Transient receptor potential (TRP) channels in the Manila clam (Ruditapes philippinarum): Characterization and expression patterns of the TRP gene family under heat stress in Manila clams based on genome-wide identification

Zhang, Yanming; Nie, Hongtao; Yan, Xiwu

doi:10.1016/j.gene.2022.147112

Cited by 6 publications

(3 citation statements)

References 73 publications

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“…Second, the observed patterns of TRP family evolution are similar to previous studies in molluscs, including oysters (68,70,71,73,74). TRP gene family members form hotspots at substantially greater levels than observed background levels per genome.…”

Section: Discussionsupporting

confidence: 85%

“…The TRPM gene family is recognized as a primary molecular sensor of temperature, including their elevated expression in response to heat stress in oysters and other molluscs (68,70,71,73,74). Upper intertidal and hydrothermal vents are both environments featuring heat extremes, and bivalve and gastropod lineages have independently entered these environments with greatly expanded TRPM gene family diversity through lineage-specific hotspots.…”

Section: Discussionmentioning

confidence: 99%

“…The selected molluscs include bivalves and gastropods species found in subtidal vs. intertidal or hydrothermal vent habitats. We also epmhasize the Transient Receptor Potential (TRP) ion channel superfamily, including the thermo-sensitive TRPM family(67–70), which are diverse and expressed under heat stress in species used here(71–79). Our findings illustrate that approaches leveraging hotspots could enable predictions of adaptation and resilience in response to environmental change.…”

Section: Introductionmentioning

confidence: 99%

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Genomic Hotspots: Localized chromosome gene expansions identify lineage-specific innovations as targets for functional biodiversity and predictions of stress resilience

Edsinger,

Moroz

2024

Preprint

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1AbstractFunctional and biodiversity genomics is essential for assessment and monitoring of planetary health and species-specific management in changing ecosystems. However, experimental knowledge of gene functions is limited to a few species, and dependencies on distantly related models. Combined with unrecognized degrees of lineage-specific gene family expansion, this means that traditional comparative methods are insufficient. Here, we clarify definitions of homology and genomic ‘dark matter’ and introduce the concept of a hotspot, defined as innovations underlying the evolution of lineage-specific biology. We illustrate hotspots using molluscs having chromosome-scale genome assemblies and focus on heat-sensing TRPM channels and species living in environments of extreme heat stress (e.g., high intertidal and hydrothermal vent gastropods and bivalves). Integrating gene family, orthogroup, and domain-based methods with genomic hotspots (local paralog expansions on chromosomes), we show that conventional approaches overlook substantial amounts of species-specific gene family diversity due to limitations of distant homology detection. In contrast, local segmental duplications are often recent, lineage-specific genetic innovations reflecting emerging adaptions and can be identified for any genome. Revealed TRPM gene family diversification highlights unique neural and behavioral mechanisms that could be beneficial in predicting species’ resilience to heat stress. In summary, the identification of hotspots and their integration with other types of analyses illuminate evolutionary (neuro)genomic strategies that do not depend on knowledge from model organisms and unbiasedly reveal evolutionarily recent lineage-specific adaptations. This strategy enables discoveries of biological innovations across species as prospective targets for modeling, management, and biodiversity conservation.

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