Bioluminescence and environmental light drive the visual evolution of deep-sea shrimp (Oplophoroidea)
Data files
Dec 02, 2024 version files 3.67 GB
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Apurp_final.fasta
205.19 MB
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Astylo_final.fasta
427.96 MB
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Eombango_final.fasta
376.62 MB
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FinalOpsinTree.treefile
57.31 KB
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Hgracil_final.fasta
506.62 MB
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Mmollis_final.fasta
477.54 MB
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Nelegans_final.fasta
264 MB
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Nensi.trinity.fasta
115.05 MB
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Ogracil_final.fasta
405.84 MB
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oplophoridae_lightingEnv.csv
469 B
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oplophoridae_opsins_binary.csv
593 B
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oplophoroidea_orthologs_newtree.rooted.pruned.treefile
766 B
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PROMALS_LWSaligned_curated.fasta
4.97 KB
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PROMALS_MWSaligned_curated_mws1.fasta
4.86 KB
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PROMALS_MWSaligned_curated_mws2.fasta
4.55 KB
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PROMALSalignment_OplophoroideaOpsins_final.fasta
383.03 KB
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README.md
5.21 KB
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Sbraueri_final.fasta
317.88 MB
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Scrist_final.fasta
570.51 MB
Abstract
Light functions as the universal language in the deep sea (> 200 m). Both bioluminescent emissions and downwelling light sources dimly illuminate the water column and can drive sensory system evolution. In pelagic environments, vertically migrating animals can experience drastic changes to their lighting environment across depth, subjecting them to unique selective pressures, possibly to distinguish between changes in ambient light and bioluminescent sources. Here we show that visual opsin diversity across a group of variable vertical migrators- bioluminescent deep-sea shrimp belonging to the Superfamily Oplophoroidea- is higher among species who migrate to shallower waters with more variable light conditions. Further, we provide evidence for adaptive visual evolution among species who have evolved an additional mode of bioluminescence (photophores), including positive selection for a putative mid-wavelength sensitive opsin that may facilitate light source discrimination. Diversification of this opsin appears to play an important role in the visual ecologies of photophore-bearing shrimp with its diversification in Oplophoroidea likely playing a critical role in the fitness and evolutionary success of this group.
README: Bioluminescence and environmental light drive the visual evolution of deep-sea shrimp (Oplophoroidea)
https://doi.org/10.5061/dryad.cz8w9gjds
Description of the data and file structure
Bioluminescent shrimp eye transcriptomes
Tissue-specific (eye) reference transcriptomes were assembled de novo for the 10 deep-sea shrimp species (Trinity v2.8.5), belonging to two families of bioluminescent shrimp- Oplophoridae (1-2 modes of bioluminescence) and Acanthephyridae (1 mode)- and one outgroup species (N. ensifer). After contaminant removal, the final reference assemblies were used in downstream analyses, including ortholog identification to build a species tree for the Superfamily Oplophoroidea and the identification and characterization of putative visual opsins (r-opsins) to test whether there was evidence of positive selection. The resulting tree was used for Ancestral State Reconstruction (ASR) of opsin type (presence/absence of expression) and for the ASR of lighting environment for Oplophoroidea. Members of this superfamily migrate vertically in the water column, but some remain in deep waters where light is limited (> 400meters) or can no longer penetrate (>1000). For ASR species were categorized based on the shallowest depth of their known species range (=highest light presence or lowest light attenuation), as either 1) epipelagic < 200m, 2) upper mesopelagic 200-400m, 3) mesopelagic 400-700m or 4) lower mesopelagic > 700m.
Files and variables
File: Astylo_final.fasta
Description: Eye transcriptome of Acanthephyra stylorostratis
File: Apurp_final.fasta
Description: Eye transcriptome of Acanthephyra purpurea
File: Eombango_final.fasta
Description: Eye transcriptome of Ephyrina ombango
File: Hgracil_final.fasta
Description: Eye transcriptome of Hymenodora gracilis
File: Mmollis_final.fasta
Description: Eye transcriptome of Meningodora mollis
File: Nelegans_final.fasta
Description: Eye transcriptome of Notostomus elegans
File: Nensi.trinity.fasta
Description: Eye transcriptome of Nematocarcinus ensifer
File: Ogracil_final.fasta
Description: Eye transcriptome of Oplophorus gracilirostris
File: Sbraueri_final.fasta
Description: Eye transcriptome of Systellaspis braueri
File: Scrist_final.fasta
Description: Eye transcriptome of Systellaspis cristata
File: FinalOpsinTree.treefile
Description: Arthropod opsin gene tree used to characterize opsins in this study, based on clade grouping with opsins with known wavelength sensitivities (lambda max).
