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De novo assembly of transcriptome and genome data from the Asia I mtCOI genetic clade of Bemisia tabaci

De novo assembly of transcriptome and genome data from the Asia I mtCOI genetic clade of Bemisia tabaci

Patel, Mitulkumar V. (2016) De novo assembly of transcriptome and genome data from the Asia I mtCOI genetic clade of Bemisia tabaci. PhD thesis, University of Greenwich.

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Abstract

Bemisia tabaci, the whitefly, is an economically important group of cryptic species that pose an ongoing and major threat to global food security. Molecular characterization from at least one of the species in the group is required urgently within whitefly community to define genetic differences across distinct populations and to facilitate the development of more effective insecticides to help farmers. In this thesis, the process of de novo assembly and characterizing transcriptome and genome data of an Asia I population is described along with steps towards the development of a genetic framework for insecticide discovery. A comprehensive transcriptome of adult females of an Asia I population was assembled from 0.864 million reads generated using the Roche 454 sequencing platform. A total of 29,418 contigs produced using CLC Genomics of which 8,563 were assigned putative functions. A draft genome 828 Mbp of the Asia I population was produced through de novo assembly of 206 million 250 bp paired-end reads generated on the Illumina MiSeq 2500 platform using Platanus. They were found to encode 41,981 PCGs and also contained 990 ncRNAs and repetitive elements (45.66%). A selection of 741 full-length genes were studied and found to contain larger intron sizes together with repetitive elements that contribute to the larger Asia I genome size and partly explain the difficulties encountered in genome assembly. Finally, in addition to the B. tabaci Asia I genome, one mitogenome and three endosymbiont genomes representing Portiera, Wolbachia and Arsenophonus were obtained from the same sequence library. The development of a genetic framework is described as a side-project which uses Drosophila essential genes as a reference to identify orthologs in other insects and validates with ChEMBL targets. The ‘omics’ data presented in this thesis provides a comprehensive sequence resource for Asia I populations and demonstrates the workflow of obtaining genetic information of host and its endosymbionts.

Item Type: Thesis (PhD)
Uncontrolled Keywords: Whitefly B. tabaci; gene structure; genome data; pest biology; insecticide discovery;
Subjects: Q Science > QL Zoology
Q Science > QR Microbiology
Faculty / Department / Research Group: Faculty of Engineering & Science > Natural Resources Institute
Last Modified: 15 Apr 2019 10:09
Selected for GREAT 2016: None
Selected for GREAT 2017: None
Selected for GREAT 2018: None
Selected for GREAT 2019: None
URI: http://gala.gre.ac.uk/id/eprint/23585

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