High-quality genome assembles from key Hawaiian coral species

Gene expression response under thermal stress in two Hawaiian corals is dominated by ploidy and genotype

Transcriptome data are frequently used to investigate coral bleaching; however, the factors controlling gene expression in natural populations of these species are poorly understood. We studied two corals, Montipora capitata and Pocillopora acuta, that inhabit the sheltered Kāne'ohe Bay, Hawai'i. M. capitata colonies in the bay are outbreeding diploids, whereas P. acuta is a mixture of clonal diploids and triploids. Populations were sampled from six reefs and subjected to either control (no stress), thermal stress, pH stress, or combined pH and thermal stress treatments. RNA-seq data were generated to test two competing hypotheses: (1) gene expression is largely independent of genotype, reflecting a shared treatment-driven response (TDE) or, (2) genotype dominates gene expression, regardless of treatment (GDE). Our results strongly support the GDE model, even under severe stress. We suggest that post-transcriptional processes (e.g., control of translation, protein turnover) modify the signal from the transcriptome, and may underlie the observed differences in coral bleaching sensitivity via the downstream proteome and metabolome.

Facultative lifestyle drives diversity of coral algal symbionts

The photosynthetic symbionts of corals sustain biodiverse reefs in nutrient-poor, tropical waters. Recent genomic data illuminate the evolution of coral symbionts under genome size constraints and suggest that retention of the facultative lifestyle, widespread among these algae, confers a selective advantage when compared with a strict symbiotic existence. We posit that the coral symbiosis is analogous to a 'bioreactor' that selects winner genotypes and allows them to rise to high numbers in a sheltered habitat prior to release by the coral host. Our observations lead to a novel hypothesis, the 'stepping-stone model', which predicts that local adaptation under both the symbiotic and free-living stages, in a stepwise fashion, accelerates coral alga diversity and the origin of endemic strains and species.

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

Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, with long-read de-novo genome assemblies now starting to be publicly available, opening the door for a wide array of 'omics-based research. Here we present a new de-novo genome assembly for the endangered Caribbean star coral, Orbicella faveolata, using PacBio circular consensus reads. Our genome assembly improved the contiguity (51 versus 1,933 contigs) and complete and single copy BUSCO orthologs (93.6% versus 85.3%, database metazoa_odb10), compared to the currently available reference genome generated using short-read methodologies. Our new de-novo assembled genome also showed comparable quality metrics to other coral long-read genomes. Telomeric repeat analysis identified putative chromosomes in our scaffolded assembly, with these repeats at either one, or both ends, of scaffolded contigs. We identified 32,172 protein coding genes in our assembly through use of long-read RNA sequencing (ISO-seq) of additional O. faveolata fragments exposed to a range of abiotic and biotic treatments, and publicly available short-read RNA-seq data. With anthropogenic influences heavily affecting O. faveolata, as well as its increasing incorporation into reef restoration activities, this updated genome resource can be used for population genomics and other 'omics analyses to aid in the conservation of this species.

Ploidy Variation and Its Implications for Reproduction and Population Dynamics in Two Sympatric Hawaiian Coral Species

Standing genetic variation is a major driver of fitness and resilience and therefore of fundamental importance for threatened species such as stony corals. We analyzed RNA-seq data generated from 132 Montipora capitata and 119 Pocillopora acuta coral colonies collected from Kāne'ohe Bay, O'ahu, Hawai'i. Our goals were to determine the extent of colony genetic variation and to study reproductive strategies in these two sympatric species. Surprisingly, we found that 63% of the P. acuta colonies were triploid, with putative independent origins of the different triploid clades. These corals have spread primarily via asexual reproduction and are descended from a small number of genotypes, whose diploid ancestor invaded the bay. In contrast, all M. capitata colonies are diploid and outbreeding, with almost all colonies genetically distinct. Only two cases of asexual reproduction, likely via fragmentation, were identified in this species. We report two distinct strategies in sympatric coral species that inhabit the largest sheltered body of water in the main Hawaiian Islands. These data highlight divergence in reproductive behavior and genome biology, both of which contribute to coral resilience and persistence.

A draft genome assembly of reef-building octocoral Heliopora coerulea

Coral reefs are under existential threat from climate change and anthropogenic impacts. Genomic studies have enhanced our knowledge of resilience and responses of some coral species to environmental stress, but reference genomes are lacking for many coral species. The blue coral Heliopora is the only reef-building octocoral genus and exhibits optimal growth at a temperature close to the bleaching threshold of scleractinian corals. Local and high-latitude expansions of Heliopora coerulea were reported in the last decade, but little is known about the molecular mechanisms underlying its thermal resistance. We generated a draft genome of H. coerulea with an assembled size of 429.9 Mb, scaffold N50 of 1.42 Mb and BUSCO completeness of 94.9%. The genome contains 239.1 Mb repetitive sequences, 27,108 protein coding genes, 6,225 lncRNAs, and 79 miRNAs. This reference genome provides a valuable resource for in-depth studies on the adaptive mechanisms of corals under climate change and the evolution of skeleton in cnidarian.

Genome assembly of the deep-sea coral Lophelia pertusa

Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated PacBio continuous long reads data for an initial assembly and proximity ligation data for scaffolding. The assembly was annotated using evidence from transcripts, proteins, and ab initio gene model predictions. This assembly is comparable to high-quality reference genomes from shallow-water scleractinian corals. The assembly comprises 2,858 scaffolds (N50 1.6 Mbp) and has a size of 556.9 Mbp. Approximately 57% of the genome comprises repetitive elements and 34% of coding DNA. We predicted 41,089 genes, including 91.1% of complete metazoan orthologs. This assembly will facilitate investigations into the ecology of this species and the evolution of deep-sea corals.

High-quality genome assembles from key Hawaiian coral species

Background

Coral reefs house about 25% of marine biodiversity and are critical for the livelihood of many communities by providing food, tourism revenue, and protection from wave surge. These magnificent ecosystems are under existential threat from anthropogenic climate change. Whereas extensive ecological and physiological studies have addressed coral response to environmental stress, high-quality reference genome data are lacking for many of these species. The latter issue hinders efforts to understand the genetic basis of stress resistance and to design informed coral conservation strategies.

Results

We report genome assemblies from 4 key Hawaiian coral species, Montipora capitata, Pocillopora acuta, Pocillopora meandrina, and Porites compressa. These species, or members of these genera, are distributed worldwide and therefore of broad scientific and ecological importance. For M. capitata, an initial assembly was generated from short-read Illumina and long-read PacBio data, which was then scaffolded into 14 putative chromosomes using Omni-C sequencing. For P. acuta, P. meandrina, and P. compressa, high-quality assemblies were generated using short-read Illumina and long-read PacBio data. The P. acuta assembly is from a triploid individual, making it the first reference genome of a nondiploid coral animal.

Conclusions

These assemblies are significant improvements over available data and provide invaluable resources for supporting multiomics studies into coral biology, not just in Hawaiʻi but also in other regions, where related species exist. The P. acuta assembly provides a platform for studying polyploidy in corals and its role in genome evolution and stress adaptation in these organisms.