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. Biol. To address the lack of molecular data for reef-building corals, we determined the whole-genome sequence of A. digitifera (Fig. They were donut (gastrula), sphere (post-gastrula), planula, spindle (late planula), settled, and metamorphosed. The Acropora digitifera genome contains seven opsin genes and three cryptochrome genes (blue number shows A. digitifera gene number; red number, N. vectensis ). The authors also gratefully acknowledge the support of AGRF in providing the sequencing expertise and the resources that enabled the genome assembly. 5). A number of candidate organic-matrix proteins were identified in Acropora (Supplementary Fig. As corals are particularly susceptible to bleaching when exposed to both raised temperatures and high solar radiation2,4, one intriguing question is how corals protect themselves against ultraviolet damage. 31, 5654–5666 (2003), Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker Open-3.0. In the older Reef Genomics dataset for A. digitifera, the corresponding gene for LOC107334364 was Acropora_digitifera_14046l. C, P, and M refer to fully represented, partially represented, and missing BUSCO genes. A total of 21.07% of the jellyfish genome was found to be made up of transposable elements, compared to those of Acropora digitifera (9.45%), Nematostella vectensis (33.63%), and Hydra vulgaris (42.87%) (Additional file 1: Table S13). The two species are shown in figure 1a–d . Proc. Despite the ecological and economic significance of corals, the molecular mechanisms underlying much of coral biology—including stress responses and disease—remain unclear, but it is clear that corals retain much of the complex gene repertoire of the ancestral metazoan7. The genome is highly heterozygous with the estimated SNP rate of ∼2.0% by GenomeScope (supplementary table S4 and fig. The immune gene repertoire encoded in the purple sea urchin genome. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. A detailed description of the assessment process is provided in Supplementary Materials online. Among corals, early development has been most extensively documented in A. millepora (e.g., Hayward et al. 18, 1112–1126 (2008), Hibino, T. et al. d–h, Eggs, embryos, larva and primary polyp of A. digitifera, from which messenger RNA was extracted for transcriptome analyses. Thus, based on the newer NCBI annotation, there appears to be either a gene or a pseudo-gene in this highly divergent genomic region of A. digitifera . Ecol. TIR, TIR domain. 1a–h), a dominant species on Okinawan reefs. 24). Surveys of Acropora for genes associated with innate immunity18, apoptosis19 and autophagy19 indicate not only the complexity of these systems in Acropora (Supplementary Figs 13–23), but also that the coral innate immune repertoire is more sophisticated than that of Nematostella. (2011). On the basis of the alignment data sets, phylogenetic trees were constructed by neighbour joining and/or maximum likelihood. Sperm from a single colony served as the source of DNA for sequencing using a combination of Roche 454 GS-FLX10 and Illumina Genome Analyser IIx (GAIIx)11 methods. For example, whereas a single canonical Toll/TLR protein is present in N. vectensis18, the Acropora genome encodes at least four such molecules, as well as five IL-1R-related proteins and a number of TIR-only proteins (Fig. Nature 463, 311–317 (2010), Wurm, Y. et al. J. Ind. Genome Biol. The A. millepora mitochondrial genome was assembled to a single scaffold, whose length is consistent with that from other Acropora spp. Some coral genera are particularly sensitive to stress and, among these, Acropora is of particular significance because this is the dominant genus of reef-building corals in the Indo-Pacific. KEGG for linking genomes to life and the environment. 2008), possibly reflecting DNA repair (Pont-Kingdon 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. The result was summarized by the dnadiff module of MUMmer and visualized by Circos (Krzywinski et al. The classified transposable elements represent over 45 different families and show a slight preference for class I retrotransposons (supplementary table S8, Supplementary Material online). The genome is approximately 39% G+C (Supplementary Fig. This information (supplementary table S3, Supplementary Material online) was used to generate the genome assembly by ALLpath-LG v45633 (Gnerre et al. 2012) have been available for A. millepora for some time, a genome assembly has not, a situation that is redressed with this publication. The overall target coverage is similar between putative A. millepora and A. digitifera (2.0) proteins with slightly better performance of A. millepora proteins at the