Bioinformatic analysis of fruit-specific expressed sequence tag libraries of Diospyros kaki Thunb.: view at the transcriptome at different developmental stages
| Autor: | Tatiana V. Tatarinova, Wan Sin Lee, Gaurav Sablok, Zhengrong Luo, Farzana Rahman, Jennifer Ann Harikrishna, Chun Luo |
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| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
Genetics
Expressed sequence tag cDNA library food and beverages Diospyros kaki GC3 biology MicroRNA Single-nucleotide polymorphism Environmental Science (miscellaneous) Biology Agricultural and Biological Sciences (miscellaneous) Homology (biology) Transcriptome SSRs Original Article SSR-FDM Indel SNPs Biotechnology |
| Zdroj: | 3 Biotech |
| Popis: | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13205-011-0005-9) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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