Unknown to Known: Advancing Knowledge of Coral Gene Function. Issue 2 (February 2020)

• Record Type: Journal Article
• Authors: Cleves, Phillip A.; Shumaker, Alexander; Lee, JunMo; Putnam, Hollie M.; Bhattacharya, Debashish
• Is Part Of: Trends in genetics. Volume 36:Issue 2(2020)
• Page Start: 93
• Page End: 104
• Publication Date: 2020-02
• Subjects: coral bleaching -- coexpression network -- genome editing -- multiomics -- thermal stress; Genetics -- Periodicals; 576.5
• DOI: 10.1016/j.tig.2019.11.001
• Languages: English
• ISSNs: 0168-9525

Abstract

Abstract : Given the catastrophic changes befalling coral reefs, understanding coral gene function is essential to advance reef conservation. This has proved challenging due to the paucity of genomic data and genetic tools available for corals. Recently, CRISPR/Cas9 gene editing was applied to these species; however, a major bottleneck is the identification and prioritization of candidate genes for manipulation. This issue is exacerbated by the many unknown ('dark') coral genes that may play key roles in the stress response. We review the use of gene coexpression networks that incorporate both known and unknown genes to identify targets for reverse genetic analysis. This approach also provides a framework for the annotation of dark genes in established interaction networks to improve our fundamental knowledge of coral gene function. Highlights: Coral reefs are under threat from warming oceans. Understanding the basis of the thermal stress response is therefore critical to devising strategies to protect corals and the diverse ecosystem services they provide. Developing a small number of coral model systems will be a necessary step to focus multiomics and functional genetics research to gain a mechanistic understanding of coral holobiont biology. The recent development of CRISPR/Cas9 methods for gene editing in corals offers the opportunity to test hypotheses about coral gene function. Along with studying orthologs of well-understood metazoan genes using reverse genetics, we advocate the use of gene coexpression networks to identify 'dark' genes of unknown function that occupy hub or peripheral network positions. Disruption of dark genes may offer novel insights into coral biology and identify species-specific adaptations.