropical and subtropical crops, presenting a complex polyploid genome of hybrid origin, bearing a challenge for the understanding of genetic processes in higher plants. In the present work a general search was carried out on the largest Sugarcane EST Database (SUCEST) that includes 237,954 ESTs aiming to identify defensin antimicrobial peptides - a class of small, basic, cysteine-rich peptides distributed throughout the kingdoms. Using a computational approach 17 new defensin isoforms could be identified. Main steps for the search, characterization and evaluation of the defensin expression profile are presented. Prevalent expression tissues were leaf roll, lateral bark, root apex, base of inflorescence, developing seed, and calli. Bioinformatics and phylogenetic analysis of the primary structure of the sugarcane defensin candidates as well as the 3D structures obtained by comparative modeling support their role as antimicrobials.

Original languageEnglish
Pages (from-to)248-254
Number of pages7
JournalCurrent Protein and Peptide Science
Volume11
Issue number3
DOIs
Publication statusPublished - 2010

Keywords

  • Comparative modeling
  • Crop evolution
  • Data mining
  • Defense system
  • Drug discovery
  • EST-database

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

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