Dataset Information

Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing.

ABSTRACT: The rice coral, Montipora capitata, is widely distributed throughout the Indo-Pacific and comprises one of the most important reef-building species in the Hawaiian Islands. Here, we describe a de novo assembly of its genome based on a linked-read sequencing approach developed by 10x Genomics. The final draft assembly consisted of 27,870 scaffolds with a N50 size of 186?kb and contained a fairly complete set (81%) of metazoan benchmarking (BUSCO) genes. Based on haploid assembly size (615?Mb) and read k-mer profiles, we estimated the genome size to fall between 600 and 700?Mb, although the high fraction of repetitive sequence introduced considerable uncertainty. Repeat analysis indicated that 42% of the assembly consisted of interspersed, mostly unclassified repeats, and almost 3% tandem repeats. We also identified 36,691 protein-coding genes with a median coding sequence length of 807?bp, together spanning 7% of the assembly. The high repeat content and heterozygosity of the genome proved a challenging scenario for assembly, requiring additional steps to merge haplotypes and resulting in a higher than expected fragmentation at the scaffold level. Despite these challenges, the assembly turned out to be comparable in most quality measures to that of other available coral genomes while being considerably more cost-effective, especially with respect to long-read sequencing methods. Provided high-molecular-weight DNA is available, linked-read technology may thus serve as a valuable alternative capable of providing quality genome assemblies of nonmodel organisms.

SUBMITTER: Helmkampf M

PROVIDER: S-EPMC6668484 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing.

Helmkampf Martin M Bellinger M Renee MR Geib Scott M SM Sim Sheina B SB Takabayashi Misaki M

Genome biology and evolution 20190701 7

The rice coral, Montipora capitata, is widely distributed throughout the Indo-Pacific and comprises one of the most important reef-building species in the Hawaiian Islands. Here, we describe a de novo assembly of its genome based on a linked-read sequencing approach developed by 10x Genomics. The final draft assembly consisted of 27,870 scaffolds with a N50 size of 186 kb and contained a fairly complete set (81%) of metazoan benchmarking (BUSCO) genes. Based on haploid assembly size (615 Mb) and ...[more]

PMID: 31243452

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Project description:Midway Atoll in the Northwestern Hawaiian Islands is home to ground nesting birds that are threatened by invasive mice. Planned rodent eradication efforts for the island involve aerial application of cereal bait pellets containing the chemical rodenticide brodifacoum. Given the nature of the application method, drift of cereal bait pellets into the coastal waters surrounding Midway Atoll is unavoidable. To understand whether cereal bait pellets impact marine invertebrates, gametes and larvae of the reef-building coral Montipora capitata were exposed to brodifacoum, cereal bait pellets containing brodifacoum, and inert cereal bait pellets without the rodenticide. Fertilization success and larval survival were assessed at nominal brodifacoum concentrations of 1, 10, and 100 ppb. Fertilization success decreased by 15% after exposure to 100 ppb brodifacoum solutions. Larval survival was not reduced by exposure to brodifacoum solutions. Cereal bait pellets containing brodifacoum reduced fertilization success at 10 ppb brodifacoum in 0.4 g per L pellet solutions by 34.84%, and inhibited fertilization at 100 ppb brodifacoum in 4 g of pellet per L solution. Inert cereal bait pellets had similar effects, reducing fertilization success at 0.4 g of pellet per L by 40.50%, and inhibiting fertilization at 4 g per L pellet solutions. Larval survival was reduced by >43% after prolonged exposure to 4 g per L pellet solutions. The highest concentration used in this study was meant to represent an extreme and unlikely condition resulting from an accidental spill. Our findings indicate large amounts of cereal bait pellets entering the coastal environment of Midway Atoll, if occurring during a coral spawning event, would reduce coral reproduction by decreasing fertilization success. It is difficult to know the ecologically relevant concentrations of cereal bait pellets in coastal environments due to unavoidable bait drift after land applications, but results indicate small amounts of pellet drifting into coastal environments would not severely reduce coral reproductive capacity. Best management practices should consider known coral reproductive periods when scheduling applications of pellets on tropical islands to reduce the risk of negative impacts of large-scale accidents on corals.

Project description:Background Corals, which form the foundation of biodiverse reef ecosystems, are under threat from warming oceans. Reefs provide essential ecological services, including food, income from tourism, nutrient cycling, waste removal, and the absorption of wave energy to mitigate erosion. Here, we studied the coral thermal stress response using network methods to analyze transcriptomic and polar metabolomic data generated from the Hawaiian rice coral Montipora capitata. Coral nubbins were exposed to ambient or thermal stress conditions over a 5-week period, coinciding with a mass spawning event of this species. The major goal of our study was to expand the inventory of thermal stress-related genes and metabolites present in M. capitata and to study gene-metabolite interactions. These interactions provide the foundation for functional or genetic analysis of key coral genes as well as provide potentially diagnostic markers of pre-bleaching stress. A secondary goal of our study was to analyze the accumulation of sex hormones prior to and during mass spawning to understand how thermal stress may impact reproductive success in M. capitata. Methods M. capitata was exposed to thermal stress during its spawning cycle over the course of 5 weeks, during which time transcriptomic and polar metabolomic data were collected. We analyzed these data streams individually, and then integrated both data sets using MAGI (Metabolite Annotation and Gene Integration) to investigate molecular transitions and biochemical reactions. Results Our results reveal the complexity of the thermal stress phenome in M. capitata, which includes many genes involved in redox regulation, biomineralization, and reproduction. The size and number of modules in the gene co-expression networks expanded from the initial stress response to the onset of bleaching. The later stages involved the suppression of metabolite transport by the coral host, including a variety of sodium-coupled transporters and a putative ammonium transporter, possibly as a response to reduction in algal productivity. The gene-metabolite integration data suggest that thermal treatment results in the activation of animal redox stress pathways involved in quenching molecular oxygen to prevent an overabundance of reactive oxygen species. Lastly, evidence that thermal stress affects reproductive activity was provided by the downregulation of CYP-like genes and the irregular production of sex hormones during the mass spawning cycle. Overall, redox regulation and metabolite transport are key components of the coral animal thermal stress phenome. Mass spawning was highly attenuated under thermal stress, suggesting that global climate change may negatively impact reproductive behavior in this species.

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Dataset Information

Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing.

Publications

Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing.

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