1
|
Marzonie MR, Nitschke MR, Bay LK, Bourne DG, Harrison HB. Symbiodiniaceae diversity varies by host and environment across thermally distinct reefs. Mol Ecol 2024; 33:e17342. [PMID: 38584356 DOI: 10.1111/mec.17342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/07/2024] [Accepted: 03/07/2024] [Indexed: 04/09/2024]
Abstract
Endosymbiotic dinoflagellates (Symbiodiniaceae) influence coral thermal tolerance at both local and regional scales. In isolation, the effects of host genetics, environment, and thermal disturbances on symbiont communities are well understood, yet their combined effects remain poorly resolved. Here, we investigate Symbiodiniaceae across 1300 km in Australia's Coral Sea Marine Park to disentangle these interactive effects. We identified Symbiodiniaceae to species-level resolution for three coral species (Acropora cf humilis, Pocillopora verrucosa, and Pocillopora meandrina) by sequencing two genetic markers of the symbiont (ITS2 and psbAncr), paired with genotype-by-sequencing of the coral host (DArT-seq). Our samples predominantly returned sequences from the genus Cladocopium, where Acropora cf humilis affiliated with C3k, Pocillopora verrucosa with C. pacificum, and Pocillopora meandrina with C. latusorum. Multivariate analyses revealed that Acropora symbionts were driven strongly by local environment and thermal disturbances. In contrast, Pocillopora symbiont communities were both partitioned 2.5-fold more by host genetic structure than by environmental structure. Among the two Pocillopora species, the effects of environment and host genetics explained four times more variation in symbionts for P. meandrina than P. verrucosa. The concurrent bleaching event in 2020 had variable impacts on symbiont communities, consistent with patterns in P. verrucosa and A. cf humilis, but not P. meandrina. Our findings demonstrate how symbiont macroscale community structure responses to environmental gradients depend on host species and their respective population structure. Integrating host, symbiont, and environmental data will help forecast the adaptive potential of corals and their symbionts amidst a rapidly changing environment.
Collapse
Affiliation(s)
- Magena R Marzonie
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
| | - Matthew R Nitschke
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Hugo B Harrison
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
- School of Biological Sciences, University of Bristol, Bristol, UK
| |
Collapse
|
2
|
Oury N, Magalon H. Investigating the potential roles of intra-colonial genetic variability in Pocillopora corals using genomics. Sci Rep 2024; 14:6437. [PMID: 38499737 PMCID: PMC10948807 DOI: 10.1038/s41598-024-57136-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/14/2024] [Indexed: 03/20/2024] Open
Abstract
Intra-colonial genetic variability (IGV), the presence of more than one genotype in a single colony, has been increasingly studied in scleractinians, revealing its high prevalence. Several studies hypothesised that IGV brings benefits, but few have investigated its roles from a genetic perspective. Here, using genomic data (SNPs), we investigated these potential benefits in populations of the coral Pocillopora acuta from Reunion Island (southwestern Indian Ocean). As the detection of IGV depends on sequencing and bioinformatics errors, we first explored the impact of the bioinformatics pipeline on its detection. Then, SNPs and genes variable within colonies were characterised. While most of the tested bioinformatics parameters did not significantly impact the detection of IGV, filtering on genotype depth of coverage strongly improved its detection by reducing genotyping errors. Mosaicism and chimerism, the two processes leading to IGV (the first through somatic mutations, the second through fusion of distinct organisms), were found in 7% and 12% of the colonies, respectively. Both processes led to several intra-colonial allelic differences, but most were non-coding or silent. However, 7% of the differences were non-silent and found in genes involved in a high diversity of biological processes, some of which were directly linked to responses to environmental stresses. IGV, therefore, appears as a source of genetic diversity and genetic plasticity, increasing the adaptive potential of colonies. Such benefits undoubtedly play an important role in the maintenance and the evolution of scleractinian populations and appear crucial for the future of coral reefs in the context of ongoing global changes.
Collapse
Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, 97744, St Denis Cedex 09, La Réunion, France.
- Laboratoire Cogitamus, Paris, France.