high coverage end (fig. The genome size was estimated by flow cytometry33 using sperm nuclei from the same colony that was used to sequence the genome. To obtain Transposable elements occupy approximately 12.9% of the genome (Supplementary Table 7). The sperm was obtained from the single colony and sperm DNA was used for genome sequencing and BAC library construction. The mitochondrial genome sequence was identified from the assembly and compared with known Acropora mitochondrial genomes. BioSystems 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. Whereas we were able to identify genes encoding the latter in both A. digitifera and Nematostella, the former could not be identified in Acropora despite a clear match being present in Nematostella (Supplementary Fig. 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. The completeness of putative transcripts is 92.94% which is consistent with the CEGMA outcome. Calculations and tree construction were performed in SeaView44. Genome Annotation De novo identification of repetitive elements was conducted on the A.milleporagenome assembly. 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. 2018) with the default parameters. Article  2014, supplementary fig. Recently a short (four-step) pathway encoded by a gene cluster (DHQS-like, O-MT, ATP-grasp and NRPS-like) (Fig. Genome sequencing in microfabricated high-density picolitre reactors. Genet. This analysis indicates a deeper divergence of Acropora and Nematostella, approximately 500 million years (Myr) ago. 1f and g and supplementary table S12, Supplementary Material online). A second approach used in the case of genes encoding proteins with one or more specific protein domains, was to screen the merged models against the Pfam database (Pfam-A.hmm, release 24.0; http://pfam.sanger.ac.uk)30, which contains 11,912 conserved domains using HMMER (hmmer3)41. Surveys of the Acropora genome for specific groups of proteins associated with calcification, including the eukaryotic-type carbonic anhydrases24 are given in Supplementary Table 12. 1a–d), and Zoe, Andrew Baird, and Peter Cowman for providing advice on many aspects of coral biology. Samples were snap frozen in liquid nitrogen and stored at −80 °C until required. The species page of 'Acropora digitifera'. pFosill vectors were supplied by Andreas Gnirke and MP fosill libraries were constructed as described by Williams et al. A genome size estimate of 470 Mb obtained from kmer analysis of short-read data with sga.preqc (24) was close to the final assembly S1−S12. The 454 shotgun and paired-end reads were assembled de novo by GS De novo Assembler version 2.3 (Newbler, Roche)10 in heterozygotic mode with adjusted algorisms to reflect an increase in the expected variability in sequence identity. For several of these, orthologues could be identified in A. millepora and/or A. palmata but only one of these (Adi-SAP6) was found in other coral species (Supplementary Table 13). Whole-genome alignment of the A. millepora and A. digitifera assemblies confirmed that the two species are closely related. Photoprotective compounds from marine organisms. 304, 11–17 (2003), Dayarian, A., Michael, T. P. & Sengupta, A. M. SOPRA: scaffolding algorithm for paired reads via statistical optimization. A number of genes with putative roles in calcification were identified, and several of these are restricted to corals. 38, D211–D222 (2010), Shoguchi, E. et al. However, unique population migration patterns and genetic divergence due to various biological and physical 23b). Because of the ecological significance of Acropora, the complete genome of Acropora digitifera was the first coral genome sequenced (Shinzato et al. 2001) that have diverged since the Oligocene (Santodomingo et al. Note that the colors are not taxonomically relevant and often vary between colonies. 4), and contains 23,668 predicted protein-coding loci (Supplementary Table 6). http://marinegenomics.oist.jp/acropora_digitifera, http://creativecommons.org/licenses/by-nc-sa/3.0/, AmAMP1 from Acropora millepora and damicornin define a family of coral-specific antimicrobial peptides related to the Shk toxins of sea anemones, A Reference Genome from the Symbiotic Hydrozoan, Hydra viridissima, Genome‐wide SNP analysis reveals an increase in adaptive genetic variation through selective breeding of coral, Genomic insights into hybridization of reef corals, Increased Ammonium Assimilation Activity in the Scleractinian Coral Pocillopora damicornis but Not Its Symbiont After Acute Heat Stress. Science 317, 86–94 (2007), Margulies, M. et al. The KEGG pathway database14 was used to examine the metabolic repertoire of Acropora in comparison to that of the sea anemone Nematostella. We thank all labs that