Bioinformatic analysis of fruit-specific expressed sequence tag libraries of 'Diospyros kaki' Thunb. : view at the transcriptome at different developmental stages

Sablok, Gaurav, Luo, Chun, Lee, Wan Sin, Rahman, Farzana, Tatarinova, Tatiana V., Harikrishna, Jennifer Ann and Luo, Zhengrong (2011) Bioinformatic analysis of fruit-specific expressed sequence tag libraries of 'Diospyros kaki' Thunb. : view at the transcriptome at different developmental stages. 3 Biotech, 1(1), pp. 35-45. ISSN (print) 2190-572X

Official URL: https://doi.org/10.1007/s13205-011-0005-9

Abstract

We present here a systematic analysis of the 'Diospyros kaki' expressed sequence tags (ESTs) generated from development stage-specific libraries. A total of 2,529 putative tentative unigenes were identified in the MF library whereas the OYF library displayed 3,775 tentative unigenes. Among the two cDNA libraries, 325 EST-Simple sequence repeats (SSRs) in 296 putative unigenes were detected in the MF library showing an occurrence of 11.7% with a frequency of 1 SSR/3.16 kb whereas the OYF library had an EST-SSRs occurrence of 10.8% with 407 EST-SSRs in the 352 putative unigenes with a frequency of 1 SSR/2.92 kb. We observed a higher frequency of SNPs and indels in the OYF library (20.94 SNPs/indels per 100 bp) in comparison to MF library showed a relatively lower frequency (0.74 SNPs/indels per 100 bp). A combined homology and secondary structure analysis approach identified a potential miRNA precursor, an ortholog of miR159, and potential miR159 targets, in the development-specific ESTs of 'D. kaki'.

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