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Proteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes Aegypti

Maringer, Kevin, Yousuf, A, Heesom, KJ, Fan, J, Lee, Diane, Fernandez-Sesma, A, Bessant, C, Matthews, DA and Davidson, AD (2017) Proteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes Aegypti BMC Genomics, 18 (101).

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Abstract

Background: Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism’s mobile genetic elements, partly due to the highly divergent nature of TEs. Furthermore, as for many non-model organisms, incomplete genome annotation has hampered proteomic studies on Ae. aegypti. Results: We analysed the Ae. aegypti proteome using our new proteomics informed by transcriptomics (PIT) technique, which bypasses the need for genome annotation by identifying proteins through matched transcriptomic (rather than genomic) data. Our data vastly increase the number of experimentally confirmed Ae. aegypti proteins. The PIT analysis also identified hotspots of incomplete genome annotation, and showed that poor sequence and assembly quality do not explain all annotation gaps. Finally, in a proof-of principle study, we developed criteria for the characterisation of proteomically active TEs. Protein expression did not correlate with a TE’s genomic abundance at different levels of classification. Most notably, long terminal repeat (LTR) retrotransposons were markedly enriched compared to other elements. PIT was superior to ‘conventional’ proteomic approaches in both our transposon and genome annotation analyses. Conclusions: We present the first proteomic characterisation of an organism’s repertoire of mobile genetic elements, which will open new avenues of research into the function of transposon proteins in health and disease. Furthermore, our study provides a proof-of concept that PIT can be used to evaluate a genome’s annotation to guide annotation efforts which has the potential to improve the efficiency of annotation projects in non-model organisms. PIT therefore represents a valuable new tool to study the biology of the important vector species Ae. aegypti, including its role in transmitting emerging viruses of global public health concern.

Item Type: Article
Subjects : Biosciences and Medicine
Divisions : Faculty of Health and Medical Sciences > School of Biosciences and Medicine
Authors :
NameEmailORCID
Maringer, Kevink.maringer@surrey.ac.ukUNSPECIFIED
Yousuf, AUNSPECIFIEDUNSPECIFIED
Heesom, KJUNSPECIFIEDUNSPECIFIED
Fan, JUNSPECIFIEDUNSPECIFIED
Lee, Dianediane.lee@surrey.ac.ukUNSPECIFIED
Fernandez-Sesma, AUNSPECIFIEDUNSPECIFIED
Bessant, CUNSPECIFIEDUNSPECIFIED
Matthews, DAUNSPECIFIEDUNSPECIFIED
Davidson, ADUNSPECIFIEDUNSPECIFIED
Date : 19 January 2017
Identification Number : 10.1186/s12864-016-3432-5
Copyright Disclaimer : © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Uncontrolled Keywords : genome annotation, non-model organism, PIT, proteomics informed by transcriptomics, transposon.
Related URLs :
Depositing User : Symplectic Elements
Date Deposited : 11 Jan 2017 12:40
Last Modified : 19 Jul 2017 08:08
URI: http://epubs.surrey.ac.uk/id/eprint/813266

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