Preliminary study on expressed sequence tags (ESTs) of papaya, pineapple and pummelo

Y.S. Sew, V. Maheswary, A. Noor Suhana, A. Hayati, A.S. Zulkifli and A.B. Umi Kalsom

Abstract

A small scale expressed sequence tags (ESTs) were studied on papaya (Carica papaya var. Eksotika 2), pineapple (Ananas comosus var. Gandul) and pummelo (Citrus grandis var. Melomas). Single pass sequencing was performed on 960 randomly selected papaya cDNA clones, ,440 pineapple cDNA clones and 547 pummelo cDNA clones. Clustering and assembly of qualified ESTs revealed 07, 78 and 48 tentative unique contigs, and 347, 30 and 302 tentative unique singletons of papaya, pineapple and pummelo, respectively. Homology search of these qualified ESTs resulted in 76.5% having significant matches (E-value ≤ 0– 0) to previously identified and registered proteins in the non-redundant database (GenBank). The ESTs sequences that are matching to GenBank nucleic acid database were further classified into 2 functional categories based on Munice Information Center for Protein Sequences (MIPS) classification. From this preliminary ESTs study, various genes that involved in cell rescue and defence, stress response as well as fruit ripening process were identified. In addition, about 5–3 % of ESTs showed no homology with the registered protein in GenBank and their functions need to be further studied. The generated EST databases can be a potential source for comparative and functional genomic studies utilizing bioinformatics.

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