1
|
Vaga CF, Seiblitz IGL, Stolarski J, Capel KCC, Quattrini AM, Cairns SD, Huang D, Quek RZB, Kitahara MV. 300 million years apart: the extreme case of macromorphological skeletal convergence between deltocyathids and a turbinoliid coral (Anthozoa, Scleractinia). INVERTEBR SYST 2024; 38:IS23053. [PMID: 38744500 DOI: 10.1071/is23053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/18/2024] [Indexed: 05/16/2024]
Abstract
The integration of morphological and molecular lines of evidence has enabled the family Deltocyathidae to be erected to accommodate Deltocyathus species that were previously ascribed to the family Caryophylliidae. However, although displaying the same morphological characteristics as other species of Deltocyathus , molecular data suggested that D. magnificus was phylogenetically distant from Deltocyathidae, falling within the family Turbinoliidae instead. To elucidate the enigmatic evolutionary history of this species and skeletal microstructural features, the phylogenetic relationships of Deltocyathidae and Turbinoliidae were investigated using nuclear ultraconserved and exon loci and complete mitochondrial genomes. Both nuclear and mitochondrial phylogenomic reconstructions confirmed the position of D. magnificus within turbinolids. Furthermore, a novel mitochondrial gene order was uncovered for Deltocyathidae species. This gene order was not present in Turbinoliidae or in D. magnificus that both have the scleractinian canonical gene order, further indicating the taxonomic utility of mitochondrial gene order. D. magnificus is therefore formally moved to the family Turbinoliidae and accommodated in a new genus (Dennantotrochus Kitahara, Vaga & Stolarski, gen. nov.). Surprisingly, turbinolids and deltocyathids do not differ in microstructural organisation of the skeleton that consists of densely packed, individualised rapid accretion deposits and thickening deposits composed of fibres perpendicular to the skeleton surface. Therefore, although both families are clearly evolutionarily divergent, macromorphological features indicate a case of skeletal convergence while these may still share conservative biomineralisation mechanisms. ZooBank: urn:lsid:zoobank.org:pub:5F1C0E25-3CC6-4D1F-B1F0-CD9D0014678E.
Collapse
Affiliation(s)
- C F Vaga
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - I G L Seiblitz
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, PL-00-818 Warsaw, Poland
| | - K C C Capel
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Invertebrate Department, National Museum of Rio de Janeiro, Federal University of Rio de Janeiro, 20940-040, Rio de Janeiro, Brazil
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - D Huang
- Lee Kong Chian Natural History Museum, National University of Singapore, Conservatory Drive, Singapore 117377, Singapore; and Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - R Z B Quek
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; and Yale-NUS College, National University of Singapore, Singapore 138527, Singapore
| | - M V Kitahara
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| |
Collapse
|
2
|
Randolph Quek ZB, Jain SS, Richards ZT, Arrigoni R, Benzoni F, Hoeksema BW, Carvajal JI, Wilson NG, Baird AH, Kitahara MV, Seiblitz IGL, Vaga CF, Huang D. A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia). Mol Phylogenet Evol 2023:107867. [PMID: 37348770 DOI: 10.1016/j.ympev.2023.107867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 05/28/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
A well-supported evolutionary tree representing most major lineages of scleractinian corals is in sight with the development and application of phylogenomic approaches. Specifically, hybrid-capture techniques are shedding light on the evolution and systematics of corals. Here, we reconstructed a broad phylogeny of Scleractinia to test previous phylogenetic hypotheses inferred from a few molecular markers, in particular, the relationships among major scleractinian families and genera, and to identify clades that require further research. We analysed 449 nuclear loci from 422 corals, comprising 266 species spanning 26 families, combining data across whole genomes, transcriptomes, hybrid capture and low-coverage sequencing to reconstruct the largest phylogenomic tree of scleractinians to date. Due to the large number of loci and data completeness (<38% missing data), node supports were high across shallow and deep nodes with incongruences observed in only a few shallow nodes. The "Robust" and "Complex" clades were recovered unequivocally, and our analyses confirmed that Micrabaciidae Vaughan, 1905 is sister to the "Robust" clade, transforming our understanding of the "Basal" clade. Several families remain polyphyletic in our phylogeny, including Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012, Caryophylliidae Dana, 1846, and Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012, and we hereby formally proposed the family name Pachyseridae Benzoni & Hoeksema to accommodate Pachyseris Milne Edwards & Haime, 1849, which is phylogenetically distinct from Agariciidae Gray, 1847. Results also revealed species misidentifications and inconsistencies within morphologically complex clades, such as Acropora Oken, 1815 and Platygyra Ehrenberg, 1834, underscoring the need for reference skeletal material and topotypes, as well as the importance of detailed taxonomic work. The approach and findings here provide much promise for further stabilising the topology of the scleractinian tree of life and advancing our understanding of coral evolution.
