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

• Published in: 3 Biotech Vol. 1; no. 1; pp. 35 - 45
• Main Authors: Sablok, Gaurav, Luo, Chun, Lee, Wan Sin, Rahman, Farzana, Tatarinova, Tatiana V., Harikrishna, Jennifer Ann, Luo, Zhengrong
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.07.2011
• Subjects: Agriculture; Bioinformatics; Biomaterials; Biotechnology; Cancer Research; Chemistry; Chemistry and Materials Science; Original; Original Article; Stem Cells; biology; MicroRNA; SSR-FDM; SSRs; SNPs; Expressed sequence tag; GC
• ISSN: 2190-572X; 2190-5738
• DOI: 10.1007/s13205-011-0005-9

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.