Vol. 6, Issue 5 (2018)
Differential gene expression analysis and putative genes identification from three developmental growth stages in fenugreek (Trigonella foenum-graecum L.)
Author(s): Shubha R and Rukam S Tomar
Abstract: Fenugreek (Trigonella foenum-graecum L.) popularly known as “Methi†belongs to family fabaceae and subfamily papilionaceae. Gujarat Methi Variety 2 was selected for transcriptome study from the three developmental stages that were vegetative stage (20-30 DAS), reproductive stage (50-60 DAS) and maturity stage (80-90 DAS) which were sequenced using Ion S5 genome sequencing machine. Differential gene expression analysis was carried out by using CLC genomic workbench (v10.0.0). In which the data generated from transcriptome sequencing of fenugreek were mapped with the reference genome Arabidopsis thaliana, the reference genome with a length of 119,667,750 bp, total number of genes present in the reference genome were 32,833 and 49,477 transcripts. In gene expression analysis from all the three developmental stages, top 10 highly expressed genes and 10 lower regulated genes were selected. In vegetative stage, the highest expression value was 474910 and RPKM was 73070.44 for highly expressed gene, with a gene length of 1223 bp and lowest expression value was 3 and RPKM was 0.291139 for lower regulated gene, with a length of 2833 bp. In reproductive stage, the highest expression value was 233210 and RPKM was 28507.21 for highly expressed gene, with a length of 1223 bp and lowest expression value was 3 and RPKM was 0.268558 for lower regulated gene, with a length of 2332 bp. In maturity stage, the highest expression value was 82652 and RPKM was 6970.07088 for highly expressed gene, with a length of 2334 bp and lowest expression value was 3 and RPKM was 1.104943625 for lower regulated gene, with a length of 468 bp. The sequence data sets were analysed through Blast2GO bioinformatic tool. A total of 445 putative genes were identified. From vegetative stage transcriptome 48 genes were identified, from reproductive stage none of the genes were identified and from maturity stage transcriptome 397 genes were identified.
Pages: 1864-1880 | 318 Views 42 Downloads
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How to cite this article:
Shubha R, Rukam S Tomar. Differential gene expression analysis and putative genes identification from three developmental growth stages in fenugreek (Trigonella foenum-graecum L.). Int J Chem Stud 2018;6(5):1864-1880.
