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Next generation transcriptome sequencing and quantitative real-time PCR technologies for characterisation of the Bemisia tabaci Asia 1 mtCOI phylogenetic clade

Next generation transcriptome sequencing and quantitative real-time PCR technologies for characterisation of the Bemisia tabaci Asia 1 mtCOI phylogenetic clade

Seal, Susan, Patel, Mitulkumar V., Collins, Carl, Colvin, John and Bailey, David (2012) Next generation transcriptome sequencing and quantitative real-time PCR technologies for characterisation of the Bemisia tabaci Asia 1 mtCOI phylogenetic clade. Journal of Integrative Agriculture, 11 (2). pp. 281-292. ISSN 2095-3119 (doi:10.1016/S2095-3119(12)60012-4)

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Abstract

A programme of functional genomics research is underway at the University of Greenwich, UK, to develop and apply genomics technologies to characterise an economically-important but under-researched Bemisia tabaci (Hemiptera: Aleyrodidae), the Asia 1 mtCOI phylogenetic group. A comparison of this putative species from India with other important B. tabaci populations and insect species may provide targets for the development of more effective whitefly control strategies. As a first step, next-generation sequencing (NGS) has been used to survey the transcriptome of adult female whitefly, with high quality RNA preparations being used to generate cDNA libraries for NGS using the Roche 454 Titanium DNA sequencing platform. Contig assemblies constructed from the resultant sequences (301 094 reads) using the software program CLC Genomics Workbench generated 3 821 core contigs. Comparison of a selection of these contigs with related sequences from other B. tabaci genetic groups has revealed good alignment for some genes (e.g., HSP90) but misassemblies in other datasets (e.g., the vitellogenin gene family), highlighting the need for manual curation as well as collaborative international efforts to obtain accurate assemblies from the existing next generation sequence datasets. Nevertheless, data emerging from the NGS has facilitated the development of accurate and reliable methods for analysing gene expression based on quantitative real-time RT-PCR, illustrating the power of this approach to enable rapid expression analyses in an organism for which a complete genome sequence is currently lacking.

Item Type: Article
Additional Information: [1] There is an errata referring to this article in Journal of Integrative Agriculture, (2012) Vol. 11, (9), p. 1433. [2] Appendix associated with this paper can be available on http://www.ChinaAgriSci.com/V2/En/appendix.htm [5] The Journal of Integrative Agriculture is an official publication of the Chinese Academy of Agricultural Sciences (CAAS).
Uncontrolled Keywords: Bemisia tabaci, whitefly, transcriptome, next generation sequencing, quantitative real-time (QRT)-PCR, Asia 1 mtCOI
Subjects: Q Science > QH Natural history > QH301 Biology
S Agriculture > SF Animal culture
Faculty / Department / Research Group: Faculty of Engineering & Science > Natural Resources Institute
Related URLs:
Last Modified: 11 Sep 2014 12:10
Selected for GREAT 2016: None
Selected for GREAT 2017: None
Selected for GREAT 2018: None
URI: http://gala.gre.ac.uk/id/eprint/10021

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