- KAUST Red Sea Research Center and Marine Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, 97744, St Denis Cedex 09, La Réunion, France
- Laboratoire Cogitamus, Paris, France
- Laboratoire d'Excellence CORAIL, Perpignan, France
| |
Collapse
|
3
|
Gong S, Liang J, Li G, Xu L, Tan Y, Zheng X, Jin X, Yu K, Xia X. Linking coral fluorescence phenotypes to thermal bleaching in the reef-building Galaxea fascicularis from the northern South China Sea. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:155-167. [PMID: 38433965 PMCID: PMC10902222 DOI: 10.1007/s42995-023-00190-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/31/2023] [Indexed: 03/05/2024]
Abstract
Coral fluorescence phenotypes have been suggested as an adaptation to a broad range of environmental conditions, yet the mechanisms linking thermal bleaching tolerance in reef-building coral populations, associated with fluorescence phenotypes due to GFP-like proteins, remains unclear. In this study, the relationship between the thermal sensitivity and phenotypic plasticity of corals was investigated using two phenotypes of Galaxea fascicularis, green and brown. The results reveal that brown G. fascicularis was more susceptible to bleaching than green G. fascicularis when exposed to a higher growth temperature of 32 °C. Both phenotypes of G. fascicularis were associated with the thermotolerant Symbiodiniaceae symbiont, Durusdinium trenchii. However, the brown G. fascicularis showed a significant decrease in Symbiodiniaceae cell density and a significant increase in pathogenic bacteria abundance when the growth temperature was raised from 29 to 32 °C. The physiological traits and transcriptomic profiles of Symbiodiniaceae were not notably affected, but there were differences in the transcriptional levels of certain genes between the two phenotype hosts of G. fascicularis. Under heat stress of 32 °C, the gene encoding green fluorescent protein (GFP)-like and chromosome-associated proteins, as well as genes related to oxidative phosphorylation, cell growth and death showed lower transcriptional levels in the brown G. fascicularis compared to the green G. fascicularis. Overall, the results demonstrate that the green form of G. fascicularis is better able to tolerate ocean warming and defend against pathogenic bacteria, likely due to higher gene transcription levels and defense ability. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00190-1.
Collapse
Affiliation(s)
- Sanqiang Gong
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Jiayuan Liang
- Coral Reef Research Center of China, Guangxi University, Nanning, 53004 China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Lijia Xu
- South China Institute of Environmental Sciences, The Ministry of Ecology and Environment of PRC, Guangzhou, 510530 China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Xinqing Zheng
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
| | - Xuejie Jin
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi University, Nanning, 53004 China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| |
Collapse
|
4
|
Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun Biol 2023; 6:566. [PMID: 37264063 DOI: 10.1038/s42003-023-04917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
Collapse
Affiliation(s)
- Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
| | | | | | | | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | | | | |
Collapse
|
5
|
Noel B, Denoeud F, Rouan A, Buitrago-López C, Capasso L, Poulain J, Boissin E, Pousse M, Da Silva C, Couloux A, Armstrong E, Carradec Q, Cruaud C, Labadie K, Lê-Hoang J, Tambutté S, Barbe V, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Allemand D, Planes S, Gilson E, Zoccola D, Wincker P, Voolstra CR, Aury JM. Pervasive tandem duplications and convergent evolution shape coral genomes. Genome Biol 2023; 24:123. [PMID: 37264421 DOI: 10.1186/s13059-023-02960-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. RESULTS In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. CONCLUSIONS At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.
Collapse
Affiliation(s)
- Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Alice Rouan
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | | | - Laura Capasso
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
- Sorbonne Université, Collège Doctoral, 75005, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Emilie Boissin
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Mélanie Pousse
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Eric Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Sylvie Tambutté
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | | | - Guillaume Iwankow
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Sarah Romac
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire Des Sciences du Climat Et de L'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-Sur-Yvette, 91191, France
| | - J Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Pierre E Galand
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls Sur Mer, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de La Mer de Villefranche Sur Mer, Sorbonne Université, Laboratoire d'Océanographie de Villefranche, Villefranche-Sur-Mer, 06230, France
- Institut Universitaire de France, Paris, 75231, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, 220 Nash Hall, Corvallis, OR, 97331, USA
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Department of Human Genetics, CHU Nice, Nice, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France.
| |
Collapse
|
6
|
Oury N, Noël C, Mona S, Aurelle D, Magalon H. From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Mol Phylogenet Evol 2023; 184:107803. [PMID: 37120114 DOI: 10.1016/j.ympev.2023.107803] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus Pocillopora, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus Pocillopora. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.
Collapse
Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France.
| | - Cyril Noël
- IFREMER - IRSI - Service de Bioinformatique (SeBiMER), Plouzané, France
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; EPHE, PSL Research University, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
| | - Didier Aurelle
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
| |
Collapse
|
7
|
Stephens TG, Lee J, Jeong Y, Yoon HS, Putnam HM, Majerová E, Bhattacharya D. High-quality genome assembles from key Hawaiian coral species. Gigascience 2022; 11:6815755. [PMID: 36352542 PMCID: PMC9646523 DOI: 10.1093/gigascience/giac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/11/2022] [Accepted: 09/22/2022] [Indexed: 11/11/2022] Open
Abstract
Background Coral reefs house about 25% of marine biodiversity and are critical for the livelihood of many communities by providing food, tourism revenue, and protection from wave surge. These magnificent ecosystems are under existential threat from anthropogenic climate change. Whereas extensive ecological and physiological studies have addressed coral response to environmental stress, high-quality reference genome data are lacking for many of these species. The latter issue hinders efforts to understand the genetic basis of stress resistance and to design informed coral conservation strategies. Results We report genome assemblies from 4 key Hawaiian coral species, Montipora capitata, Pocillopora acuta, Pocillopora meandrina, and Porites compressa. These species, or members of these genera, are distributed worldwide and therefore of broad scientific and ecological importance. For M. capitata, an initial assembly was generated from short-read Illumina and long-read PacBio data, which was then scaffolded into 14 putative chromosomes using Omni-C sequencing. For P. acuta, P. meandrina, and P. compressa, high-quality assemblies were generated using short-read Illumina and long-read PacBio data. The P. acuta assembly is from a triploid individual, making it the first reference genome of a nondiploid coral animal. Conclusions These assemblies are significant improvements over available data and provide invaluable resources for supporting multiomics studies into coral biology, not just in Hawaiʻi but also in other regions, where related species exist. The P. acuta assembly provides a platform for studying polyploidy in corals and its role in genome evolution and stress adaptation in these organisms.
