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The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)

Citation

Drozdova, Polina; Kizenko, Alena; Saranchina, Alexandra; Timofeyev, Maxim (2021), The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae), Dryad, Dataset, https://doi.org/10.5061/dryad.fj6q573r9

Abstract

Vision is a crucial sense for the evolutionary success of many animal groups. In this work, we explore the diversity of opsins in over 100 amphipod (Crustacea: Amphipoda) species with sequenced transcriptomes and concluded that it is generally restricted to middle wavelength-sensitive (MWS) and long wavelength-sensitive (LWS) opsins. We found that multiple lineages of amphipods, including two lineages from the deep and ancient Lake Baikal in Eastern Siberia, lost the expression of MWS opsins. We provide reassembled transcriptomes and list of opsin sequences.

Methods

Raw sequencing reads were downloaded from the sequence read archive (SRA) NCBI database with the fastq-dump command from NCBI SRA toolkit v2.9.2 (http://ncbi.github.io/sra-tools/). Data quality control was performed with
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) v0.11.8 and summarized with MultiQC v1.2. Read trimming was performed with trimmomatic v0.36 in the pair-end mode. Transcriptome reassemblies were obtained with Trinity v2.8.5 or rnaSPAdes v3.13.1. Assembly completeness was estimated with BUSCO v3.0.2.

Funding

Russian Science Foundation, Award: 19-74-00045