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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