Volume 9, Issue 3, November 2014, Pages 1416–1427
Diky S. Diningrat1, Srinanan M. Widiyanto2, Adi Pancoro3, Iriawati4, Donghwan Shim5, Bhargavi Panchangam6, Nicole Zembower7, and John E. Carlson8
1 School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung-40132, Indonesia
2 School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung-40132, Indonesia
3 School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung-40132, Indonesia
4 School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung-40132, Indonesia
5 Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, Indonesia
6 Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, Indonesia
7 Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, Indonesia
8 Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, Indonesia
Original language: English
Copyright © 2014 ISSR Journals. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Teak (Tectona grandis L.f) is highly famous woody plant species for the quality and durability. Teak has two main problems on long reproductive cycle and produces low seeds. Both problems are basically related to mechanism of flower development. Hence, the determination of the genetic pathways and specific genes involved in teak flowering development could be beneficial for teak productivity improvement. 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 teak bud tissues. Libraries were sequenced using Illumina MiSeq technology which generated 3,778,316 in vegetative and 3,701,878 in generative paired-end reads sequences. The sequences were combined QC tested, trimmed, and de novo assembled conducted using CLCGenomics Workbench. The sequence reads assembled de novo into 87,365 transcript contigs consisting of 42,435,728 bases with N50 of 498bp. 64,961 (74.36%) of assembled contigs exhibited similarity BLASTN to Arabidopsis thaliana database. The assembled contigs were annotated through high stringency BLASTX analysis to proteome of A. thaliana. 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 transition stage. The functionally protein datasets characterized by gene ontology (GO) annotation and KEGG metabolic pathways assignments for the result of DEG analysis. This study allowed us compare the transcriptomes of vegetative and generative tissues of teak in flowering developmental stage, and identify potential biological processes involved in teak flowering developmental stage.
Author Keywords: de novo assembly, teak flowering, NGS, DEG, Gene Ontology, EST, non model plant.
Diky S. Diningrat1, Srinanan M. Widiyanto2, Adi Pancoro3, Iriawati4, Donghwan Shim5, Bhargavi Panchangam6, Nicole Zembower7, and John E. Carlson8
1 School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung-40132, Indonesia
2 School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung-40132, Indonesia
3 School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung-40132, Indonesia
4 School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung-40132, Indonesia
5 Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, Indonesia
6 Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, Indonesia
7 Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, Indonesia
8 Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, Indonesia
Original language: English
Copyright © 2014 ISSR Journals. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Teak (Tectona grandis L.f) is highly famous woody plant species for the quality and durability. Teak has two main problems on long reproductive cycle and produces low seeds. Both problems are basically related to mechanism of flower development. Hence, the determination of the genetic pathways and specific genes involved in teak flowering development could be beneficial for teak productivity improvement. 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 teak bud tissues. Libraries were sequenced using Illumina MiSeq technology which generated 3,778,316 in vegetative and 3,701,878 in generative paired-end reads sequences. The sequences were combined QC tested, trimmed, and de novo assembled conducted using CLCGenomics Workbench. The sequence reads assembled de novo into 87,365 transcript contigs consisting of 42,435,728 bases with N50 of 498bp. 64,961 (74.36%) of assembled contigs exhibited similarity BLASTN to Arabidopsis thaliana database. The assembled contigs were annotated through high stringency BLASTX analysis to proteome of A. thaliana. 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 transition stage. The functionally protein datasets characterized by gene ontology (GO) annotation and KEGG metabolic pathways assignments for the result of DEG analysis. This study allowed us compare the transcriptomes of vegetative and generative tissues of teak in flowering developmental stage, and identify potential biological processes involved in teak flowering developmental stage.
Author Keywords: de novo assembly, teak flowering, NGS, DEG, Gene Ontology, EST, non model plant.
How to Cite this Article
Diky S. Diningrat, Srinanan M. Widiyanto, Adi Pancoro, Iriawati, Donghwan Shim, Bhargavi Panchangam, Nicole Zembower, and John E. Carlson, “Transcriptomes of Teak (Tectona grandis, L.f) in Vegetative to Generative Transition Stage Development,” International Journal of Innovation and Applied Studies, vol. 9, no. 3, pp. 1416–1427, November 2014.
