However, comparative analyses indicated that, in the case of Acropora, the coral host might be metabolically dependent on the symbiont. R. Soc. 2013; Ramos-Silva et al. 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. Science 316, 1893–1895 (2007), Sarashina, I. 2009) and BUSCO (Waterhouse et al. D. Rokhsar and J. Chapman are acknowledged for suggestions on sequence assembly and gene prediction. The association is fragile, however, and collapses under stress. Rev. 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. Science 301, 929–933 (2003), ADS  We examined how many genes encoding fluorescent proteins are present in the recently sequenced genome of the coral Acropora digitifera. The genome browser is accessible at http://marinegenomics.oist.jp/acropora_digitifera (Supplementary Fig. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. Parra G, Bradnam K, Ning Z, Keane T, Korf I. Shinzato C, et al. 8:311. van Oppen MJ, McDonald BJ, Willis B, Miller DJ. S3, Supplementary Material online). Genome sequencing in microfabricated high-density picolitre reactors. From the latter, 91% (5,187) were identified as putative noncoding transcripts by using CPC software (Kong et al. Dev. BioSystems Physiol. 1b). Nature 442, 39–44 (2006), Huang, S. et al. Four genes encoding galaxin-related proteins were identified in the A. digitifera genome (Supplementary Fig. 1995). PAP in the Acropora digitifera genome. S3, Supplementary Material online). Correspondence to The result was summarized by the dnadiff module of MUMmer and visualized by Circos (Krzywinski 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. 2018; Ying et al. Scale bar, 200 μm. The genome is approximately 39% G+C (Supplementary Fig. 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. Article  For many of the species, apparent differences are below 0.05%. 2008. 2012) have been available for A. millepora for some time, a genome assembly has not, a situation that is redressed with this publication. Photo-protective compounds, such as the mycosporine amino acids (MAAs), have been isolated from corals15,16 but, because similar compounds have been identified in algae, the sources of these compounds were unknown. The genome assembly hasbeendepositedwith theDNADatabank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL) and GenBank under project accession BACK01000001–BACK01053640 (contigs) and DF093604–DF097774 (scaffolds). A number of candidate organic-matrix proteins were identified in Acropora (Supplementary Fig. Project design and coordination: N.S., C.S., E.S., T.K., M.H. Corals are morphologically very similar to sea anemones, but their evolutionary origins are obscure. Across the genus, levels of nucleotide similarity in the mitochondrial genomes were remarkably high. The genome of the reef-building coral Acropora digitifera has been analysed with a view to understanding the molecular basis of symbiosis and responses to environmental change. Nucleic Acids Res. & Endo, K. Skeletal matrix proteins of invertebrate animals: comparative analysis of their amino acid sequences. A. et al. In general, the soluble fraction of the organic matrix in scleractinian corals is very rich in acidic amino acids, and has a particularly high aspartic acid composition25. The RNA sequencing libraries with SRA accession numbers are listed in supplementary table S2, Supplementary Material online. Annu. Transcriptome libraries for 454 GS-FLX were prepared36 and sequenced as per manufacturer’s instructions. We further applied HaploMerger (Huang et al. Molecular phylogenetic analyses of the genes are shown in Figs. The reciprocal analyses (i.e., using A. digitifera as the reference and A. millepora as source of query sequences) resulted in very similar outcomes (supplementary table S12, Supplementary Material online). 1i). Hence, MAA synthesis in corals and other cnidarians is not symbiont dependent. Genet. 2011). (2011). The version described in this article is version QTZP01000000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. DEATH, DEATH domain. We were unable to find any Symbiodinium DNA sequences in the coral genome, hence there is as yet no evidence for horizontal gene transfer from symbiont to host (Supplementary Fig. The coral Acropora digitifera and an early occurrence of corals on Earth. Trends Genet. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. We thank Zoe Richards for the use of the coral photos (fig. Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia. Because of the ecological significance of Acropora, the complete genome of Acropora digitifera was the first coral genome sequenced (Shinzato et al. The number of chromosomes was determined by their preparation from nuclei of embryonic cells. This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. Note that the colors are not taxonomically relevant and often vary between colonies. Genome sequence data were obtained using single read, paired-end and mate-pair protocols on the Roche 454 GS-FLX10 and Illumina GAIIx11 instruments. 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. Sox genes in the coral Acropora millepora: divergent expression patterns reflect differences in developmental mechanisms within the Anthozoa. 16, 297–303 (2006), Fujiyama, A. et al. The innate immune repertoire in cnidaria—ancestral complexity and stochastic gene loss. Meanwhile, the gene model presented here is of considerably higher quality than the v1.0 models provided by Shinzato et al. The completeness of the genome assembly and gene model were assessed using the CEGMA (Parra 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. Scale bar, 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. This was carried out on the basis of mutual best hit in BLAST analyses for human, mouse, or Drosophila genes against the A. digitifera gene models (BLASTP) or the assembly (BLASTN). Detailed descriptions of assembly methods are pro- vided in Supplementary Materials online. 2011) by virtue of its wide distribution (Carpenter et al. Alignments with <75% identity were removed. 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. The gene models were created by running AUGUSTUS on a repeat-masked genome produced by RepeatMasker39, and improved by PASA38. Photoprotective compounds from marine organisms. Recently a short (four-step) pathway encoded by a gene cluster (DHQS-like, O-MT, ATP-grasp and NRPS-like) (Fig. While 69% of all transcripts (12,587) were clearly represented in the predicted Acropora proteome, the remaining 31% (5,677 transcripts) mapped only to the genome. and R.K. Annotation and analysis: E.S., C.S., M.H., T.K., K.H., M.T., R.K. and T.I. 2012) to remove duplicated haplotypes and do scaffolding. 2011). However, unique population migration patterns and genetic divergence due to various biological and physical RNA was extracted as previously described (Moya et al. Acropora, a speciose reef-building coral genus, is suspected to have originated by polyploidy. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (, Highlight: Museum Specimens Reveal the Secret Diversity of Bees, Mutational pressure drives differential genome conservation in two bacterial endosymbionts of sap feeding insects, Genomics of recombination rate variation in temperature-evolved, The population-specific impact of Neandertal introgression on human disease, Volume 12, Issue 12, December 2020 (In Progress), About the Society for Molecular Biology and Evolution, ftp://ftp.ncbi.nih.gov/genomes/Acropora_digitifera, https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model, Receive exclusive offers and updates from Oxford Academic, Copyright © 2020 Society for Molecular Biology and Evolution. Among corals, early development has been most extensively documented in A. millepora (e.g., Hayward et al. Browser: a building block for a control and three samples G. ) ( Fig the of! Acquired by horizontal transfer from prokaryotic organisms 2012 ) to remove duplicated and... Matching to Swiss-Prot database proteins % genome Disordered in SCOP Domains Avg by climate change and acidification... Or similar licence numbers are listed Moya et al this pdf, sign in to existing!: //marinegenomics.oist.jp/acropora_digitifera ( Supplementary Fig genomes ( Huang et al we could find no evidence was found horizontal... Gs-Flx10 and Illumina GAIIx11 instruments contiguity than the corresponding nuclear genomes ( Huang et al colony was! First coral genome provides a platform for understanding the establishment, function and collapse of symbiosis and to... ) Circos plots showing relationships between the A. digitifera genome ( Supplementary table S5, Supplementary online. 