Vol. 7, Issue 2 (2019)
A Draft Genome Sequencing of Dill (Anethum graveolens L.) Using Ion Torrent Sequencing Technology
Author(s): Shiwani, MK Mandavia and RS Tomar
Abstract: Dill (Anethum graveolens L.) is one of the important spice crops. Dill is an important medicinal and industrial plant. Considering the importance of this herbal spice plant various biochemical studies has been carried out and which are still going on including traditional and modern approaches. In present study, Ion Torrent Genome Sequencing (Ion S5) technology was used to generate dill draft genome using genotype Gujarat Dill 1. For the measurement of the genome size, flow cytometer (Accuri C6) was used, and genome size of the dill haploid cell was found 2.6 Gb approximately. Gujarat Dill-1 genotype was sequenced using next generation sequencing platform Ion S5 which yielded 10.44 Gb of raw data. The data was checked for quality. After quality check and its control total of 3.2 Gb of data was remained in the data set. This 3.2 Gb data was de novo assembled. de novo assembly of 15,940,402 reads had yield data of 321,805,497 base pairs (321 Mb). In order to maintain the quality of assembled data contigs were filtered, after filter 32 contigs were remained with 5000 bp of minimum, 42,775 bp of maximum and 9,568 bp of average contig length. In Blast2go total 32 sequence (32 contigs) were functionally annotated out of which 31.84 (99.5%) were showed positive interpro, while 30 (93.75%) were got Blast hits. 87.5% (28) and 65.62% (21) sequences were mapped and annotated respectively. Quality filter of assembly yielded data of 306 Kb (306,184 bp). This data was selected for functional annotation. Through functional annotation of assembled data, total of 542 putative genes were identified which were involved in 498 putative function. It included biological processes, molecular function and cellular components. Sequence similarity was also tested based on protein domain conserved region through InterProScan. Out of 32 sequences, all most all sequences showed positive InterPro result. 47 IPS IDs were identified, among them 30 were IPS domain, 14 were IPS family and 4 were IPS active sites. Assembled sequences of dill (Gujarat dill-1) were divided in to four main classes which covered 18 sequences. Among them 11 sequences were grouped into class oxidoreductases followed by class transferases (3 sequences), class hydrolases (2 sequences) and class lyases (2 sequences).
Pages: 1034-1042 | 344 Views 77 Downloads
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How to cite this article:
Shiwani, MK Mandavia, RS Tomar. A Draft Genome Sequencing of Dill (Anethum graveolens L.) Using Ion Torrent Sequencing Technology. Int J Chem Stud 2019;7(2):1034-1042.
