DOI: 10.5061/dryad.9ghx3ffp8
title: Putative photosensitivity in internal light organs (organs of Pesta) of deep-sea sergestid shrimps

description: Many marine species can regulate the intensity of bioluminescence from
 their ventral photophores in order to counterilluminate, a camouflage
 technique whereby animals closely match the intensity of the downwelling
 illumination blocked by their bodies, thereby hiding their silhouettes.
 Recent studies on autogenic cuticular photophores in deep-sea shrimps
 indicate that the photophores themselves are light-sensitive. Here, our
 results further suggest photosensitivity in a second type of
 autogenic photophore, the internal organs of Pesta, found in deep-sea
 sergestid shrimps. Experiments were conducted ship-board on live
 specimens, exposing the animals to bright light, which resulted in
 ultrastructural changes that matched those seen in crustacean eyes during
 the photoreceptor membrane turnover, a process that is crucial for the
 proper functioning of photosensitive components. In addition, RNA-seq
 studies demonstrated the expression of visual opsins and phototransduction
 genes in organs of Pesta tissue that are known to play a role in light
 detection, and electrophysiological measurements indicated that the light
 organs are responding to light received by the eyes. The long-sought-after
 mechanism of counterillumination remains unknown, but evidence of
 photosensitivity in photophores may indicate a dual functionality of light
 detection and emission.
description: Biological replicates of <em>Parasergestes
 armatus</em> (n=4) were immediately preserved in RNAlater and stored
 at -80 °C upon live collection. Organs of Pesta were carefully dissected
 in chilled RNAlater to prevent degradation of nucleic acids and
 homogenized in TRIzol reagent (ThermoFisher Scientific). Total RNA was
 extracted following recommendations in DeLeo <em>et al</em>.
 (2018) and mRNA libraries were prepared using the NEBNext Ultra II
 Directional RNA Library Prep Kit for Illumina. Pippin Prep (Sage Science)
 was used for size selection on barcoded libraries and all samples (n=4)
 were sequenced on an Illumina HiSeq4000. FastQC was
 used to assess the quality of raw sequencing data and adaptor sequences
 were trimmed with Trimmomatic v0.36 (parameters:
 <em>adapter.clip</em> 2:30:10:1:true,
 <em>crop</em> 135, <em>headcrop</em> 15,
 <em>trim.leading</em> 3, <em>trim.trailing</em> 3,
 <em>sliding.window</em> 4:20,
 <em>min.read.length</em> 36). Rcorrector and BBnorm were used
 to error-correct reads and normalize read coverage. Tissue-specific
 transcriptomes were assembled <em>de novo</em> using Trinity
 v2.6.5 (minimum contig length of 200bp, k-mer size of 23) and
 contamination was removed using Kraken v1.0 with default parameters and
 NCBI’s (Refseq) bacteria, archaea, and viral databases. BBduk and dedupe
 (BBTools suite, available at:
 http://sourceforge.net/projects/bbmap) were used to
 remove duplicate transcripts and rRNA. All voucher specimens are archived
 in the Florida International Crustacean Collection (FICC, HBG
 #8487-8490).  The organ of Pesta transcriptome was
 analyzed using a modified Phylogenetically-Informed Annotation (PIA) Tool
 which can be used to identify putative visual opsins and phototransduction
 genes using custom databases (including both visual and non-visual opsins
 as well as other light detection genes, in precomputed phylogenies which
 enables the discrimination between false positives and/or paralogous genes
 following a series of BLAST searches). To further
 characterize putative opsins recovered by PIA, these sequences were
 aligned with PROMALS3D using a reference invertebrate opsin dataset
 (n=283). This dataset included visual opsins across a range of spectral
 sensitivities as well as non-visual opsins and related G-protein coupled
 receptors (GPCR) (see DeLeo and Bracken-Grissom 2020 for a list of all
 taxa included). Model testing and opsin gene tree reconstruction were done
 with IQ-TREE using an LG general amino acid replacement matrix, under a
 FreeRate model with 9 rate categories, and empirical base frequencies
 (LG+R9+F), based on recommendations from ModelFinder. Support was assessed
 using 1) a Shimodaira–Hasegawa–like approximate likelihood ratio test
 (SH-aLRT; 10,000 replicates), 2) an approximate Bayes test and 3) an
 Ultra-fast bootstrap approximation (UFBoot; 10,000 replicates). False
 positives aligning with non-visual opsins or outgroups were
 removed.
description: Alignment viewer (i.e., Aliview or Genewiz) and/or a Text
 editor
description: # Title of Dataset: Putative photosensitivity in internal light organs
 (organs of Pesta) of deep-sea sergestid shrimps --- This dataset contains
 a tissue-specific transcriptome (organs of Pesta) assembled de novo from
 replicate (n=4) RNAseq data for the deep-sea sergestid shrimp
 *Parasergestes armatus*. The organs of Pesta are a type of type of
 autogenic photophore, with our results indicating putative
 photosensitivity in addition to light emission. This dataset also contains
 the putative visual opsin genes curated from the assembly using
 phylogenetically informed annotation tools, and associated alignment files
 used in subsequent analyses. These data support additional lines of
 evidence presented in the paper that the organs of Pesta are light
 sensitive. ## Description of the Data and file structure
 trinity_Parmatus_organsPesta.fasta - Tissue-specific de novo transcriptome
 assembly file generated from organs of Pesta, autogenic photophores, from
 the deep-sea sergestid shrimp Parasergestes armatus.
 Parmatus_organsPesta_LWS_ropsins.fasta - File containing the putative
 long-wavelength sensitive (LWS) visual r-opsins curated from the P.
 armatus organs of Pesta transcriptome using phylogenetically informed
 annotation.
 Parmatus_organsPesta_Sdebilis_photo_LWS_ropsins_alignment.fasta -
 Alignment file of the putative LWS opsins recovered from P. armatus organs
 of Pesta and putative visual opsins recovered from another type of
 autogenic photophore from the deep-sea shrimp, Systellaspis debilis. Prior
 studies also suggest S. debilis photophores are photosensitive. ##
 Sharing/access Information Links to other publicly accessible locations of
 the data: