Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes
Kevin Maringer1,2,3, Amjad Yousuf4,5, Kate J Heesom6
1School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK. K.Maringer@surrey.ac.uk.
BMC Genomics
|January 21, 2017
Summary
This study introduces proteomics informed by transcriptomics (PIT) to analyze the Aedes aegypti proteome, revealing insights into transposable elements and improving genome annotation for this disease vector.
Area of Science:
- Genomics
- Proteomics
- Vector Biology
Background:
- Aedes aegypti mosquitoes transmit dengue, Zika, chikungunya, and yellow fever viruses.
- Transposable elements (TEs) constitute nearly half of the Ae. aegypti genome and are implicated in viral persistence.
- Studying TE proteomes is challenging due to TE divergence and incomplete genome annotation in non-model organisms.
Purpose of the Study:
- To characterize the proteome of mobile genetic elements in Ae. aegypti.
- To develop and validate a novel proteomics technique for non-model organisms.
- To assess genome annotation quality and guide future annotation efforts.
Main Methods:
- Proteomics informed by transcriptomics (PIT) was employed, bypassing traditional genome annotation.
- Transcriptomic data was used to identify proteins, vastly expanding the confirmed proteome.
- Criteria were established for characterizing proteomically active TEs.
Main Results:
- The study identified a significantly larger number of experimentally confirmed Ae. aegypti proteins.
- PIT revealed hotspots of incomplete genome annotation, independent of sequence quality.
- Long terminal repeat (LTR) retrotransposons were found to be enriched in the proteome, with expression not correlating to genomic abundance.
Conclusions:
- This research presents the first proteomic characterization of mobile genetic elements in any organism, opening new research avenues.
- The PIT technique serves as a proof-of-concept for evaluating and improving genome annotation in non-model organisms.
- PIT is a valuable tool for studying Ae. aegypti biology and its role in transmitting global health-threatening viruses.
Keywords:
Aedes aegyptiGenome annotationNon-model organismPITProteomics informed by transcriptomicsTransposonMore Related Videos
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