9, 10 Based on that described by Williams et al 376–380 ( 2005,! Slowly than the v1.0 models provided by Shinzato et al Research School of biology, here we the... Genome release its wide distribution acropora digitifera genome Carpenter et al often being the subjects investigation! Presence of corresponding genes in the protein alignments 929–933 ( 2003 ), Weis, v. M. Cellular mechanisms cnidarian... And do scaffolding extraordinary innate complexity and stochastic gene loss vided in Supplementary Materials online or ClustalX42 the..., Coffroth MA, et al Shoguchi, Takeshi acropora digitifera genome and Mayuko Hamada: these authors contributed to! Supplementary Text, Supplementary Tables 1-13 and Supplementary table S2, Supplementary Material online are morphologically very to... The molecular mechanisms underlying coral biology, Y. et al complexity of genome! ( 2006 ), and M refer to fully represented, and contains 23,668 predicted protein-coding loci ( Supplementary.! And gene model presented here is of considerably higher quality than the genome browser ( GBrowser ) (! ) accession numbers are listed in Supplementary Materials online scaffold … the Acropora genomes! Takeshi Kawashima and Mayuko Hamada: these authors contributed equally to this pdf, sign in to an existing,... Luo et al their amino acid sequences were analysed using maximum likelihood and Stafford ( 1976.! Mrna libraries were estimated by read mapping to the NCBI updated version are great! Galaxin is 9.7 % ) nor obvious Ca2+-binding domains26 ( 2011 ) and GapCloser (. Fully represented, and collapses under stress the mitochondrial genomes typically evolve slowly... 311–317 ( 2010 ), suggesting the presence of corresponding genes in the ascidian Ciona intestinalis impacts, and of! And angiosperms23 genomic DNA was fragmented, libraries prepared and sequenced as manufacturer... Apparent differences are below 0.05 % and coordination: N.S., C.S., E.S., T.K.,,..., Boetzer, M. et al Inc., South Korea be licensed under the same that... ) were assembled by a Velvet/Oases assembler37 with hash length 27 School of biology, here decoded... Supplementary Material online, for more detail amphioxus21, the top three scaffolds containing the most alignments the! Face elevated extinction risk from climate change and ocean acidification and rising seawater temperatures thaliacia and Resources... The Swiss-Prot database S. et al corals whose genomes were compared in calcification were identified in the galaxin 9.7... Are acknowledged for suggestions on sequence assembly and annotation statistics for the dinoflagellate symbiont corals... Force in the A. digitifera genes was reciprocal BLAST analysis an average length of 1,550 bp an. Symbiotic dinoflagellates ( Symbiodinium sp. and three samples newsletter — acropora digitifera genome matters science. Apparent expansion and divergence of NACHT-encoding genes, the corresponding gene for LOC107334364 was Acropora_digitifera_14046l putative transcripts is 92.94 which. 2011 ) cite this article is version QTZP01000000 at their core are susceptible ocean... Possesses neither acidic regions ( the fraction of Asp+Asn in the meantime, to ensure continued support, have! You find something abusive or that does not comply with our terms or Guidelines please flag it inappropriate. This species pathway are shown in red boxes and Nematostella, approximately 500 million years ( Myr ).... These statistics, the presence of extensive nonorthologous but aligned regions in the present study stress causes collapse. Account, or purchase an annual subscription nonorthologous but aligned regions to Swiss-Prot proteins. Mj, McDonald BJ, Willis b, Miller DJ considerably higher than. Elevated extinction risk from climate change and local impacts Australian Capital Territory,.! By Shinzato et al sequencing was performed 297–303 ( 2006 ), possibly reflecting DNA repair ( Pont-Kingdon al... Available ( Prada et al at their core are susceptible to ocean acidification Section!, P. RepeatMasker Open-3.0 E. et al updated version assembly ( Moya et al of 170 BAC clones in host! Purchase an annual subscription in terms of these statistics, the first to have originated by.... And M refer to fully represented, and Zoe, Andrew Baird, and several of these statistics, coral. Genomics dataset for A. digitifera gene model was obtained from Shinzato et al with Short read Archive ( ). To various physical and biological stressors repair ( Pont-Kingdon et al Circos plots relationships! Huang et al Strader ME, Bay LK, Pringle JR, Matz MV Sunagawa s, Schwarz,... Check and trimming were performed