DOI: 10.5061/dryad.djh9w0w6s
title: Data from: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve

description: Photosymbioses between heterotrophic hosts and autotrophic symbionts are
 evolutionarily prevalent and ecologically significant. However, molecular
 mechanisms behind such symbioses remain less elucidated, which hinders our
 understanding of their origin and adaptive evolution. This study compared
 gene expression patterns in a photosymbiotic bivalve (Fragum sueziense)
 and a closely related non-symbiotic species (Trigoniocardia granifera)
 under different light conditions to detect potential molecular pathways
 involved in mollusk photosymbiosis. We discovered that the presence of
 algal symbionts greatly impacted host gene expression in
 symbiont-containing tissues. We found that the host immune functions were
 suppressed under normal light compared to those in the dark. In addition,
 we found that cilia in the symbiont-containing tissues play important
 roles in symbiont regulation or photoreception. Interestingly, many
 potential photosymbiosis genes could not be annotated or do not exhibit
 orthologs in T. granifera transcriptomes, indicating unique molecular
 functions in photosymbiotic bivalves. Overall, we found both novel and
 known molecular mechanisms involved in animal-algal photosymbiosis within
 bivalves. Given that many of the molecular pathways are shared among
 distantly related host lineages, such as mollusks and cnidarians, it
 indicates that parallel and/or convergent evolution is instrumental in
 driving host-symbiont adaptations in diverse organisms.
description: <em>Fragum sueziense</em> were collected in Family
 Beach, Guam and <em>Trigoniocardia granifera</em> were
 collected near Isla Venado, Panama. 30 <em>F. sueziense</em>
 and 37 <em>T. granifera</em> were randomly assigned into 3
 groups evenly and placed under different light intensities: 1. Under an
 ambient light-dark cycle, which the animals were exposed to in the natural
 habitats; 2. At reduced light during the day by blocking sunlight with
 black meshes; and 3. Under constant darkness by blocking sunlight with
 multiple layers of black meshes. Specimens were treated for 3 days then
 processed. See detailed collecting and processing information in
 electronic supplementary material text in Li et al. 2024.
description: # Comparative transcriptomics revealed parallel evolution and innovation
 of photosymbiosis molecular mechanisms in a marine bivalve
 [https://doi.org/10.5061/dryad.djh9w0w6s](https://doi.org/10.5061/dryad.djh9w0w6s) ## Description of the data and file structure unigene_FS_final.fasta: Meta-transcriptome of *Fragum sueziense* unigene_TG_final.fasta: Meta-transcriptome of *Trigoniocardia granifera* FS.emapper.annotations: Emapper Annotation of *Fragum sueziense* meta-transcriptome TG.emapper.annotations: Emapper Annotation of *Trigoniocardia granifera* meta-transcriptome list3.genelist_filtered: Genes that are highly possible to be involved in photosymbiosis in list 3 list4.genelist_filtered: Genes that are highly possible to be involved in photosymbiosis in list 4 ## Softwares unigene_FS_final.fasta & unigene_TG_final.fasta: meta-transcriptome (including all treatments and tissue types) for each bivalve species was assembled using Trinity v2.13. FS.emapper.annotations & TG.emapper.annotations: The meta-transcriptomes were annotated with eggnog mapper with default settings list3.genelist_filtered: For *F. sueziense*, genes showing upregulation in the mantles under ambient conditions (normal photosymbiosis) compared to total dark (photosynthetic shut down) were retrieved from the DEG analyses (unfiltered list 1). Genes upregulated within mantle tissues (symbiont-bearing) compared to foot tissues (no symbionts) under ambient condition were identified as a second gene set (unfiltered list 2). Subsequently, genes were excluded from unfiltered list 1* *and* *2 if their orthologs exhibited similar expression patterns in the non-symbiotic species *T. granifera* because similar expression patterns in the non-symbiotic species indicated that these genes were more likely to be involved in light-dark regulation or mantle/foot specific functions, instead of photosymbiosis. After exclusion, the intersection of lists 1 and 2 were identified as list 3. list4.genelist_filtered: *F. sueziense* genes which were not assigned to orthogroups in the first step could represent novel genes associated with photosymbiosis. Therefore, the same approaches which generated unfiltered lists 1 and 2 were performed on the unassigned genes in *F. sueziense*. The intersection of the two sets of genes were grouped into list 4.