De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly

Authors: FRAZIER, MONIKA - University Of Hawaii; HELMKAMPF, MARTIN - University Of Hawaii; BELLINGER, RENEE - University Of Hawaii; Geib, Scott; TAKABAYASHI, MISAKI - University Of Hawaii

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/28/2017
Publication Date: 9/11/2017
Citation: Frazier, M., Helmkampf, M., Bellinger, R., Geib, S.M., Takabayashi, M. 2017. De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly Biomed Central (BMC) Genomics. https://doi.org/10.1186/s12864-017-4090-y.

Interpretive Summary: Corals are a vital component of reef ecosystems, and are of significant cultural and economic value worldwide. Recently, there has been a worldwide decline in coral health and growth, due to human and naturally caused stressors. One cause of coral decline is a disease called growth anomaly, which, for example, is found wide-spread throughout coral communities across the Hawaiian Islands. Despite its presence, the cause and the pathology associated with the disease is not clearly understood, including what impacts the disease has on the coral host itself, or on obligate symbionts of the coral, such as algal species. This study used deep sequencing of the genes expressed by healthy and diseased coral to characterize the communities associated with both types of coral and to gain some understanding at the molecular and biochemical level about the impact of growth anomaly on the coral community. This foundational research will hopefully lead to better understanding of this disease and how it can be managed and prevented to maintain healthy coral ecosystems.

Technical Abstract: Background 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 use RNA-seq along with de novo transcriptome assembly and homolog assignment to identify coral genes that are expressed by healthy and GA-affected Montipora capitata colonies. We conducted pairwise comparisons of three distinct tissue types: tissue from healthy corals ("healthy"), GA lesion tissue from diseased corals ("GA-affected") and apparently healthy tissue from diseased corals ("GA-unaffected"). Results The quality-filtered de novo-assembled metatranscriptome contained 76,063 genes, of which 13,643 were identified as putative coral genes. A total of 105 unique coral genes were found differentially expressed among tissue types, and included genes putatively involved in immune system pathways, regulation of apoptosis, bone development and growth, as well as genes associated with disease pathology in other eukaryotes. Pairwise comparisons revealed the greatest number of differentially expressed genes between healthy and GA-affected tissue (93 genes), followed by healthy and GAunaffected tissue (33 genes), and GA-affected and -unaffected tissue (7 genes). This finding suggests that GA has a variety of genetic effects at the colony level. Differentially expressed genes of interest include deleted in malignant brain tumors 1, tumor necrosis factor receptor-associated factors 3, 5 and 6, low-density lipoprotein receptor-related proteins 4, 5 and 6, and bone morphogenetic protein 1. Conclusion The expression pattern of several genes linked to oncogenesis and bone growth in mammalian model organisms indicates that GA may represent a form of neoplasia, in disagreement with some earlier studies. 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 and metatranscriptome assembly developed through this study represent a significant addition to the molecular information available to further our understanding of GA.