Collapse
Affiliation(s)
- Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, NJ 08901, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University , Daegu, Buk-gu 41566, Korea
| | - YuJin Jeong
- Department of Oceanography, Kyungpook National University , Daegu, Buk-gu 41566, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University , Suwon 16419, Korea
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island , Kingston, RI 02881, USA
| | - Eva Majerová
- Hawaiʻi Institute of Marine Biology , Kāneʻohe, HI 96744, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, NJ 08901, USA
| |
Collapse
|
8
|
Johnston EC, Cunning R, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae). Mol Ecol 2022; 31:5368-5385. [PMID: 35960256 PMCID: PMC9805206 DOI: 10.1111/mec.16654] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 01/09/2023]
Abstract
The congruence between phylogenies of tightly associated groups of organisms (cophylogeny) reflects evolutionary links between ecologically important interactions. However, despite being a classic example of an obligate symbiosis, tests of cophylogeny between scleractinian corals and their photosynthetic algal symbionts have been hampered in the past because both corals and algae contain genetically unresolved and morphologically cryptic species. Here, we studied co-occurring, cryptic Pocillopora species from Mo'orea, French Polynesia, that differ in their relative abundance across depth. We constructed new phylogenies of the host Pocillopora (using complete mitochondrial genomes, genomic loci, and thousands of single nucleotide polymorphisms) and their Symbiodiniaceae symbionts (using ITS2 and psbAncr markers) and tested for cophylogeny. The analysis supported the presence of five Pocillopora species on the fore reef at Mo'orea that mostly hosted either Cladocopium latusorum or C. pacificum. Only Pocillopora species hosting C. latusorum also hosted taxa from Symbiodinium and Durusdinium. In general, the Cladocopium phylogeny mirrored the Pocillopora phylogeny. Within Cladocopium species, lineages also differed in their associations with Pocillopora haplotypes, except those showing evidence of nuclear introgression, and with depth in the two most common Pocillopora species. We also found evidence for a new Pocillopora species (haplotype 10), that has so far only been sampled from French Polynesia, that warrants formal identification. The linked phylogenies of these Pocillopora and Cladocopium species and lineages suggest that symbiont speciation is driven by niche diversification in the host, but there is still evidence for symbiont flexibility in some cases.
Collapse
Affiliation(s)
- Erika C. Johnston
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| | - Ross Cunning
- Daniel P. Haerther Center for Conservation and ResearchJohn G. Shedd AquariumChicagoIllinoisUSA
| | - Scott C. Burgess
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| |
Collapse
|
9
|
Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circa-Dian Genes. Int J Mol Sci 2022; 23:ijms231911135. [PMID: 36232445 PMCID: PMC9570262 DOI: 10.3390/ijms231911135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.
Collapse
|
10
|
Cowen LJ, Putnam HM. Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience. Annu Rev Biomed Data Sci 2022; 5:205-231. [PMID: 35537462 DOI: 10.1146/annurev-biodatasci-122120-030732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Lenore J Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA;
| |
Collapse
|
11
|
Levy S, Elek A, Grau-Bové X, Menéndez-Bravo S, Iglesias M, Tanay A, Mass T, Sebé-Pedrós A. A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity. Cell 2021; 184:2973-2987.e18. [PMID: 33945788 PMCID: PMC8162421 DOI: 10.1016/j.cell.2021.04.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/24/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023]
Abstract
Stony corals are colonial cnidarians that sustain the most biodiverse marine ecosystems on Earth: coral reefs. Despite their ecological importance, little is known about the cell types and molecular pathways that underpin the biology of reef-building corals. Using single-cell RNA sequencing, we define over 40 cell types across the life cycle of Stylophora pistillata. We discover specialized immune cells, and we uncover the developmental gene expression dynamics of calcium-carbonate skeleton formation. By simultaneously measuring the transcriptomes of coral cells and the algae within them, we characterize the metabolic programs involved in symbiosis in both partners. We also trace the evolution of these coral cell specializations by phylogenetic integration of multiple cnidarian cell type atlases. Overall, this study reveals the molecular and cellular basis of stony coral biology.
Collapse
Affiliation(s)
- Shani Levy
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simón Menéndez-Bravo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Iglesias
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel.
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|