Collapse
Affiliation(s)
- Z B Randolph Quek
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Yale-NUS College, National University of Singapore, Singapore 138527, Singapore.
| | - Sudhanshi S Jain
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia 6102, Australia; Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms, Genoa Marine Centre, Stazione Zoologica Anton Dohrn-National Institute of Marine Biology, Ecology and Biotechnology, 16126 Genoa, Italy
| | - Francesca Benzoni
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Bert W Hoeksema
- Taxonomy, Systematics and Geodiversity Group, Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 CC Groningen, The Netherlands
| | - Jose I Carvajal
- Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia
| | - Nerida G Wilson
- Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia; School of Biological Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Andrew H Baird
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Marcelo V Kitahara
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, United States of America
| | - Isabela G L Seiblitz
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - Claudia F Vaga
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117377, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore; Centre for Nature-based Climate Solutions, National University of Singapore, Singapore 117558, Singapore.
| |
Collapse
|
3
|
Quattrini AM, Snyder KE, Purow-Ruderman R, Seiblitz IGL, Hoang J, Floerke N, Ramos NI, Wirshing HH, Rodriguez E, McFadden CS. Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes. Sci Rep 2023; 13:7443. [PMID: 37156831 PMCID: PMC10167242 DOI: 10.1038/s41598-023-34059-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/24/2023] [Indexed: 05/10/2023] Open
Abstract
Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial (mt)-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mt genomes and reconstruct phylogenies for comparisons to phylogenies inferred from hundreds of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and > 50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by introgressive hybridization and unique properties of mt genomes, including slow rates of evolution driven by strong purifying selection and substitution rate variation. Strong purifying selection across the mt genomes caution their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mt genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mt genome assembly and adds to the growing knowledge of anthozoan evolution.
Collapse
Affiliation(s)
- Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA.
| | - Karen E Snyder
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | | | - Isabela G L Seiblitz
- Centre for Marine Biology, University of São Paulo, São Sebastião, 11612-109, Brazil
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-900, Brazil
| | - Johnson Hoang
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Natasha Floerke
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Nina I Ramos
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Herman H Wirshing
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Estefanía Rodriguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | | |
Collapse
|
4
|
Matias AMA, Popovic I, Thia JA, Cooke IR, Torda G, Lukoschek V, Bay LK, Kim SW, Riginos C. Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef. Evol Appl 2023; 16:293-310. [PMID: 36793689 PMCID: PMC9923489 DOI: 10.1111/eva.13435] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/20/2022] [Accepted: 05/29/2022] [Indexed: 11/26/2022] Open
Abstract
Genomic studies are uncovering extensive cryptic diversity within reef-building corals, suggesting that evolutionarily and ecologically relevant diversity is highly underestimated in the very organisms that structure coral reefs. Furthermore, endosymbiotic algae within coral host species can confer adaptive responses to environmental stress and may represent additional axes of coral genetic variation that are not constrained by taxonomic divergence of the cnidarian host. Here, we examine genetic variation in a common and widespread, reef-building coral, Acropora tenuis, and its associated endosymbiotic algae along the entire expanse of the Great Barrier Reef (GBR). We use SNPs derived from genome-wide sequencing to characterize the cnidarian coral host and organelles from zooxanthellate endosymbionts (genus Cladocopium). We discover three distinct and sympatric genetic clusters of coral hosts, whose distributions appear associated with latitude and inshore-offshore reef position. Demographic modelling suggests that the divergence history of the three distinct host taxa ranges from 0.5 to 1.5 million years ago, preceding the GBR's formation, and has been characterized by low-to-moderate ongoing inter-taxon gene flow, consistent with occasional hybridization and introgression typifying coral evolution. Despite this differentiation in the cnidarian host, A. tenuis taxa share a common symbiont pool, dominated by the genus Cladocopium (Clade C). Cladocopium plastid diversity is not strongly associated with host identity but varies with reef location relative to shore: inshore colonies contain lower symbiont diversity on average but have greater differences between colonies as compared with symbiont communities from offshore colonies. Spatial genetic patterns of symbiont communities could reflect local selective pressures maintaining coral holobiont differentiation across an inshore-offshore environmental gradient. The strong influence of environment (but not host identity) on symbiont community composition supports the notion that symbiont community composition responds to habitat and may assist in the adaptation of corals to future environmental change.