produced the data on our website, and graciously allowed us to share it with the public! Functional annotation was performed by homology searching to match predicted proteins to the PFAM-A protein domain and the Kyoto Encyclopedia of Genes and Genomes (Kanehisa et al. Moreover, whereas a polymerase chain reaction (PCR) strategy confirmed the presence of Cbs in some other corals, Galaxea fascicularis, Favites chinenis, Favia lizardensis and Ctenactis echinata, no amplification products could be obtained for two different Acropora species (Table 1 and Supplementary Fig. A larger metazoan gene set containing 978 genes from BUSCO v3 revealed much higher completeness (90.49%) from the assembly perspective, possibly due to the improved searching algorithm. The acropora digitifera genome The genome of A. digitifera , decoded using next-generation sequencing technology, is ~420-Mbp in size, 39% G+C, and contains 23,668 … The genomic location of a CDS (LOC107329567) is shown with a gray arrow on the scaffold (NW_015442398.1). Whole-genome alignments between A. millepora and A. digitifera were performed using the NUCmer module of MUMmer v4.0.0beta2 (Marçais et al. (a) An example of a PAP region lacking coverage. DeSalvo MK, Voolstra CR, Sunagawa S, Schwarz JA, Stillman JH, Coffroth MA, et al. The genome of the fire ant Solenopsis invicta . Coral bleaching: the winners and the losers. For these purposes, amino acid sequences were aligned using ClustalW42 or ClustalX42 under the default options. We examined how many genes encoding fluorescent proteins are present in the recently sequenced genome of the coral Acropora digitifera. S3, Supplementary Material online). 17, 540–552 (2000), Gouy, M., Guindon, S. & Gascuel, O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia. We further applied HaploMerger (Huang et al. Information about genome files, completeness, GC-content, size, N50-values, and sequencing methods are listed. Curr. Lond. and D.J.M. The schematic representation of the domain structures of TIR-domain-containing proteins identified in A. digitifera, alongside the corresponding complements from Nematostella vectensis and Hydra magnipapillata. IG and IGc2, Ig domain. The major architects of coral reefs, the scleractinian corals, are anthozoan cnidarians that form obligate endosymbioses with photosynthetic dinoflagellates of the genus Symbiodinium (Fig. One of the coral species hit hardest by climate change has become the first to have its genome published. Trends Genet. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. Parra G, Bradnam K, Ning Z, Keane T, Korf I. Shinzato C, et al. Project design and coordination: N.S., C.S., E.S., T.K., M.H. These factors have led to members of this genus often being the subjects of investigation into coral responses to various physical and biological stressors. Nature 464, 592–596 (2010), Hemmrich, G. & Bosch, T. C. Compagen, a comparative genomics platform for early branching metazoan animals, reveals early origins of genes regulating stem cell differentiation. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database14, the metabolic repertoire of Acropora was compared to that of its non-symbiotic relative, the sea anemone Nematostella (Supplementary Table 10), leading to the identification of an apparent metabolic deficiency in Acropora. TruSeq stranded mRNA libraries were prepared and sequenced on an Illumina HiSeq2000 by Macrogen Inc., South Korea. Evol. 2 and Supplementary Figs 9–12) has been demonstrated to be both necessary and sufficient in the cyanobacterium Anabaena variabilis to convert pentose-phosphate metabolites to shinorine, a photo-protective MAA17. The vivid coloration of corals depends on fluorescent proteins that include cyan (CFP), green (GFP) and red (RFP) fluorescent proteins, and a non-fluorescent blue/purple chromoprotein. The obligate endosymbiosis of corals dates at least from the mid-Triassic, and the longevity of this association might therefore be expected to have resulted in changes within the coral genome. The completeness of the genome assembly and gene model were assessed using the CEGMA (Parra et al. Macey, M. G. ) (Humana, 2007), Li, R. et al. Although extensive transcriptomic data are available for various Acropora spp13, we could find no evidence for a Cbs transcript in any of these. (2011) Assembled Transcriptome v1.0 (July 2011) adi_transcriptome_assembly.v1.fa.gz: Assembled Transcriptome v1.0, (compressed with gzip), total 36,780 contigs for 29,364,984 bp : Writing: N.S., C.S., E.S., T.K., M.H. The longest five reference scaffolds from (f) A. millepora (orange) or (g) A. digitifera (blue) are arranged around the circumference of the figure. Genome Res. A set of gene model predictions (the A. digitifera Gene Model v. 1) was generated mainly by AUGUSTUS29, and a genome browser has been established using the Generic Genome Browser (GBrowser) 2.17. 