Nature 463, 311–317 (2010), Wurm, Y. et al. A set of gene model predictions (the A. digitifera Gene Model v. 1) was generated using AUGUSTUS29. Biol. The genomic location of a CDS (LOC107329567) is shown with a gray arrow on the scaffold (NW_015442398.1). 2012; Denton et al. Proc. Nucleic Acids Res. 2011) by virtue of its wide distribution (Carpenter et al. (2011). During the writing of this article, we became aware of the online availability of an unpublished A millepora draft genome assembly at https://przeworskilab.com/data/, last accessed April 1, 2019. The genomic DNA was fragmented, libraries prepared and sequencing conducted according to the manufacturer’s protocols. 6b), suggesting the presence of a considerable number of coral-specific genes. Transposable elements occupy approximately 12.9% of the genome (Supplementary Table 7). 2002, 2004, 2015) and molecular technologies, including in situ hybridization (e.g., Grasso et al. Shinzato, C., Shoguchi, E., Kawashima, T. et al. Although the analyses presented here do not rigorously exclude the presence of Cbs activity in Acropora, they raise the intriguing possibility of a metabolic basis for the obligate nature of symbiosis in Acropora; differences in dependency could potentially explain not only the phenomenon of symbiont selectivity, but also the high sensitivity of Acropora to environmental challenges. The coral repertoire of genes with predicted roles in skeleton deposition is of particular interest given the likely impact of ocean acidification resulting from rising atmospheric CO2 on coral calcification. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Using the Acropora digitifera genome to understand coral responses to environmental change. Prior to genome assembly, quality check and trimming were performed on raw sequencing reads. A number of candidate organic-matrix proteins were identified in Acropora (Supplementary Fig. Reef-building corals are iconic animals that are in global decline as a consequence of increasing anthropogenic pressure, but the development of strategies to ensure their conservation is constrained by our limited understanding of the molecular bases of many aspects of coral biology. In the meantime, to ensure continued support, we are displaying the site without styles B 274, 3079–3085 (2007), Meylan, E., Tschopp, J. You are using a browser version with limited support for CSS. We thank Zoe Richards for the use of the coral photos (fig. The genome is highly heterozygous with the estimated SNP rate of ∼2.0% by GenomeScope (supplementary table S4 and fig. Mol. BMC Bioinformatics 11, 345 (2010), Boetzer, M. et al. 304, 11–17 (2003), Dayarian, A., Michael, T. P. & Sengupta, A. M. SOPRA: scaffolding algorithm for paired reads via statistical optimization. 12, 1599–1610 (2002), Eddy, S. R. Profile hidden Markov models. 2001) that have diverged since the Oligocene (Santodomingo et al. On average, there are seven exons per gene, and the mean transcript length is 1,818 bp. The biosynthesis of cysteine from homocysteine and/or serine requires the activities of two enzymes, cystathionine β-synthase (Cbs) and cystathionase (cystathionine γ-lyase; Cth) (Table 1). The genome browser is accessible at http://marinegenomics.oist.jp/acropora_digitifera (Supplementary Fig. 2), indicating that both the coral and the sea anemone have the ability to carry out de novo synthesis of ultraviolet-protective compounds. We thank all labs that produced the data on our website, and graciously allowed us to share it with the public! To overcome potential assembly errors arising from tandem repeats, sequences that were aligned to another sequence over 50% of the length by BLASTN (1 × 10−50) were removed from the assembly35. Nature The genome of A. digitifera, decoded using next-generation sequencing technology, is ~420-Mbp in size, 39% G+C, and contains 23,668 predicted protein-coding loci (Shinzato et al., 2011).The coral gene set is comparable in size and composition to those of Nematostella vectensis (Putnam et al., 2007) and Hydra magnipapillata (Chapman et al., 2010). 4, 122–131 (2001), Article Bioinformatics 23, 2947–2948 (2007), Castresana, J. Genome Res. Across the genus, levels of nucleotide similarity in the mitochondrial genomes were remarkably high. The sperm was obtained from the single colony and sperm DNA was used for genome sequencing and BAC library construction. (c) An Acropora digitifera colony and (d) a corresponding close up. In terms of these statistics, the A. millepora genome data therefore outperform the updated (v2.0) NCBI A. digitifera genome release. Sperm were collected from a single A. millepora colony at Magnetic Island, Queensland (19°08′S, 146°50′E), snap frozen in liquid nitrogen and stored at −80 °C until needed. This work was supported by the Australian Research Council through the Centre of Excellence for Coral Reef Studies, the Centre for Molecular Genetics of Development and Discovery Grants DP0209460, DP0344483, and DP1095343. 