File: PROMALS_LWSaligned_curated.fasta
Description: Alignment of long-wavelength sensitive (LWS) opsins recovered from the shrimp eye transcriptomes.
File: oplophoroidea_orthologs_newtree.rooted.pruned.treefile
Description: Species tree for the Superfamily Oplophoroidea based on 622 orthologous genes, with the outgroup removed after rooting for Ancestral State Reconstruction analyses.
File: PROMALS_MWSaligned_curated_mws1.fasta
Description: Alignment of mid-wavelength sensitive (MWS1) opsins (clade1) recovered from the shrimp eye transcriptomes.
File: PROMALS_MWSaligned_curated_mws2.fasta
Description: Alignment of mid-wavelength sensitive (MWS2) opsins (clade2) recovered from the shrimp eye transcriptomes.
File: PROMALSalignment_OplophoroideaOpsins_final.fasta
Description: Alignment of Oplophoroidea opsins recovered from the shrimp eye transcriptomes.
File: oplophoridae_lightingEnv.csv
Description: Ancestral State Reconstruction coding for the lighting environment, based on the shallowest depth each species migrates to (=highest light presence or lowest light attenuation): epipelagic < 200m, upper mesopelagic 200-400m, mesopelagic 400-700m or lower mesopelagic > 700m
Variables
- Assembly: Transcriptome assembly
- LE: Lighting environment category
File: oplophoridae_opsins_binary.csv
Description: Ancestral State Reconstruction coding for the presence/absence of expression of each opsin type in the shrimp eye transcriptomes. Opsin clade corresponds to clade identified with the opsin gene tree (FinalOpsinTree.treefile).
Variables
- Assembly: Transcriptome assembly
- S1: short wavelength sensitive opsin (SWS1)
- S2: short wavelength sensitive opsin (SWS2)
- SM: short/mid wavelength sensitive opsin (SWS/MWS)
- M1: mid wavelength sensitive opsin (MWS1)
- M2: mid wavelength sensitive opsin (MWS2)
- L: long wavelength sensitive opsin (LWS2)
Code/software
Assembly files
Transcriptomes can be viewed using a text editor (e.g. Sublime) or through command-line tools (e.g. nano)
Alignment files
Text editors (e.g. Sublime) can be used to view the alignments, or free software programs like AliView to view in more detail.
Tree files
Tree viewing software like FigTree can be used to view the tree files.
ASR coding files (.csv)
The .csv files can be viewed with a text editors (e.g. Sublime) or using excel.
Methods
Specimens were collected from the Gulf of Mexico and Florida Straits aboard the RV Point Sur (2015-2018), RV Sonne and RV Walton Smith (2016, 2017), respectively. Collections were done by a 9-meter2 Tucker trawl fitted with a light-tight, thermally insulated cod-end MOC-10 system. All animals were sorted shipboard under dim red light and preserved and frozen in RNAlater. Eye tissues were dissected in RNAlater from three biological replicates for a majority of the shrimp species, except for Systellaspis braueri where only two replicates preserved for RNA work were available and the outgroup species N. ensifer (n=1). Total RNA was discretely extracted from tissues using Trizol/Chloroform reagents and rDNase (Macherey-Nagel) treated. RNAseq libraries were constructed from high-quality RNA using the NEBNext® UltraTM II Directional library prep kit for Illumina® using the manufacturer’s protocol for use with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Libraries had a target amplicon size of 330 bp and contained NEBNext Multiplex Oligos for Illumina® dual index adaptors. Libraries were pooled and sequenced on an Illumina HiSeq4000 to obtain 150 bp paired-end reads at the GENEWIZ® Core Facility (South Plainfield, NJ).
Raw Illumina data was quality assessed (FastQC) prior to trimming with Trimmomatic v0.36 (adapter.clip 4:30:10, min.read.length 30). Reads were then error-corrected (Rcorrector) and tissue-specific (eye) reference transcriptomes were assembled de novo for each species with Trinity v2.8.5 (using in silico read normalization, a minimum contig length of 200 bp and a k-mer size of 23). Contamination was removed from each assembly (default parameters and the bacteria, archaea and viral database Minikraken2, v2). Duplicate transcripts and rRNA were removed using BBduk and dedupe (BBTools suite, available at: http://sourceforge.net/projects/bbmap).