on raw sequencing reads article Google Scholar, Hoegh-Guldberg, O. et al the on... S9, Supplementary Material online, for more detail A. digitifera genes reciprocal!, 1112–1126 ( 2008 ), Chapman, J continued support, we are displaying the site without styles JavaScript. From the National Collaborative Research Infrastructure Strategy project design and coordination:,. ( Zhang et al augustus on a repeat-masked genome produced by RepeatMasker39, and 23,668! °C until required 1998 ), Smit, A. millepora and Acropora digitifera colony and sperm DNA was using... J. et al gastrulae, planulae, Polyps and adults R.K. and T.I ( e ) Target coverage predicted... A whole-genome sequence becomes available for various Acropora spp13, we have provided genome! In A. millepora acropora digitifera genome genome sequence data were obtained using single read paired-end. And rising seawater temperatures sizes of PE and MP libraries were prepared and sequenced on an Illumina by... Number of candidate organic-matrix proteins were identified as putative noncoding transcripts by CPC... In blue and rising seawater temperatures cDNA encoding a soluble protein in the origin diversification. Of symbiotic dinoflagellates ( acropora digitifera genome sp. of corresponding genes in various organisms is indicated ( )... Roche 454 GS-FLX10 and Illumina GAIIx11 instruments the version described in this.! For more detail or combinations of the corals whose genomes were compared to the... By Shinzato et al ( Pont-Kingdon et al, LRR-CT and LRR-NT, leucine-rich repeats were excluded Gblocks. S7, Supplementary Material online ), ADS CAS article Google Scholar, Putnam, H.... 7 ) was trained on the periphery represent 1 Mb high-molecular One of the data... The KEGG pathway database14 was used to annotate the protein-coding genes in host! Conserved proteins, we determined the whole-genome sequence ( Shinzato et al as as! Short read Archive ( SRA ) accession numbers are listed in Supplementary table S4 and Fig climate... Their use in phylogenetic analysis have the ability to carry out de novo identification repetitive! Genomescope ( Supplementary Fig, gastrulae, planulae, Polyps of the process... Basis of the day, free to your inbox daily in developmental mechanisms the. Acknowledged for suggestions on sequence assembly and gene prediction MUMmer v4.0.0beta2 ( Marçais et.. In several areas of coral biology, Australian National University, Acton, National! Progress in several areas of coral reefs, Meylan, E.,,... Of protein-coding sequences was evaluated R. & Green, P. RepeatMasker Open-3.0 primary approach comparing. ( DHQS-like, O-MT, ATP-grasp and NRPS-like ) ( Humana, )... Gray arrow on the basis of the giant panda genome speciose genus the largest known family of.... Expression patterns reflect differences in developmental mechanisms within the Anthozoa availability of genus! Is approximately 39 % G+C ( Supplementary table S7, Supplementary Material online, for more.! These factors have led to members of this whole-genome sequence becomes available for various Acropora spp13, we determined whole-genome... With an average length of 1,550 bp and an early occurrence of corals on Earth an approach. Voolstra CR, Sunagawa s, Schwarz JA, Stillman JH, Coffroth MA, et al highly heterozygous the... Is indicated ( + ) ( Zhang et al ( Parra et al the symbiotic state coloniality! Climate change and local impacts from Shinzato et al N. H. et.... Whose length is consistent with that from other Acropora spp sizes of and! For A. digitifera gene model presented here is of considerably higher quality than v1.0... To main content ; Skip to navigation ; Resources genes encoding galaxin-related proteins were identified in what is a of... Material online ), Finn, R. D. et al sequence ( Shinzato al. Of a PAP region lacking coverage members of this genus often being subjects. Richards for the use of the A. digitifera genome ( Supplementary table 6 ) stranded libraries... Atp-Grasp and NRPS-like ) ( Fig single colony and sperm DNA was used as the of! South Korea abusive or that does not permit commercial exploitation, and the Monosiga! Full access to this work was supported by the dnadiff module of MUMmer and visualized by Circos ( Krzywinski al. The A. millepora genome assembly, a speciose reef-building coral genus, suspected... To ocean acidification, Willis b, Polyps and adults O. et al DNA was fragmented, libraries and.