PXD003799

PXD003799 is an original dataset announced via ProteomeXchange.

Title	Proteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes aegypti
Description	The incomplete genome annotation of non-model organisms hampers molecular and proteomic studies. Proteomics informed by transcriptomics (PIT) is suited to non-model organisms because peptides are identified using transcriptomic, not genomic, data. Aedes aegypti is the mosquito vector for the (re-)emerging dengue, chikungunya, yellow fever and Zika viruses. An Ae. aegypti genome sequence is available, however experimental evidence for >90% of the Ae. aegypti proteome or the activity of transposable elements (TEs) that constitute 50% of the Ae. aegypti genome is lacking. We used PIT to characterise the proteome of the Aedes aegypti derived cell line Aag2. Hotspots of incomplete genome annotation were identified which are not explained by poor sequence and assembly quality. We developed criteria for the characterisation of proteomically active TEs and demonstrate that protein expression does not correlate with a TE’s genomic abundance. Finally, we identify Phasi Charoen-like virus as an unrecognised contaminant of Aag2 cells. We therefore present the first proteomic characterisation of mobile genetic elements, and provide proof-of-principle that PIT can evaluate a genome’s annotation to guide annotation efforts.
HostingRepository	PRIDE
AnnounceDate	2017-02-15
AnnouncementXML	Submission_2017-02-15_01:43:58.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrew Davidson
SpeciesList	scientific name: Aedes aegypti aegypti; NCBI TaxID: 1424507;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-03-16 07:10:40	ID requested
⏵ 1	2017-02-15 01:43:59	announced

Maringer K, Yousuf A, Heesom KJ, Fan J, Lee D, Fernandez-Sesma A, Bessant C, Matthews DA, Davidson AD, Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti. BMC Genomics, 18(1):101(2017) [pubmed]

curator keyword: Biological

submitter keyword: LC-MS/MS, Aedes aegypti, PIT, proteomics informed by transcriptomics

Andrew Davidson
contact affiliation	School of Cellular and Molecular Medicine, Faculty of Biomedical Sciences, University of Bristol, Bristol, BS81TD
contact email	andrew.davidson@bristol.ac.uk
lab head
Andrew Davidson
contact affiliation	University of Bristol, Bristol UK
contact email	andrew.davidson@bristol.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD003799
     1. Label: PRIDE project
     2. Name: Proteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes aegypti