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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. 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.

SUBMITTER: Sablok G

PROVIDER: S-EPMC3339603 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

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

Sablok Gaurav G Luo Chun C Lee Wan Sin WS Rahman Farzana F Tatarinova Tatiana V TV Harikrishna Jennifer Ann JA Luo Zhengrong Z

3 Biotech 20110421 1

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 ha ...[more]

PMID: 22558534

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Project description:Background'Taishuu' has a crisp texture, abundant juice, and sweet flavor with hints of cantaloupe. The availability of mitochondrial genome data of Diospyros species is far from the known number of species.ResultsThe sequencing data were assembled into a closed circular mitochondrial chromosome with a 421,308 bp length and a 45.79% GC content. The mitochondrial genome comprised 40 protein-coding, 24 tRNA, and three rRNA genes. The most common codons for arginine (Arg), proline (Pro), glycine (Gly), tryptophan (Trp), valine (Val), alanine (Ala), and leucine (Leu) were AGA, CCA, GGA, UGG, GUA, GCA, and CUA, respectively. The start codon for cox1 and nad4L protein-coding genes was ACG (ATG), whereas the remaining protein-coding genes started with ATG. There are four types of stop codons: CGA, TAA, TAG, and TGA, with TAA being the most frequently used stop codon (45.24%). In the D. kaki Thunb. 'Taishuu' mitochondrial genome, a total of 645 repeat sequences were identified, including 125 SSRs, 7 tandem repeats, and 513 dispersed repeats. Collinearity analysis revealed a close relationship between D. kaki Thunb. 'Taishuu' and Diospyros oleifera, with conserved homologous gene fragments shared among these species in large regions of the mitochondrial genome. The protein-coding genes ccmB and nad4L were observed to undergo positive selection. Analysis of homologous sequences between chloroplasts and mitochondria identified 28 homologous segments, with a total length of 24,075 bp, accounting for 5.71% of the mitochondrial genome. These homologous segments contain 8 annotated genes, including 6 tRNA genes and 2 protein-coding genes (rrn18 and ccmC). There are 23 homologous genes between chloroplasts and nuclei. Mitochondria, chloroplasts, and nuclei share two homologous genes, which are trnV-GAC and trnW-CCA.ConclusionIn conclusion, a high-quality chromosome-level draft genome for D. kaki was generated in this study, which will contribute to further studies of major economic traits in the genus Diospyros.

Project description:Research on crop sexuality is important for establishing systems for germplasm innovation and cultivating improved varieties. In this study, androecious persimmon trees were treated with various concentrations of ethrel (100, 500, and 1,000 mg/L) and zeatin (1, 5, and 10 mg/L) to investigate the morphological, physiological, and molecular characteristics of persimmon. Ethrel at 1,000 mg/L and zeatin at 10 mg/L both significantly reduced the stamen length and pollen grain diameter in androecious trees. Ethrel treatment also led to reduced stamen development with degenerated cellular contents; zeatin treatment promoted the development of arrested pistils via maintaining relatively normal mitochondrial morphology. Both treatments altered carbohydrate, amino acid, and endogenous phytohormone contents, as well as genes associated with hormone production and floral organ development. Thereafter, we explored the combined effects of four chemicals, including ethrel and zeatin, as well as zebularine and 5-azacytidine, both of which are DNA methylation inhibitors, on androecious persimmon flower development. Morphological comparisons showed that stamen length, pollen viability, and pollen grain diameter were significantly inhibited after combined treatment. Large numbers of genes involving in carbohydrate metabolic, mitogen-activated protein kinase (MAPK) signaling, and ribosome pathways, and metabolites including uridine monophosphate (UMP) and cyclamic acid were identified in response to the treatment, indicating complex regulatory mechanisms. An association analysis of transcriptomic and metabolomic data indicated that ribosomal genes have distinct effects on UMP and cyclamic acid metabolites, explaining how male floral buds of androecious persimmon trees respond to these exogenous chemicals. These findings extend the knowledge concerning sexual differentiation in persimmon; they also provide a theoretical basis for molecular breeding, high-yield cultivation, and quality improvement in persimmon.

Dataset Information

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

Publications

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

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