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|Title: ||Bioinformatic analysis of fruit-specific expressed sequence tag libraries of Diospyros kaki Thunb.: view at the transcriptome at different developmental stages|
|Authors: ||Rahman, Farzana|
Tatarinova, Tatiana V.
|Issue Date: ||26-Apr-2012|
|Citation: ||Sablok, G., Luo, C., Lee, W. S., Rahman, F., Tatarinova, T.V., Harikrishna, J. A. and Luo, Z. (2011) 'Bioinformatic analysis of fruit-specific expressed sequence tag libraries of Diospyros kaki Thunb.: view at the transcriptome at different developmentalstages', 3 Biotech, 1(1), pp: 35-45.|
|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|
|Appears in Collections:||Mathematics|
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