Development of an integrated genomic map for a threatened Caribbean coral (Orbicella faveolata)

Abstract

Genomic methods are powerful tools for studying evolutionary responses to selection, but the application of these tools in non-model systems threatened by climate change has been limited by the availability of genomic resources in those systems. High-throughput DNA sequencing has enabled development of genome and transcriptome assemblies in non-model systems including reef-building corals, but the fragmented nature of early draft assemblies often obscures the relative positions of genes and genetic markers, and limits the functional interpretation of genomic studies in these systems. To address this limitation and improve genomic resources for the study of adaptation to ocean warming in corals, we've developed a genetic linkage map for the mountainous star coral, Orbicella faveolata. We analyzed genetic linkage among multilocus SNP genotypes to infer the relative positions of markers, transcripts, and genomic scaffolds in an integrated genomic map. To illustrate the utility of this resource, we tested for genetic associations with bleaching responses and fluorescence phenotypes, and estimated genomewide patterns of population differentiation. Mapping the significant markers identified from these analyses in the integrated genomic resource identified hundreds of genes linked to significant markers, highlighting the utility of this resource for genomic studies of corals. The functional interpretations drawn from genomic studies are often limited by the availability of genomic resources linking genes to genetic markers. The resource developed in this study provides a framework for comparing genetic studies of O. faveolata across genotyping methods or references, and illustrates an approach for integrating genomic resources that may be broadly useful in other non-model systems.

Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing

“…Previous work has suggested that the potential karyotype of O. faveolata is 16 chromosomes [48]. In our study, telomeric repeat analysis identified regions at either one (telocentric, 12 scaffolds) or both (metacentric, seven scaffolds) ends of 19 of the 51 scaffolds (TeloScafs) (Fig.…”

“…With the high percentage BUSCO completion of the telomere containing scaffolds, this further suggests that several scaffolds likely represent complete chromosomes. The number of identified TeloScafs is however larger than the potential karyotype of 16 for O. faveolata [48] suggesting that we missed some repetitive sections of the genome such as centromeric repeats. This may also be due to only utilizing HiFi reads for our assembly.…”

Trends in the Application of “Omics” to Ecotoxicology and Stress Ecology

“…Within the cnidaria, Orbicella (previously Montastrea) faveolata was the most often investigated organism. A wide range of sequencing data is available for this endangered reef-building coral, from whole-genome assemblies to RNA-seq data [50][51][52]. Notably, there is little information on proteomic, metabolomic, and multiomic responses within the cnidaria, indicating a knowledge gap for molecular responses in cnidaria beyond the transcriptional level (Figure 2).…”

Valuing Caribbean Biodiversity Knowledge

“…SNPs allow for targeted research into specific aspects of a species' ecology on the molecular level. Questions about the effectiveness of marine protected areas, organism's response to climate change and anthropogenic stressors as well as identification of genetically distinct populations, can be answered using SNPs technology [41,42]. SNP libraries can and have been developed for numerous species for conservation and management purposes.…”

“…SNP libraries can and have been developed for numerous species for conservation and management purposes. In the Caribbean, SNP technology has been applied across various taxa including endangered corals (Acropora palmata and Orbicella faveolata), fish (Nassau grouper), invertebrates (spiny lobster) and an invasive angiosperm (Halophila stipulacea) [42][43][44][45][46].…”