Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages

Ying, Hua, Cooke, Ira, Sprungala, Susanne, Wang, Weiwen, Hayward, David C., Tang, Yurong, Huttley, Gavin, Ball, Eldon E., Forêt, Sylvain, and Miller, David J. (2018) Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages. Genome Biology, 19. 175.

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Background Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there are two major clades, Complexa and Robusta, but the genomic bases of significant differences between them remain unclear.

Results Draft genome assemblies and annotations were generated for three coral species: Galaxea fascicularis (Complexa), Fungia sp., and Goniastrea aspera (Robusta). Whilst phylogenetic analyses strongly support a deep split between Complexa and Robusta, synteny analyses reveal a high level of gene order conservation between all corals, but not between corals and sea anemones or between sea anemones. HOX-related gene clusters are, however, well preserved across all of these combinations. Differences between species are apparent in the distribution and numbers of protein domains and an apparent correlation between number of HSP20 proteins and stress tolerance. Uniquely amongst animals, a complete histidine biosynthesis pathway is present in robust corals but not in complex corals or sea anemones. This pathway appears to be ancestral, and its retention in the robust coral lineage has important implications for coral nutrition and symbiosis.

Conclusions The availability of three new coral genomes enabled recognition of a de novo histidine biosynthesis pathway in robust corals which is only the second identified biosynthetic difference between corals. These datasets provide a platform for understanding many aspects of coral biology, particularly the interactions of corals with their endosymbionts.

Item ID: 57285
Item Type: Article (Research - C1)
ISSN: 1474-760X
Keywords: Scleractinia; complex coral; robust coral; nucleotide substitution model; HOX cluster; ParaHox; gene family expansion; histidine biosynthesis
Copyright Information: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
Funders: Australian Government National Collaborative Research Infrastructure Strategy (NCRIS), Rio Tinto, Great Barrier Reef Foundation (GBRF), Australian Research Council (ARC), ARC Centre of Excellence for Coral Reef Studies, James Cook University (JCU)
Projects and Grants: ARC Grant CE140100020
Date Deposited: 04 Mar 2019 04:51
FoR Codes: 31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310410 Phylogeny and comparative analysis @ 50%
31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310204 Genomics and transcriptomics @ 50%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 100%
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