Dataset Information

Integration of transcriptome and proteome annotation in the naive Ixodes ricinus midgut with genome sequencing

ABSTRACT: In Europe, ticks are the most important vectors of diseases threatening humans, livestock, wildlife and companion animals. Nevertheless, genomic sequence information and functional annotation of proteins of the most important European tick, Ixodes ricinus, is limited. Here we present the first analysis of the I. ricinus genome and of the transcriptome of the unfed I. ricinus midgut. We combined and integrated data from genome, transcriptome and proteome. The de novo assembly of 1 billion paired-end sequences identified 6,415 putative genes providing an unprecedented insight into the I. ricinus genome. Mapping of our midgut mRNA reads to the assembled contigs let us estimate to cover around two third of the unique genomic sequences. In addition, more than 10,000 transcripts from naïve midgut were annotated functionally and/or locally. By combining the alignment-based with a motif-search based annotation approach, we could double the number of annotations throughout all groups without shifting the dataset. Moreover, 1,175 proteins expressed in the naïve midgut were identified by mass spectrometry confirming the high completeness of our transcriptome database, and 608 were significantly annotated for function and/or localization. This multiple-omics study vastly extends the publicly available DNA, RNA and protein databases for I. ricinus and ticks in general.

OTHER RELATED OMICS DATASETS IN: PRJNA270959

INSTRUMENT(S): AB SCIEX TOF/TOF T2D file

ORGANISM(S): Ixodes Ricinus

TISSUE(S): Midgut

SUBMITTER: Wibke Cramaro

LAB HEAD: Claude P Muller

PROVIDER: PXD001796 | Pride | 2015-11-04

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	ID14196.mzxml	Mzxml
	ID14196_Arthropoda.dat-pride.xml.gz	Xml
	ID14196_Ixodes.dat-pride.pride.mgf.gz	Mgf
	ID14196_Ixodes.dat-pride.pride.mztab.gz	Mztab
	ID14196_Ixodes.dat-pride.xml.gz	Xml

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Integration of Ixodes ricinus genome sequencing with transcriptome and proteome annotation of the naïve midgut.

Cramaro Wibke J WJ Revets Dominique D Hunewald Oliver E OE Sinner Regina R Reye Anna L AL Muller Claude P CP

BMC genomics 20151028

<h4>Background</h4>In Europe, Ixodes ricinus ticks are the most important vectors of diseases threatening humans, livestock, wildlife and companion animals. Nevertheless, genomic sequence information is missing and functional annotation of transcripts and proteins is limited. This lack of information is restricting studies of the vector and its interactions with pathogens and hosts. Here we present and integrate the first analysis of the I. ricinus genome with the transcriptome and proteome of t ...[more]

PMID: 26510422

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