DOI: 10.5061/dryad.mkkwh7111
title: Data from: Analysis of the opsin repertoire in the tardigrade Hypsibius dujardini provides insights into the evolution of opsin genes in Panarthropoda

description: Screening of a deeply sequenced transcriptome using Illumina sequencing as
 well as the genome of the tardigrade Hypsibius
 exemplaris (referred to as Hypsibius dujardini in the
 published article) revealed a set of five opsin genes.To clarify
 the phylogenetic position of these genes and to elucidate the evolutionary
 history of opsins in Panarthropoda (Onychophora +Tardigrada+Arthropoda),
 we reconstructed the phylogeny of broadly sampled metazoan opsin genes
 using maximum likelihood and Bayesian inference methods in conjunction
 with carefully selected substitution models. According to our findings,
 the opsin repertoire of H. exemplaris comprises representatives of all
 three major bilaterian opsin clades, including one r-opsin, three
 c-opsins, and a Group 4 opsin (neuropsin/opsin-5). The identification of
 the tardigrade ortholog of neuropsin/opsin-5 is the first record of this
 opsin type in a protostome,but our screening of available metazoan genomes
 revealed that it is also present in other protostomes. Our opsin phylogeny
 further suggests that two r-opsins, including an “arthropsin”, were
 present in the last common ancestor of Panarthropoda. Although both
 r-opsin lineages were retained in Onychophora and Arthropoda, the
 arthropsin was lost in Tardigrada. The single (most likely visual) r-opsin
 found in H. exemplaris supports the hypothesis of monochromatic vision in
 the panarthropod ancestor, whereas two duplications of the ancestral
 panarthropod c-opsin have led to three c-opsins in tardigrades. Although
 the early-branching nodes are unstable within the metazoans, our findings
 suggest that the last common ancestor of Bilateria possessed six opsins:
 Two r-opsins, one c-opsin, and three Group 4 opsins, one of which (Go
 opsin) was lost in the ecdysozoan lineage.
description: Specimens of <em>Hypsibius exemplaris</em> (Gąsiorek,
 2018) (Eutardigrada, Hypsibiidae) were obtained commercially from Sciento
 (Manchester, UK). Several hundred specimens were used to extract total RNA
 using TRIzol reagent (Invitrogen, Carlsbad, CA) and RNeasy MinElute
 Cleanup Kit (Qiagen, Hilden, Germany) according to the manufacturers’
 protocols. Library preparation for double indexing (Meyer and Kircher
 2010; Kircher et al. 2012), 76 cycles paired-end sequencing on an Illumina
 Genome Analyzer IIx (San Diego, CA), and postsequencing processing
 (adapter trimming, removal of reads with falsely paired indices and
 filtering of reads at three different levels of stringency; Filter15:
 reads with more than five bases below a phred quality score of 15 were
 removed; Filter30: reads with less than 20 bases in a row with a phred
 quality score of at least 30 were removed; Filter25: same as Filter30 but
 the threshold value was set to 25 to keep as many high-quality reads as
 possible) were performed as described by Hering et al. (2012). Each of the
 three obtained data sets (Filter15, Filter25, and Filter30) was then
 assembled <em>de novo</em> using two different software
 packages to assess the occurrence of opsin transcripts in a broader
 methodological framework: CLC Genomics Workbench v5.1 (CLC bio, Århus,
 Denmark), and IDBA-Tran v1.1.0 (Peng et al. 2013). The IDBA-Tran
 assemblies were done twice, allowing for the retention of one or up to
 three isoforms of a transcript, respectively, using the --max_isoforms
 option (for details see statistics_and_BUSCO_values.xls).
description: An explanation of each file is given in the README.txt file.