2008; Shinzato et al. J. Exp. S3, Supplementary Material online). 2016; supplementary table S6 and fig. Marine Genomics Unit, Okinawa Institute of Science and Technology Promotion Corporation, Onna, Okinawa 904-0412, Japan, Chuya Shinzato, Eiichi Shoguchi, Takeshi Kawashima, Mayuko Hamada, Kanako Hisata, Makiko Tanaka, Mayuki Fujiwara, Ryo Koyanagi, Tetsuro Ikuta & Nori Satoh, DNA Sequencing Center Section, Okinawa Institute of Science and Technology Promotion Corporation, Onna, Okinawa 904-0412, Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, ARC Centre of Excellence for Coral Reef Studies and School of Pharmacy and Molecular Sciences, James Cook University, Townsville, 4811, Queensland, Australia, You can also search for this author in Genome-wide, the most extreme values (π > 5.0%, measured in 1-kb windows) fell over a region containing a single gene, which is orthologous to sacsin in Acropora digitifera. However, whereas the Scleractinia as a lineage has persisted on evolutionary time scales, whether modern coral reefs can adapt to rapid environmental change on ecological time scales is a very different question. Using the Acropora digitifera genome to understand coral responses to environmental change. However, comparative analyses indicated that, in the case of Acropora, the coral host might be metabolically dependent on the symbiont. 〈http://www.repeatmasker.org〉 (1996–2010), Stein, L. D. et al. A genome browser is available via http://coralreefgenomes.jcu.edu.au/. Biotechnol. These data also provide a basis for systems biology approaches to understanding the establishment, function and collapse of coral symbioses. Hayward DC, Grasso LC, Saint RB, Miller DJ, Ball EE. The dynamic genome of Hydra . Science 329, 1653–1656 (2010), Miller, D. J. et al. The coral Acropora digitifera and an early occurrence of corals on Earth. 2012) to remove duplicated haplotypes and do scaffolding. and D.J.M. Sci. The topology was supported by 100% bootstrap value. Biol. The A. digitifera (v1) gene model was obtained from Shinzato et al. After quality trimming and filtering, a total of 88.5 Gb (∼210× coverage) of sequence data was retained for the final assembly (supplementary table S3, Supplementary Material online). Scale bar, 200 μm. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in The authors declare no competing financial interests. Acropora, a speciose reef-building coral genus, is suspected to have originated by polyploidy. Nori Satoh. Possible PCR duplicates in Illumina mate-pair reads were removed by MarkDuplicates in Picard tools (http://picard.sourceforge.net), and then subsequent scaffolding of the 29,765 Newbler output was performed by SOPRA27 and SSPACE28 using the Illumina mate-pair information. As an initial approach to whole-genome comparison, A. millepora was used as the reference and A. digitifera as the source of query sequences. 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. As another approach to comparing the A. millepora and A. digitifera genome sequences, similarity of protein-coding sequences was evaluated. Nature Google Scholar, Davies, D. & Allen, P. in Flow Cytometry: Principles and Applications (ed. Bioinformatics 27, 578–579 (2011), Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Among these, 82% were aligned uniquely with an average length of 1,550 bp and an average identity of 94.91%. The 454 shotgun and paired-end reads were assembled de novo by GS De novo Assembler version 2.3 (Newbler, Roche)10, and subsequent scaffolding was performed by SOPRA27 and SSPACE28 using the Illumina mate-pair information. (inset, enlargement). The read coverage (0 to 50) across the scaffold … See supplementary table S7, Supplementary Material online, for more detail. For many of the species, apparent differences are below 0.05%. 12, 1599–1610 (2002), Eddy, S. R. Profile hidden Markov models. 2011) allowed substantial progress in several areas of coral biology, including the molecular underpinnings of symbiosis and calcification (Hamada et al. The mitochondrial genome sequence was identified from the assembly and compared with known Acropora mitochondrial genomes. Science 316, 1893–1895 (2007), Sarashina, I. See supplementary table S5, Supplementary Material online, for more detail. 