Comparative de novo assembly and annotation of mantle tissue transcriptomes from the Mytilus edulis species complex (M. edulis, M. galloprovincialis, M. trossulus).

Knöbel, Loreen, Breusing, Corinna, Bayer, Till , Sharma, Virag, Hiller, Michael, Melzner, Frank and Stuckas, Heiko (2019) Comparative de novo assembly and annotation of mantle tissue transcriptomes from the Mytilus edulis species complex (M. edulis, M. galloprovincialis, M. trossulus). Marine Genomics . p. 100700. DOI 10.1016/j.margen.2019.100700.

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Abstract

Mytilus mussels (Mytilus edulis (ME), M. trossulus (MT), and M. galloprovincialis (MG)) are of interest in many fields of marine science and have been used as model in evolutionary research. For instance, they form mosaic hybrid zones or hybrid swarms in areas of secondary contact and hence are suited to address questions related to the evolution of reproductive barriers, adaptive hybridization or speciation. While existing genomic information mostly focuses on single species (ME, MG), this project generated RNA seq data of all three species from allopatric populations, i.e. samples representing genetically pure specimens. We investigated adult mantle tissue (four specimens per species), which is functionally involved in processes such as reproduction or biomineralization. The project provides three assembled transcriptomes (post filtering total transcript numbers for ME: 353339, MT: 437827, MG: 290267) representing genes annotated to at least 40 level 2 GO-terms (number (percentage) of annotated transcripts for ME: 44434 (12.6%), MT: 43960 (10%), MG: 60064 (20.7%)). Annotation showed that the most abundant 40 GO-terms are equally well covered by contigs of the three Mytilus transcriptomes. Therefore, this project lays a basis for evolutionary research by providing candidate genes representing various molecular functions such as reproduction, cellular processes or immune response. The potential of the new transcriptomes to address evolutionary questions is further exemplified by a pilot study on ME and MT transcriptomes that used reciprocal blast to identify 7652 one-to-one orthologue pairs of transcripts

Document Type: Article
Keywords: RNA-seq; Mollusca; Hybridization; GO-term annotation; Mantle tissue
Research affiliation: OceanRep > GEOMAR > FB3 Marine Ecology > FB3-EV Marine Evolutionary Ecology
OceanRep > GEOMAR > FB3 Marine Ecology > FB3-EOE-B Experimental Ecology - Benthic Ecology
Refereed: Yes
Open Access Journal?: No
DOI etc.: 10.1016/j.margen.2019.100700
ISSN: 1874-7787
Date Deposited: 20 Aug 2019 10:32
Last Modified: 20 Aug 2019 11:23
URI: http://oceanrep.geomar.de/id/eprint/47524

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