Revealing the Gene Diversity and Candidate Gene Family for Adaption to Environment Depth in Leucosiid Crabs Comparing the Transcriptome Assembly

Abstract

The study of gene diversity in interspecies contributes to our understanding of the environmental adaptation, evolutionary history, origin, and stability of biodiversity. Crabs are the main component of the macrobenthos community; therefore, how crabs adapt to different environments can be a guide to understand how to maintain community diversity. Previous studies on environmental adaptation have focused on differences in morphology, organ structure, and function, but there is a lack of research that explores this topic from the perspective of gene diversity in benthonic crabs. In this study, the leucosiid crab was selected for transcriptome assembly and was analyzed as this superfamily is one of the main clades in brachyuran crabs. Their transcriptome data were used to understand the gene diversity, phylogeny, and divergence time estimations. Subsequently, candidate gene families for depth adaptation were found in eight species that live in habitats with different depths. The results indicated that the number of total unigene sequences was between 65,617 (Philyra malefactrix) and 98,279 (Arcania heptacantha) in eight species. The total length of the genes was counted to be between 48,006,211 and 95,471,088 bp. The age of the superfamily Leucosioidea is over 150 Ma, dating back to at least the Jurassic geological period. The divergence of the family Leucosiidae would have occurred in the middle Cretaceous (around 100 Ma). After dividing into groups of three depth types, which carried the gene families, it was found that the three groups shared the solute carrier family, whereas bile acid secretion, organic solute transporter subunit alpha-like, and solute carrier organic anion transporter families only existed in the shallow group. This result shown that the gene function of ion concentration regulation might one of the candidate gene families related to the environmental adaptation of the leucosiid crab. Hence, these gene families will be analyzed in future studies to understand the mechanism of depth adaptation regulation in crabs.

Adaptations to Subterranean Environments

“…The genes that displayed signatures of convergent, intensified selection in the test and reference branches analyzed (schemes 1 and 2) were primarily associated with hematopoietic and metabolic processes. Among these genes were MVD, which is necessary for cell survival (Wong et al, 2021); SCARA5, previously identified to exclusively express on epithelial cells in vertebrates (Yap et al, 2015); SLC4A1AP, an ion transporter gene identified in crabs (Shih et al, 2023); STARD7, which is thought to play an essential role in morphogenesis and respiration in mammals (Horibata et al, 2020); and PDK4, previously found to have increased levels of expression in fasting in chickens and mice (Connaughton et al, 2009). The identification of intensified selection on genes associated with hematopoietic and metabolic processes in our dataset may suggest that selection exerts ongoing pressures on a limited number of genes that are crucial for ensuring the survival of fishes in cave environments characterized by limited food availability .…”

Transcriptomic analysis of the Brazilian blind characid, Stygichthys typhlops, reveals convergent selection with Astyanax mexicanus and other cavefishes

“…The genes that displayed signatures of convergent, intensified selection in the test and reference branches analyzed (schemes 1 and 2) were primarily associated with hematopoietic and metabolic processes. Among these genes were MVD, which is necessary for cell survival (Wong et al, 2021); SCARA5, previously identified to exclusively express on epithelial cells in vertebrates (Yap et al, 2015); SLC4A1AP, an ion transporter gene identified in crabs (Shih et al, 2023); STARD7, which is thought to play an essential role in morphogenesis and respiration in mammals (Horibata et al, 2020); and PDK4, previously found to have increased levels of expression in fasting in chickens and mice (Connaughton et al, 2009). The identification of intensified selection on genes associated with hematopoietic and metabolic processes in our dataset may suggest that selection exerts ongoing pressures on a limited number of genes that are crucial for ensuring the survival of fishes in cave environments characterized by limited food availability (Poulson and Lavoie, 2000).…”