Mining of Transcriptome of a climacteric fruit species Diospyros kaki Thunb for functional genomics

Mehedi Hassan, Farzana Rahman, Tatiana Tatarinova, Gaurav Sblok

Allbwn ymchwil: Pennod mewn Llyfr/Adroddiad/Trafodion CynhadleddCyfraniad i gynhadleddadolygiad gan gymheiriaid

Crynodeb

Our current research focuses on developing computational resources for analysis of genome of persimmon (Diospyros kaki). Persimmon is an economically important climacteric fruit species, which has promising medicinal values. The genus Diospyros is widely distributed in Asia, Africa, and America and is characterised by complex ploidy level. In order to provide an insight into the developmental stages of D. kaki, we conducted a comparative analysis of developmental stage specific ESTs libraries. A total of 2,529 putative tentative unigenes were identified in the Mature Fruit (MF) library whereas 3,775 tentative unigenes were identified in the Ovary and Young Fruit (OYF) library.Comparative mining of SSRs between two ESTs libraries showed 325 EST-SSRs in 296 putative unigenes which were detected in the MF library showing an occurrence of 11.7% with a frequency of 1 SSR/3.16 kb and the OYF library showed an EST-SSRs occurrence of 10.8% with 407 EST- SSRs in the 352 putative unigenes with a frequency of 1 SSR/2.92kb. SNPs and indels were also identified and compared among the two cDNA libraries using redundancy and co-segregation based approach. Overall, the OYF library has 20.94 SNPs/indels per 100 bp, whereas the MF library has only 0.74 SNPs/indels per 100 bp. We detected 506 SSRs primer pairs that can be utilized to infer genetic diversity in persimmon. We also found potentially conserved 159 miRNA family expressed during the developmental stages in OYF library which correlates the potential involvement of miR159 family in development and relative distribution of SNP and SSR-FDMs markers.
Iaith wreiddiolSaesneg
TeitlN/A
StatwsCyhoeddwyd - 1 Ion 2011
Digwyddiad 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology - Vienna
Hyd: 15 Jul 201119 Jul 2011

Cynhadledd

Cynhadledd 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology
Cyfnod15/07/1119/07/11

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