Plant Genomics

Biography

Biography: S.Vimala Devi

Abstract

Pongamia, or pongam or Indian beech tree, (Pongamia pinnata (L.) Pierre), a preferred species among tree borne oilseeds for its immense utility in reclamation of soils through nitrogen fixation, tolerance to drought and salinity and biodiesel suitable oil quantity and quality. A Native of Southeast Asia grows in wide edapho-climatic region of the Indian Subcontinent and also occurs naturally in Australia. Pongamia’s oilrich seeds have sparked considerable attention as a source of high quality biodiesel. To understand the oil related traits at molecular level, novel high-throughput next generation sequencing (NGS) using Illumina Hiseq 2500 were employed in pongmaia seeds.A 292.0 (ng/µl) of RNA extracted from mature seeds with 378 ng/µl of Qubit concentration with RIN value of 6.1 was used for construction of paired end library prep. De novo transcriptome analysis was done by fastq quality check, transcriptome assembly and filter, expression estimate, differential expression analysis and transcriptome annotation. A 97,816,682 number of total reads and 48,908,341 number of paired-end reads with 9.78 Gb base pairs and 42.78 % GC content data was generated. The average base quality was above Q30 (error-probability >= 0.001) for 90% of bases and the average GC content of the reads in the sample followed a normal distribution. After various high stringency quality control steps, 83.23 M nuclear reads were processed CANoPI – Contig Annotator Pipeline, yielding 106832 unique contigs of > than 200bp. The final assembly encompassed 106,832 unique contigs. Sequence alignment with several reference genomes, including Glycine max and other tree borne oilseed species, coupled with functional comparisons such as GO, revealed a gamout of expected assortment of expressed genes viz., 2,620 involved in biological process, 2,542 in molecular fuctions and 1,319 in cellular components. In addition, a total of 42,235 SSRs were predicted from 106,832 unique contigs, belonging to 6 classes of microsatellites. Among the 9,558,848 organellar transcripts obtained 317 unique transcripts were obtained which related to 42 biological process and 87 molecular functions and 83 cellular components. 159 SSRs were predicted from 317 unique contigs, which can be used for diversity analysis in the germplasm collections and other molecular analysis.