1a–h), a dominant species on Okinawan reefs. 24). 2018) with the default parameters. The major architects of coral reefs, the scleractinian corals, are anthozoan cnidarians that form obligate endosymbioses with photosynthetic dinoflagellates of the genus Symbiodinium (Fig. See supplementary table S5, Supplementary Material online, for more detail. Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis . R. Soc. However, the protein alignment on these orthologs based on gene model predictions from each genome suggested much lower levels of similarity that those based on coding sequence and whole-genome alignment. The coral Acropora digitifera and an early occurrence of corals on Earth. AUGUSTUS 2.0.4 was trained on the 877 EST assemblies recommended by PASA38 for this purpose. The Acropora digitifera genome contains seven opsin genes and three cryptochrome genes (blue number shows A. digitifera gene number; red number, N. vectensis ). Science 291, 1913–1914 (2001), Wilkinson, C. Status of Coral Reefs of the World (Australian Institute of Marine Studies, 2004), Miller, D. J., Ball, E. E. & Technau, U. Cnidarians and ancestral genetic complexity in the animal kingdom. Gaps and ambiguous areas were excluded using Gblocks 0.91b43 with the default parameters and then checked manually. RNA was isolated from eggs, gastrulae, planulae, polyps and adults. 1b). Internet Explorer). The immune gene repertoire encoded in the purple sea urchin genome. BioSystems Google Scholar, Hoegh-Guldberg, O. et al. Despite being classified on the basis of skeletal characteristics into different species groups sensu Wallace and Wolstenholme (1998), molecular data indicate that A. millepora and A. digitifera are close relatives (e.g., van Oppen et al. D. Rokhsar and J. Chapman are acknowledged for suggestions on sequence assembly and gene prediction. 2011), and additional coral genomic data are becoming available (Prada et al. (2020), Frontiers in Marine Science Not only are Acropora species the dominant reef-building corals of the Indo-Pacific, but they are also among the most sensitive of corals to increased seawater temperatures8. Acropora species is the dominant reef‐building coral of the Indo‐Pacific 7, and Acropora digitifera (Staghorn coral) is the dominant coral on Okinawan reefs. Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity. 2012). (a) An example of a PAP region lacking coverage. The genome assembly statistics (table 1) show better contiguity than the genome assembly by Shinzato et al. A number of genes with putative roles in calcification were identified, and several of these are restricted to corals. Samples were snap frozen in liquid nitrogen and stored at −80 °C until required. Science 316, 1893–1895 (2007), Sarashina, I. (zooxanthellae), these resources will together provide additional perspectives on the symbiosis and a powerful resource for understanding the response of the holobiont to environmental stresses such as raised seawater temperatures or ocean acidification. Genome sequence data were obtained using single read, paired-end and mate-pair protocols on the Roche 454 GS-FLX10 and Illumina GAIIx11 instruments. The authors also gratefully acknowledge the support of AGRF in providing the sequencing expertise and the resources that enabled the genome assembly. 2012) to remove duplicated haplotypes and do scaffolding. The mitochondrial genome sequence was identified from the assembly and compared with known Acropora mitochondrial genomes. Here we report the whole-genome sequence of a second Acropora species, A. millepora, which has been the most extensively studied Acropora species at the molecular level (reviewed in Miller et al. Genome and EST sequencing and assembly: C.S., T.K., E.S., K.H., M. Fujie, M. Fujiwara, M.T., M.H., A.F. This colony is maintained in aquarium culture at the Sesoko Station, University of the Ryukyus, and is thus available for further investigation of the genome. Genome Res. It contains several genes with roles in protection from ultraviolet light that may have been acquired by horizontal transfer from prokaryotic organisms. 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)5. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. (2020). The estimated genome size was between 371 and 454 Mb from k-mer analysis (supplementary table S4, Supplementary Material online), which is in line with the 420-Mb genome size estimate for A. digitifera based on flow cytometry (Shinzato et al. We further applied HaploMerger (Huang et al. This work was supported in part by Grants-in-Aids from MEXT and JSPS, Japan. Although extensive transcriptomic data are available for various Acropora spp13, we could find no evidence for a Cbs transcript in any of these. This genome contains approximately 23,700 gene models. The sequence and de novo assembly of the giant panda genome. These statistics are in line with the A. digitifera gene models annotated using the sophisticated NCBI Eukaryotic Genome Annotation pipeline (supplementary table S10, Supplementary Material online). Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. Parra G, Bradnam K, Ning Z, Keane T, Korf I. Shinzato C, et al. 2016; supplementary table S6 and fig. Genome Biol. 32). Google Scholar, Putnam, N. H. et al. Whole-genome alignments between A. millepora and A. digitifera were performed using the NUCmer module of MUMmer v4.0.0beta2 (Marçais et al. A primary approach to the identification of putative orthologues of A. digitifera genes was reciprocal BLAST analysis. Here we decoded the 420-Mbp genome of the reef-building coral Acropora digitifera, with the aim of providing a platform for understanding the molecular basis of symbiosis and responses to environmental change. The scale bar represents 0.1 expected substitutions per site in the aligned regions. The same genic region also has a highly elevated value of the h 12 statistic ( 47 ), which measures the frequencies of the two most common haplotypes ( Fig. On the basis of the alignment data sets, phylogenetic trees were constructed by neighbour joining and/or maximum likelihood. The repertoire of Toll/TLR, IL-1R-like and TIR-only proteins is significantly more complex in the case of A. digitifera than in N. vectensis or H. magnipapillata. Scale bar, 200 μm. These factors have led to members of thi… Reef-building Scleractinia first appeared in the fossil record in the mid-Triassic (approximately 240 million years ago)5, but were already highly diversified, suggesting much earlier origins. The genome of the fire ant Solenopsis invicta . Bioinformatics 14, 755–763 (1998), Larkin, M. A. et al. & Karin, M. Intracellular pattern recognition receptors in the host response. and D.J.M. A preliminary assembly was first conducted using Velvet (Zerbino and Birney 2008). A genome browser has been established using the assembled genome sequences using the Generic Genome Browser (GBrowser) 2.17 (ref. Nucleic Acids Res. 2008. 38, D211–D222 (2010), Shoguchi, E. et al. Coral reefs are among the most biologically diverse ecosystems on the planet and are of great economic importance. Anthozoan mitochondrial genomes typically evolve more slowly than the corresponding nuclear genomes (Huang et al. Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata Natl Acad. In the older Reef Genomics dataset for A. digitifera, the corresponding gene for LOC107334364 was Acropora_digitifera_14046l. Supplementary data are available at Genome Biology and Evolution online. In terms of completeness, the genome assembly and associated gene predictions are of similar quality to the recent NCBI-generated version (2.0) of the A. digitifera genome. Hua Ying, David C Hayward, Ira Cooke, Weiwen Wang, Aurelie Moya, Kirby R Siemering, Susanne Sprungala, Eldon E Ball, Sylvain Forêt, David J Miller, The Whole-Genome Sequence of the Coral Acropora millepora, Genome Biology and Evolution, Volume 11, Issue 5, May 2019, Pages 1374–1379, https://doi.org/10.1093/gbe/evz077. The availability of fully sequenced genomes for three cnidarians—Acropora (the present study), Nematostella9 and Hydra12— allowed the estimation of the depth of the divergence between corals and other metazoans. 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. The failure to identify A. digitifera matches for the remaining 17.65% of A. millepora sequences is most likely due to the presence of unclosed gaps (Ns) in both genomes. The genome was sequenced to approximately 151-fold coverage (Supplementary Table 1), enabling the generation of an assembly comprising a total of 419 Mbp (Supplementary Tables 2–5; contig N50 = 10.7 kbp and scaffold N50 = 191.5 kbp; Supplementary Fig. 1-25 with legends ( see table of Contents for details ) underlying coral biology here. Access, we have provided a genome browser is accessible at http: //marinegenomics.oist.jp/acropora_digitifera ( Supplementary table )... ≥15 ) were identified as putative noncoding transcripts by using CPC software ( Kong et al to. Online, for more detail millepora and Acropora digitifera colony and sperm DNA was fragmented, libraries prepared sequencing. Sequencing methods are pro- vided in Supplementary Materials online the reference and A. were! 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