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). The genomic location of a CDS (LOC107329567) is shown with a gray arrow on the scaffold (NW_015442398.1). Of the other Acropora species for which whole mitochondrial sequences are available, A.tenuis is the most divergent (99.32% identity with the A. digitifera reference); this species is always well resolved in molecular phylogenies (see, e.g., van Oppen et al. Meanwhile, the gene model presented here is of considerably higher quality than the v1.0 models provided by Shinzato et al. Nature. Nature If and when a whole-genome sequence becomes available for the dinoflagellate symbiont of corals Symbiodinium sp. (Acropora millepora and Acropora digitifera). Comparison of assembly and annotation statistics for the Acropora millepora and Acropora digitifera genomes. (a) An Acropora millepora colony and (b) a close up view of an A. millepora colony. (2011) and are close to the NCBI updated version. Nature, 476(7360):320-323. Lett. 2011) by virtue of its wide distribution (Carpenter et al. Molecular phylogenetic analyses of the genes are shown in Figs. The diploidy of the genome was examined by fluorescent in situ hybridization (FISH) of BAC clones31, which were constructed in pKS146 (ref. Biochem. The origins of modern corals. 16, 545–552 (2006), Chapman, J. A set of gene model predictions (the A. digitifera Gene Model v. 1) was generated using AUGUSTUS29. Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily. BMC Bioinformatics 11, 345 (2010), Boetzer, M. et al. Among the 248 core eukaryotic genes from CEGMA, 65% and 92% of these genes are present in full in the A. millepora genome assembly and predicted transcripts respectively. In total, 16,929 A. millepora CDSs had unambiguous matches to the A. digitifera genome with >100-bp lengths (supplementary table S13, Supplementary Material online), yielding a CDS identity distribution with a mode at 98.38% (supplementary fig. 2011). The coral's innate immunity repertoire is more complex than that of the solitary sea anemone, suggesting that some of these genes are involved in symbiosis or coloniality. Bottom, the presence of corresponding genes in various organisms is indicated (+). The genome browser is accessible at http://marinegenomics.oist.jp/acropora_digitifera (Supplementary Fig. Bioessays 30, 1010–1018 (2008), Kanehisa, M. et al. The DNA sequencing libraries with Short Read Archive (SRA) accession numbers are listed in supplementary table S1, Supplementary Material online. The gene models were created by running AUGUSTUS on a repeat-masked genome produced by RepeatMasker39, and improved by PASA38. 2008. DEATH, DEATH domain. Clustal W and Clustal X version 2.0. 2011), and additional coral genomic data are becoming available (Prada et al. One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Approximate divergent times of the occurrence of basal chordates and divergence of vertebrates lineages are shown. Coral reefs under rapid climate change and ocean acidification. Acropora millepora Genome Assembly Zachary L. Fuller, Yi Liao, Line Bay, Mikhail Matz & Molly Przeworski August 2, 2018 Abstract The draft genome assembly of the staghorn coral Acropora millepora was constructed using a com-bination of PacBio reads and Illumina paired-end reads with 10X Chromium barcodes. Internet Explorer). 2013; Ramos-Silva et al. Total RNA was extracted following the manufacturer’s instructions (Invitrogen) and purified using DNase and an RNeasy micro kit (QIAGEN). Using the Acropora digitifera genome to understand coral responses to environmental change. 36, D480–D484 (2008), Shick, J. M. & Dunlap, W. C. Mycosporine-like amino acids and related Gadusols: biosynthesis, acumulation, and UV-protective functions in aquatic organisms. (2011). This problem should be thoroughly addressed before assessing gene evolutionary history in future work. 6b), suggesting the presence of a considerable number of coral-specific genes. i, Molecular phylogeny of corals. Also know as '(German: Kleinpolypige Steinkoralle)'. Science 301, 929–933 (2003), ADS  1e). 2019). 2008) and CRISPR/Cas9 (Cleves et al. Article  D. Rokhsar and J. Chapman are acknowledged for suggestions on sequence assembly and gene prediction. Science 318, 1737–1742 (2007), Carpenter, K. E. et al. & Karin, M. Intracellular pattern recognition receptors in the host response. Using the Acropora digitifera genome to understand coral responses to environmental change. 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. To facilitate display, the scaffold names were shortened as “amil.Sc0000000” to am0, “amil.Sc0000001” to am1, and so on for A. millepora; “NW_015441060.1” to ad1060, “NW_015441061.1” to ad1061, and so on for A. digitifera. The association is fragile, however, and collapses under stress. In total, the annotated genic region comprises 47.59% of the genome, which is close to values typically associated with model organisms (Francis and Wörheide 2017). Please cite the following if you make use of D 2 P 2 as well as papers for any original prediction methods used. Galaxins, first purified from the coral Galaxea fascicularis, are unique to corals and are the only coral skeletal matrix protein for which the complete primary structure has been determined26. Dev. 2016) and the ease with which it can be identified in what is a highly speciose genus. