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Comparative de novo assembly and annotation of mantle tissue transcriptomes from the Mytilus edulis species complex (M. edulis, M. galloprovincialis, M. trossulus)
Marine Genomics ( IF 1.9 ) Pub Date : 2019-08-12 , DOI: 10.1016/j.margen.2019.100700
Loreen Knöbel , Corinna Breusing , Till Bayer , Virag Sharma , Michael Hiller , Frank Melzner , Heiko Stuckas

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.



中文翻译:

比较从头组装和注释的披风组织转录组的紫贻贝物种复杂(蓝藻M. galloprovincialistrossulus

贻贝贻贝(Mytilus edulis(ME),trossulus(MT)和galloprovincialis(MG))在海洋科学的许多领域中受到关注,并已被用作进化研究的模型。例如,它们在次级接触区域形成镶嵌杂种区或杂种群,因此适合解决与生殖障碍,适应性杂交或物种形成有关的问题。尽管现有的基因组信息主要集中在单个物种(ME,MG)上,但该项目从异源种群中获得了所有三个物种的RNA seq数据,即代表基因纯净标本的样品。我们调查了成年地幔组织(每个物种四个标本),该组织在功能上涉及繁殖或生物矿化等过程。该项目提供了三个组装的转录组(过滤后的总转录本编号为ME:353339,MT:437827,MG:290267)代表注释了至少40个2级GO术语的基因(注释的成绩单数量(百分比):ME:44434(12.6%),MT:43960(10%),MG:60064(20.7%))。注释显示,最丰富的40个GO术语同样被三个重叠群覆盖Mytilus转录组。因此,该项目通过提供代表各种分子功能(例如生殖,细胞过程或免疫应答)的候选基因,为进化研究奠定了基础。新的转录组解决进化问题的潜力进一步通过对ME和MT转录组的试点研究得到了进一步证明,该研究使用了相互冲击来鉴定7652个一对一的直向同源物。

更新日期:2019-08-12
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