Dataset Information

Genome analysis of the rice coral Montipora capitata.

ABSTRACT: Corals comprise a biomineralizing cnidarian, dinoflagellate algal symbionts, and associated microbiome of prokaryotes and viruses. Ongoing efforts to conserve coral reefs by identifying the major stress response pathways and thereby laying the foundation to select resistant genotypes rely on a robust genomic foundation. Here we generated and analyzed a high quality long-read based ~886 Mbp nuclear genome assembly and transcriptome data from the dominant rice coral, Montipora capitata from Hawai'i. Our work provides insights into the architecture of coral genomes and shows how they differ in size and gene inventory, putatively due to population size variation. We describe a recent example of foreign gene acquisition via a bacterial gene transfer agent and illustrate the major pathways of stress response that can be used to predict regulatory components of the transcriptional networks in M. capitata. These genomic resources provide insights into the adaptive potential of these sessile, long-lived species in both natural and human influenced environments and facilitate functional and population genomic studies aimed at Hawaiian reef restoration and conservation.

SUBMITTER: Shumaker A

PROVIDER: S-EPMC6385260 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome analysis of the rice coral Montipora capitata.

Shumaker Alexander A Putnam Hollie M HM Qiu Huan H Price Dana C DC Zelzion Ehud E Harel Arye A Wagner Nicole E NE Gates Ruth D RD Yoon Hwan Su HS Bhattacharya Debashish D

Scientific reports 20190222 1

Corals comprise a biomineralizing cnidarian, dinoflagellate algal symbionts, and associated microbiome of prokaryotes and viruses. Ongoing efforts to conserve coral reefs by identifying the major stress response pathways and thereby laying the foundation to select resistant genotypes rely on a robust genomic foundation. Here we generated and analyzed a high quality long-read based ~886 Mbp nuclear genome assembly and transcriptome data from the dominant rice coral, Montipora capitata from Hawai' ...[more]

PMID: 30796282

Similar Datasets

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:Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of coral reefs, understanding coral health is critical to help preserve these ecosystems. Growth anomaly (GA) is a coral disease that has significant negative impacts on coral biology, yet our understanding of its etiology and pathology is lacking. In this study we used RNA-seq along with de novo metatranscriptome assembly and homology assignment to identify coral genes that are expressed in three distinct coral tissue types: tissue from healthy corals ("healthy"), GA lesion tissue from diseased corals ("GA-affected") and apparently healthy tissue from diseased corals ("GA-unaffected"). We conducted pairwise comparisons of gene expression among these three tissue types to identify genes and pathways that help us to unravel the molecular pathology of this coral disease.The quality-filtered de novo-assembled metatranscriptome contained 76,063 genes, of which 13,643 were identified as putative coral genes. Overall gene expression profiles of coral genes revealed high similarity between healthy tissue samples, in contrast to high variance among diseased samples. This indicates GA has a variety of genetic effects at the colony level, including on seemingly healthy (GA-unaffected) tissue. A total of 105 unique coral genes were found differentially expressed among tissue types. Pairwise comparisons revealed the greatest number of differentially expressed genes between healthy and GA-affected tissue (93 genes), followed by healthy and GA-unaffected tissue (33 genes), and GA-affected and -unaffected tissue (7 genes). The putative function of these genes suggests GA is associated with changes in the activity of genes involved in developmental processes and activation of the immune system.This is one of the first transcriptome-level studies to investigate coral GA, and the first metatranscriptome assembly for the M. capitata holobiont. The gene expression data, metatranscriptome assembly and methodology developed through this study represent a significant addition to the molecular information available to further our understanding of this coral disease.

Dataset Information

Genome analysis of the rice coral Montipora capitata.

Publications

Genome analysis of the rice coral Montipora capitata.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets