Using the Acropora digitifera genome to understand coral responses to environmental change

By Chuya Shinzato, E. Shoguchi, T. Kawashima, M. Hamada, K. Hisata, Makiko Tanaka, Manabu Fujie, M. Fujiwara, R. Koyanagi, T. Ikuta and 3 more. Nature, 2011

838 citations recorded by the source corpus.

Despite the enormous ecological and economic importance of coral reefs, the keystone organisms in their establishment, the scleractinian corals, increasingly face a range of anthropogenic challenges including ocean acidification and seawater temperature rise. To understand better the molecular mechanisms underlying coral biology, here we decoded the approximately 420-megabase genome of Acropora digitifera using next-generation sequencing technology. This genome contains approximately 23,700 gene models. Molecular phylogenetics indicate that the coral and the sea anemone Nematostella vectensis diverged approximately 500 million years ago, considerably earlier than the time over which modern corals are represented in the fossil record (∼240 million years ago). Despite the long evolutionary history of the endosymbiosis, no evidence was found for horizontal transfer of genes from symbiont to host. However, unlike several other corals, Acropora seems to lack an enzyme essential for cysteine biosynthesis, implying dependency of this coral on its symbionts for this amino acid. Corals inhabit environments where they are frequently exposed to high levels of solar radiation, and analysis of the Acropora genome data indicates that the coral host can independently carry out de novo synthesis of mycosporine-like amino acids, which are potent ultraviolet-protective compounds. In addition, the coral innate immunity repertoire is notably more complex than that of the sea anemone, indicating that some of these genes may have roles in symbiosis or coloniality. A number of genes with putative roles in calcification were identified, and several of these are restricted to corals. The coral genome provides a platform for understanding the molecular basis of symbiosis and responses to environmental changes.

Subfields: Biotechnology, Ecology, Paleontology

View Paper: https://www.semanticscholar.org/paper/495001d1ec5e790bb0010441bb7d04eb90180001

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Biotechnology

In Ecology

In Paleontology

Citations in the corpus

Animal Phylogeny and Its Evolutionary Implications (2014, background): “The sampling of cnidarian genomes is only slightly better (Chapman et al. 2010, Putnam et al. 2007, Shinzato et al. 2011).”
The new systematics of scleractinia: Integrating molecular and morphological evidence (2016, background): “The assembly of the complete Acropora digitifera genome (Shinzato et al. 2011) has provided a much-needed reference to identify and utilise orthologous regions for phylogenetic analyses.”
Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean (2017, background): “…of the coral microbiome, including integrated databases (Franklin et al., 2012; Madin et al., 2016), a growing number of host and microbial genomes (Shinzato et al., 2011; Bayer et al., 2012; Neave et al., 2017), and laboratory amendable “model” systems (Weis et al., 2008; Baumgarten et al., 2015).”
Cell Biology of Cnidarian-Dinoflagellate Symbiosis (2012, background): “Ultimately, metabolomic data can be integrated with transcriptomic and genomic data (328) to provide a comprehensive account of an organism’s metabolic pathways.”
FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads (2012, methodology): “These duplicates might have a serious impact on research applications, such as scaffolding in whole-genome sequencing [2] and discovering large-scale genome variations [8], and are usually removed.”
Thermal and pCO2 Stress Elicit Divergent Transcriptomic Responses in a Resilient Coral (2016, methodology): “…and genomes were obtained from public databases and assembled into four distinct databases (Table 3; Putnam et al., 2007; Zhang et al., 2007; Shinzato et al., 2011; Bayer et al., 2012; Ladner and Palumbi, 2012; Lehnert et al., 2012; Moya et al., 2012; Barshis et al., 2013; Kenkel et al.,…”