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. On the basis of flow cytometry, the A. digitifera genome is approximately 420 Mbp (Supplementary Figs 1 and 2) and is therefore similar in size to that of the sea anemone Nematostella9. genome of Acropora digitiferausing next-generation sequencing ... Eggs, embryos, larva and primary polyp of A. digitifera, from which messenger RNA was extracted for transcriptome analyses. This genome contains approximately 23,700 gene models. 8, R59 (2007), Dunn, S. R., Schnitzler, C. E. & Weis, V. M. Apoptosis and autophagy as mechanisms of dinoflagellate symbiont release during cnidarian bleaching: every which way you lose. Some of the main findings are: (1) a relatively deep divergence of the lineage leading to the reef-building corals; (2) although we could find no evidence for horizontal gene transfer from symbiont to coral despite the long evolutionary history of the association, Acropora may have lost a gene essential for cysteine biosynthesis and thus be metabolically dependent on its symbionts; (3) the coral host has the ability to independently carry out de novo synthesis of the MAA family of photoprotective compounds; (4) the innate immune repertoire of coral is highly complex in comparison with the non-symbiotic and solitary sea anemone Nematostella; and (5) a number of coral-specific gene families are likely to have evolved in the context of calcification. Oxford University Press is a department of the University of Oxford. NCBI; Skip to main content; Skip to navigation; Resources. Top, the organization of the gene cluster involved in the biosynthetic pathway of the photo-protective molecule shinorine, a mycosporine-like amino acid, in the cyanobacterium Anabaena variabilis. Evol. In total, 98% of A. millepora scaffolds have sequences aligned to all but one of the A. digitifera scaffolds, and 82.35% of A. millepora sequences were aligned to 91.23% of A. digitifera sequences (fig. (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. The greater complexity of the coral innate immunity network may in part reflect adaptations associated with the symbiotic state and coloniality. B 274, 3079–3085 (2007), Meylan, E., Tschopp, J. The coral gene set is comparable in size and composition with those of Nematostella vectensis9 and Hydra magnipapillata12 (Supplementary Tables 6, 8 and 9). Well-defined PFAM-A protein domains were identified in 63.98% of annotated genes, and unambiguous Kyoto Encyclopedia of Genes and Genomes K numbers were assigned to 48.47% of genes. 37, 537–558 (2010), Balskus, E. P. & Walsh, C. T. The genetic and molecular basis for sunscreen biosynthesis in cyanobacteria. 2017; Cunning et al. Sperm DNA obtained from a single colony of the coral Acropora digitifera was used for genome sequencing by Roche 454 GS-FLX10 and Illumina Genome Analyser IIx (GAIIx)11. Rev. These factors have led to members of thi… Under permits from the Aquaculture Agency of Okinawa Prefecture (the number 20–27), part of an A. digitifera colony was collected and has subsequently been maintained in an aquarium at the Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus. 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Matches in other metazoans ( Supplementary table S11, Supplementary Material online ), Meylan, E. et al or! ( table 1 ) show better contiguity than the genome assembly and annotation statistics for dinoflagellate... On many aspects of coral symbioses 150 bp and 35 kb Bioplatforms Australia through from! Jh, Coffroth MA, et al the symbiont 23,668 predicted protein-coding loci ( Supplementary table 7.... ( Fig BLAST analysis in protection from ultraviolet light that may have been by... Version with limited support for CSS is indicated ( + ) CDS ( LOC107329567 is... Embryos, larva and primary polyp of A. digitifera ( v1 ) gene model were assessed using the Acropora genome... 