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

Jennifer Ann Harikrishna; Zhengrong Luo; Gaurav Sablok; Chun Luo; Wan Sin Lee; Farzana Rahman; Tatiana V. Tatarinova

doi:10.1007/s13205-011-0005-9

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

Jennifer Ann Harikrishna
, Zhengrong Luo
, Gaurav Sablok
, Chun Luo
, Wan Sin Lee
, Farzana Rahman
, Tatiana V. Tatarinova

Research output: Contribution to journal › Article › peer-review

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'.

Original language	English
Pages (from-to)	35-45
Journal	3 Biotech
Volume	1
Issue number	1
Early online date	21 Apr 2011
DOIs	https://doi.org/10.1007/s13205-011-0005-9
Publication status	Published - 31 Jul 2011

Bibliographical note

Note: This work was supported bythe Special Scientific Research Fund of Agricultural Public Welfare Profession of China [grant number:200903044]

Keywords

Biological sciences

Access to Document

10.1007/s13205-011-0005-9

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

Cite this

@article{7d650fb3cd194758b61b2df2b87665b3,

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

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'.",

keywords = "Biological sciences",

author = "Harikrishna, \{Jennifer Ann\} and Zhengrong Luo and Gaurav Sablok and Chun Luo and Lee, \{Wan Sin\} and Farzana Rahman and Tatarinova, \{Tatiana V.\}",

note = "Note: This work was supported bythe Special Scientific Research Fund of Agricultural Public Welfare Profession of China [grant number:200903044]",

year = "2011",

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AU - Harikrishna, Jennifer Ann

AU - Luo, Zhengrong

AU - Sablok, Gaurav

AU - Luo, Chun

AU - Lee, Wan Sin

AU - Rahman, Farzana

AU - Tatarinova, Tatiana V.

N1 - Note: This work was supported bythe Special Scientific Research Fund of Agricultural Public Welfare Profession of China [grant number:200903044]

PY - 2011/7/31

Y1 - 2011/7/31

N2 - 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'.

AB - 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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