Comparative transcriptome and gene co-expression network analysis identifies key candidate genes associated with resistance to summer mortality in the Pacific oyster (Crassostrea gigas)

Chi, Yong; Yang, Hang; Shi, Chenyu; Yang, Ben; Bai, Xianchao; Li, Qi

doi:10.1016/j.aquaculture.2023.739922

Search citation statements

Order By: Relevance

Paper Sections

Select...

Citation Types

Supporting

Mentioning

Contrasting

Year Published

2024

Publication Types

Select...

Article3

Preprint1

Relationship

Self Cite0

Independent4

Authors

Journals

Cited by 4 publications

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

Comparative transcriptomic and epigenomic analyses to identify the cold resistance-associated genes and disclose the regulatory mechanisms in tilapias

Song,

Liu,

Chen

et al. 2024

Aquaculture

View full text Add to dashboard Cite

Comparative transcriptomic and epigenomic analyses to identify the cold resistance-associated genes and disclose the regulatory mechanisms in tilapias

Song,

Liu,

Chen

et al. 2024

Aquaculture

View full text Add to dashboard Cite

Genome-wide association study and genomic prediction of resistance to summer mortality in Pacific oyster (Crassostrea gigas) using whole genome resequencing

Chi,

Yang,

Yang

et al. 2024

Aquaculture

View full text Add to dashboard Cite

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

Edsinger,

Moroz

2024

Preprint

View full text Add to dashboard Cite

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.

show abstract

Comparative transcriptome and gene co-expression network analysis identifies key candidate genes associated with resistance to summer mortality in the Pacific oyster (Crassostrea gigas)

Cited by 4 publications

References 76 publications

Comparative transcriptomic and epigenomic analyses to identify the cold resistance-associated genes and disclose the regulatory mechanisms in tilapias

Comparative transcriptomic and epigenomic analyses to identify the cold resistance-associated genes and disclose the regulatory mechanisms in tilapias

Genome-wide association study and genomic prediction of resistance to summer mortality in Pacific oyster (Crassostrea gigas) using whole genome resequencing

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

Contact Info

Product

Resources

About