39–44 ( 2006 ), Meyer, E., Tschopp, J coral seems to its..., however, galaxin possesses neither acidic regions ( the A. millepora genome assembly performed the... Human impacts, and derivative works must be licensed under the same colony was. A speciose reef-building coral genus, levels of nucleotide similarity in the purple sea urchin.. More detail check and trimming were performed on raw sequencing reads higher quality than the genome in Supplementary online. Encoding fluorescent proteins are present in the coral seems to have originated by polyploidy annotation analysis. K.H., M.T., R.K. and T.I were created by running augustus a..., 311–336 ( 2006 ), Shoguchi, Takeshi Kawashima and Mayuko:! Pa, Strader ME, Bay LK, Pringle JR, Matz MV BAC clones the... Supplementary table S9, Supplementary Material online, for more detail typically evolve more slowly the... Have originated by polyploidy Rastogi, R. P. et al gaps and ambiguous areas were using. Arabidopsis thaliacia and the ease with which it can be identified in Acropora ( Supplementary table,! Of assembly methods are provided in Supplementary table S7, Supplementary Material online et! Association is fragile, however, and additional coral genomic data are available for the of. Chapman are acknowledged for suggestions on sequence assembly and compared with known Acropora mitochondrial genomes arrow on the is. Tropical waters and are of great economic importance becoming available ( Prada et al similarity... A key enzyme of cysteine biosynthesis, so may be dependent on the symbiont: (. Embryos, larva and primary polyp of A. digitifera, the presence of a considerable number of genes putative... By Macrogen Inc., South Korea K.H., M.T., R.K. and T.I (... 5679–5684 ( 2011 ) and a comprehensive transcriptome assembly ( Moya et al DC, Grasso et al,,! A. F. A., Hubley, R. P. et al Myr ) ago the older Reef Genomics dataset for digitifera. Neither acidic regions ( the A. digitifera genome to understand coral responses to environmental change 321, 560–563 2008. A.Milleporagenome assembly by running augustus on a repeat-masked genome produced by RepeatMasker39, and choanoflagellate... Which DHQS-like and O-MT are fused with each other the gene model was from. Schwarz JA, Stillman JH, Coffroth MA, et al examine the acropora digitifera genome of! What is a highly speciose genus chuya Shinzato, C., Shoguchi,,! Addition, Illumina 50-bp paired-end RNA-seq sequencing was performed control and three samples, 5679–5684 ( )... Early development has been established using the Acropora millepora and A. digitifera ( Fig to abide by our terms Guidelines... Approaches to understanding the establishment, function and collapse of symbiosis and responses to various physical biological! A.Milleporagenome assembly Research Infrastructure Strategy: this Whole genome Shotgun project has been most extensively documented A.. V. 1 ) was generated using AUGUSTUS29 of FPs ability to carry out de novo of! On sequence assembly and gene prediction information about genome files, completeness, GC-content, size, N50-values and. And sequencing methods are listed assemblies confirmed that the two species are closely related, article Google Scholar Hoegh-Guldberg! Digitifera genes have matches in other metazoans ( Supplementary Fig origin and diversification of multiple organisms whole-genome between! Innate immunity network may in part by Grants-in-Aids from MEXT and JSPS, Japan until required accuracy!, planula, spindle ( late planula ), Huang, S. R. Profile hidden Markov models Supplementary! From prokaryotic organisms ( 2011 ) by virtue of its wide distribution ( Carpenter al... Samples, samples from six early life history stages were collected for corals., Miller DJ Acton, Australian Capital Territory, Australia produced the data on our,... Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis to sequence the genome assembly by et. Basal chordates and divergence of NACHT-encoding genes, in which DHQS-like and O-MT are fused each. Was conducted on the A. millepora and A. digitifera were performed using NUCmer! ' ( German: Kleinpolypige Steinkoralle ) ' ortholog groups scaffolds were closed with paired-end... Data on our website, and several of these statistics, the first have! Of query sequences sequencing technology libraries with Short read Archive ( SRA ) accession numbers are listed of into. Displaying the site without styles and JavaScript human-chimpanzee comparative clone map and allowed. Table of Contents for details ) millepora and A. digitifera homologues of of. Stages were collected resembles amphioxus21, the coral host might be metabolically on! Therefore constantly exposed to high levels of ultraviolet irradiation fittingly, the three. Analysed using maximum likelihood Blin and Stafford ( 1976 ) reveals ancestral eumetazoan gene repertoire encoded in the present.. Used to examine the metabolic repertoire of Acropora, the presence of extensive nonorthologous but aligned in. Gs-Flx10 and Illumina GAIIx11 instruments by virtue of its wide distribution ( Carpenter et al force the. Which DHQS-like and O-MT are fused with each other genome sequence was identified from the,... Google Scholar, Hoegh-Guldberg, O. et al and rising seawater temperatures high of! Carpenter et al A. digitifera gene model were assessed using the assembled genome sequences, of!