title: RNA-Seq of the Caribbean reef-building coral Orbicella faveolata (Scleractinia-Merulinidae) under bleaching and disease stress expands models of coral innate immunity.
abstract: Climate change-driven coral disease outbreaks have led to widespread declines in coral populations. Early work on coral genomics established that corals have a complex innate immune system, and whole-transcriptome gene expression studies have revealed mechanisms by which the coral immune system responds to stress and disease. The present investigation expands bioinformatic data available to study coral molecular physiology through the assembly and annotation of a reference transcriptome of the Caribbean reef-building coral, Orbicella faveolata. Samples were collected during a warm water thermal anomaly, coral bleaching event and Caribbean yellow band disease outbreak in 2010 in Puerto Rico. Multiplex sequencing of RNA on the Illumina GAIIx platform and de novo transcriptome assembly by Trinity produced 70,745,177 raw short-sequence reads and 32,463 O. faveolata transcripts, respectively. The reference transcriptome was annotated with gene ontologies, mapped to KEGG pathways, and a predicted proteome of 20,488 sequences was generated. Protein families and signaling pathways that are essential in the regulation of innate immunity across Phyla were investigated in-depth. Results were used to develop models of evolutionarily conserved Wnt, Notch, Rig-like receptor, Nod-like receptor, and Dicer signaling. O. faveolata is a coral species that has been studied widely under climate-driven stress and disease, and the present investigation provides new data on the genes that putatively regulate its immune system.
authors.affiliation: Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Marine Sciences, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico, United States of America.
authors.forename: David A
authors.identifier: 0000-0001-9286-5789
authors.initials: DA
authors.lastname: Anderson
authors.affiliation: Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin , United States of America.
authors.forename: Marcus E
authors.initials: ME
authors.lastname: Walz
authors.affiliation: Department of Marine Sciences, University of Puerto Rico at Mayagüez , Mayagüez, Puerto Rico , United States of America.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Weil
authors.affiliation: Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America; Department of Biomedical Informatics, Harvard Medical School, Harvard University, Boston, Massachusetts, United States of America.
authors.forename: Peter
authors.identifier: 0000-0003-0658-1734
authors.initials: P
authors.lastname: Tonellato
authors.affiliation: School of Freshwater Sciences, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin , United States of America.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Smith
keywords: Cnidaria; Coral; Disease; Innate immunity; RNA-seq