Transcriptome of teak (Tectona grandis, l.f) in vegetative to generative stages development

D. S. Diningrat, S. M. Widiyanto, A. Pancoro, Iriawati, D. Shim, B. Panchangam, N. Zembower, John Edward Carlson

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Teak is one of the highly famous woody plant species for its premier quality of wood. Teak has problem on productivity because of long reproductive cycle. The problem is basically related to mechanism of flower development. The aim of this study was preliminary development of expressed gene database to characterize the floral transcriptome in teak. Two subtracted cDNA libraries were constructed from vegetative and generative bud tissues. Libraries were sequenced using Illumina MiSeq technology which generated paired-end read sequences 3,778,316 for vegetative and 3,701,878 for generative. The sequences assembled de novo into 87,365 transcript contigs consisting of 42,435,728 bases with N50 of 498 bp using CLC-Genomics Workbench. 76,169 (87.18%) of the 87,365 assembled contigs exhibited significant similarity BLASTN to Solanum lycopersicum database (www.phytozome.com). The assembled contigs were annotated through high stringency BLASTX analysis to proteome of S. lycopersicum. Distribution of contigs abundance between vegetative and generative stages analyzed using the DEGseq approach. The numbers of contigs distribution are 24,730 in vegetative, 28,912 in generative and 33,723 in both stages. The functionally protein datasets characterized by Gene Ontology (GO) annotation and KEGG metabolic pathways assignments for the result of DEG analysis. These contigs, 18,756 (75.84%) from vegetative, 22,089 (76.40%) from generative and 22,917 (67.96%) from both stages were assigned to GO classes. A total of 1455 (13.77%) were mapped to 30 pathways from vegetative, 1,638 (13.70%) were mapped to 27 pathways from generative and 1,652 (12.20%) were mapped to 30 pathways from both by BLAST comparison against the KEGG database. The biological processes of flowering developments were identified in the biological process dataset and the numbers of contigs were discovered different between stages. This transcriptome dataset information will act as a aluable resource for further molecular genetic studies teak, as well as for isolation and characterization of functional genes involved in flowering development pathways.

Original languageEnglish (US)
Pages (from-to)1-14
Number of pages14
JournalJournal of Plant Sciences
Volume10
Issue number1
DOIs
StatePublished - Jan 1 2015

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Tectona grandis
transcriptome
Solanum lycopersicum
flowering
wood quality
genes
proteome
woody plants
cDNA libraries
molecular genetics
biochemical pathways
buds
genomics
proteins

All Science Journal Classification (ASJC) codes

  • Agronomy and Crop Science
  • Plant Science

Cite this

Diningrat, D. S. ; Widiyanto, S. M. ; Pancoro, A. ; Iriawati ; Shim, D. ; Panchangam, B. ; Zembower, N. ; Carlson, John Edward. / Transcriptome of teak (Tectona grandis, l.f) in vegetative to generative stages development. In: Journal of Plant Sciences. 2015 ; Vol. 10, No. 1. pp. 1-14.
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title = "Transcriptome of teak (Tectona grandis, l.f) in vegetative to generative stages development",
abstract = "Teak is one of the highly famous woody plant species for its premier quality of wood. Teak has problem on productivity because of long reproductive cycle. The problem is basically related to mechanism of flower development. The aim of this study was preliminary development of expressed gene database to characterize the floral transcriptome in teak. Two subtracted cDNA libraries were constructed from vegetative and generative bud tissues. Libraries were sequenced using Illumina MiSeq technology which generated paired-end read sequences 3,778,316 for vegetative and 3,701,878 for generative. The sequences assembled de novo into 87,365 transcript contigs consisting of 42,435,728 bases with N50 of 498 bp using CLC-Genomics Workbench. 76,169 (87.18{\%}) of the 87,365 assembled contigs exhibited significant similarity BLASTN to Solanum lycopersicum database (www.phytozome.com). The assembled contigs were annotated through high stringency BLASTX analysis to proteome of S. lycopersicum. Distribution of contigs abundance between vegetative and generative stages analyzed using the DEGseq approach. The numbers of contigs distribution are 24,730 in vegetative, 28,912 in generative and 33,723 in both stages. The functionally protein datasets characterized by Gene Ontology (GO) annotation and KEGG metabolic pathways assignments for the result of DEG analysis. These contigs, 18,756 (75.84{\%}) from vegetative, 22,089 (76.40{\%}) from generative and 22,917 (67.96{\%}) from both stages were assigned to GO classes. A total of 1455 (13.77{\%}) were mapped to 30 pathways from vegetative, 1,638 (13.70{\%}) were mapped to 27 pathways from generative and 1,652 (12.20{\%}) were mapped to 30 pathways from both by BLAST comparison against the KEGG database. The biological processes of flowering developments were identified in the biological process dataset and the numbers of contigs were discovered different between stages. This transcriptome dataset information will act as a aluable resource for further molecular genetic studies teak, as well as for isolation and characterization of functional genes involved in flowering development pathways.",
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Diningrat, DS, Widiyanto, SM, Pancoro, A, Iriawati, Shim, D, Panchangam, B, Zembower, N & Carlson, JE 2015, 'Transcriptome of teak (Tectona grandis, l.f) in vegetative to generative stages development', Journal of Plant Sciences, vol. 10, no. 1, pp. 1-14. https://doi.org/10.3923/jps.2015.1.14

Transcriptome of teak (Tectona grandis, l.f) in vegetative to generative stages development. / Diningrat, D. S.; Widiyanto, S. M.; Pancoro, A.; Iriawati; Shim, D.; Panchangam, B.; Zembower, N.; Carlson, John Edward.

In: Journal of Plant Sciences, Vol. 10, No. 1, 01.01.2015, p. 1-14.

Research output: Contribution to journalArticle

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T1 - Transcriptome of teak (Tectona grandis, l.f) in vegetative to generative stages development

AU - Diningrat, D. S.

AU - Widiyanto, S. M.

AU - Pancoro, A.

AU - Iriawati,

AU - Shim, D.

AU - Panchangam, B.

AU - Zembower, N.

AU - Carlson, John Edward

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Diningrat DS, Widiyanto SM, Pancoro A, Iriawati, Shim D, Panchangam B et al. Transcriptome of teak (Tectona grandis, l.f) in vegetative to generative stages development. Journal of Plant Sciences. 2015 Jan 1;10(1):1-14. https://doi.org/10.3923/jps.2015.1.14