Data from: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve
Data files
Apr 04, 2024 version files 266.87 MB
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FS.emapper.annotations
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list3.genelist_filtered
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list4.genelist_filtered
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README.md
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TG.emapper.annotations
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unigene_FS_final.fasta
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unigene_TG_final.fasta
Abstract
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.
README: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve
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.
Methods
Fragum sueziense were collected in Family Beach, Guam and Trigoniocardia granifera were collected near Isla Venado, Panama. 30 F. sueziense and 37 T. granifera 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.