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Articles by J.E. Carlson
Total Records ( 2 ) for J.E. Carlson
  D.S. Diningrat , S.M. Widiyanto , A. Pancoro , Iriawati , D. Shim , B. Panchangam , N. Zembower and J.E. Carlson
  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 ( 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 valuable resource for further molecular genetic studies teak, as well as for isolation and characterization of functional genes involved in flowering development pathways.
  D.S. Diningrat , S.M. Widiyanto , A. Pancoro , Iriawati , D. Shim , B. Panchangam , N. Zembower and J.E. Carlson
  Teak is woody plants; a member of the Lamiaceae family. Teak is a plant that has a very high quality timber. Teak has constraints due to low reproductive rates and slow growth of the wood after entering the reproductive phase. Teak genetic engineering efforts by delaying flowering time was facing difficulties due to the lack of information about the role of genes regulating flowering identity in teak. Teak has indeterminate inflorescence same as the model plant Arabidopsis. In Arabidopsis, the role of Terminal Flowering 1 (TFL1) gene as a member of the Floral Meristem Identity (FMI) in regulating the vegetative to generative transition is by down regulation, so that, the downstream of the FMI genes up-regulation which resulted in the development towards the formation of flowers. In teak, this mechanism is not well known. The development of NGS technology-transcriptome analysis has allowed us to identify specific interest genes from non-model plant rapidly and cheaply relative. To determine the activity of the interest genes in silico can be undertaken with RNA-seq and QRT-PCR analysis approaches. In this study, it is identified that, TFL1 genes in teak with NGS transcriptome analysis approach that is annotated with S. lycopersicum. The TFL1 genes obtained from EST teak derived from vegetative and generative shoots buds RNA. The TFL1 genes activities on the tissues are done with RNA-seq analysis approach in order to obtain Digitally Gene Expression (DGE) of TFL1. The TFL1 gene activity was then validated in silico by QRT-PCR analysis. The results of the analysis showed that the TFL1-14 gene activity equivalent to the TFL1 gene activity in the model plant.
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