Collapse
Affiliation(s)
- Ambrocio Melvin A Matias
- Institute of Biology University of the Philippines Diliman Quezon City Philippines.,School of Biological Sciences The University of Queensland St. Lucia Queensland Australia
| | - Iva Popovic
- School of Biological Sciences The University of Queensland St. Lucia Queensland Australia
| | - Joshua A Thia
- Bio21 Institute, School of BioSciences The University of Melbourne Parkeville Victoria Australia
| | - Ira R Cooke
- College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Queensland Australia
| | - Gergely Torda
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Queensland Australia
| | - Vimoksalehi Lukoschek
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Queensland Australia.,Gold Coast University Hospital QLD Health Southport Queensland Australia
| | - Line K Bay
- Australian Institute of Marine Science Townsville Queensland Australia
| | - Sun W Kim
- School of Biological Sciences The University of Queensland St. Lucia Queensland Australia
| | - Cynthia Riginos
- School of Biological Sciences The University of Queensland St. Lucia Queensland Australia
| |
Collapse
|
5
|
Vaga CF, Seiblitz IGL, Capel KCC, Kitahara MV. The mitochondrial genomes of Crispatotrochus rubescens and Crispatotrochus rugosus (Hexacorallia; Scleractinia): new insights on the phylogeny of the family Caryophylliidae. Mol Biol Rep 2022; 49:12269-12273. [PMID: 36264418 DOI: 10.1007/s11033-022-08029-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Caryophylliidae is one of the most diverse scleractinian families, however it was recovered as polyphyletic in multiple molecular studies. Recently, the mitochondrial gene order was proposed as a character for a taxonomic revision of the family. Here we describe the first mitogenome of the caryophylliid genus Crispatotrochus, whose phylogenetic position remains uncertain. METHODS AND RESULTS The complete mitochondrial genomes of Crispatotrochus rubescens and Crispatotrochus rugosus were sequenced, assembled, and annotated. The two mitogenomes are identical and circular, have a length of 16,536 bp, a GC content of 35.9%, and contain 13 protein-coding genes, 2 ribosomal RNAs and 2 transfer RNAs. Both species have a transposition of a three gene block - cob, nad2, and nad6 - similarly to a group of caryophylliid genera that were recovered as monophyletic, including the type genus (Caryophyllia) of the family. The phylogenetic analyses recovered Crispatotrochus within the clade that presents the gene rearrangement and specifically as sister taxa of the genus Caryophyllia, a result consistent with previous studies and the similar gross morphology of the two genera. CONCLUSIONS We determined the mitochondrial genomes of the genus Crispatotrochus to investigate their relations within Scleractinia. Results from this study provide insights on the phylogenetic position of the genus and corroborate that the mitochondrial gene order could be used as taxonomic character for the family Caryophylliidae.
Collapse
Affiliation(s)
- C F Vaga
- Centre for Marine Biology, University of Sao Paulo, Sao Sebastiao, 11612-109, Brazil. .,Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil.
| | - I G L Seiblitz
- Centre for Marine Biology, University of Sao Paulo, Sao Sebastiao, 11612-109, Brazil.,Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
| | - K C C Capel
- Centre for Marine Biology, University of Sao Paulo, Sao Sebastiao, 11612-109, Brazil.,Department of Marine Science, Federal University of Sao Paulo, Santos, 11070-100, Brazil
| | - M V Kitahara
- Centre for Marine Biology, University of Sao Paulo, Sao Sebastiao, 11612-109, Brazil.,Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, MRC 163, PO Box 37012, Washington, DC, 20013-7012, USA
| |
Collapse
|
6
|
Seiblitz IGL, Vaga CF, Capel KCC, Cairns SD, Stolarski J, Quattrini AM, Kitahara MV. Caryophylliids (Anthozoa, Scleractinia) and mitochondrial gene order: insights from mitochondrial and nuclear phylogenomics. Mol Phylogenet Evol 2022; 175:107565. [PMID: 35787457 DOI: 10.1016/j.ympev.2022.107565] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 10/17/2022]
Abstract
Molecularly, the family Caryophylliidae is polyphyletic and different sets of genetic data converge towards a consensus that a taxonomic review of this family is necessary. Overall, the order of genes in the mitochondrial genome (mitogenome) together with DNA sequences have been used to successfully untangle evolutionary relationships in several groups of organisms. Published mitogenomes of two caryophylliid genera (Desmophyllum and Solenosmilia) present a transposition of the gene block containing cob, nad2, and nad6, which is located between nad5 5' exon and trnW, while that of Polycyathus chaishanensis presents the same gene order as the majority of scleractinian corals. In molecular-based evolutionary reconstructions, caryophylliids that have the mitochondrial gene rearrangement were recovered as a monophyletic lineage ("true" caryophylliids), while members of the genus Polycyathus were placed in a different position. In this study, additional mitogenomes of this family were assembled and included in evolutionary reconstructions of Scleractinia in order to improve our understanding on whether the mitogenome gene rearrangement is limited to and, therefore, could be a synapomorphy of the actual members of Caryophylliidae. Specimens of Caryophyllia scobinosa, Premocyathus sp., Heterocyathus sulcatus, and Trochocyathus caryophylloides, as well as Desmophyllum pertusum and Solenosmilia variabilis from the Southwest Atlantic were sequenced using Illumina platforms. Then, mitochondrial genomes were assembled and annotated, and nuclear datasets were recovered in-silico from assembled contigs using a previously published set of baits. Evolutionary reconstructions were performed using mitochondrial and nuclear datasets and based on Maximum Likelihood and Bayesian Inference. Obtained mitogenomes are circular and range between 15,816 and 18,225 bp in size and from 30.76% to 36.63% in GC content. The gene rearrangement is only seen in C. scobinosa, D. pertusum, Premocyathus sp., and S. variabilis, which were recovered as a monophyletic clade in both mitochondrial and nuclear phylogenies. On the other hand, the "caryophylliids" with the canonical mitogenome gene order were not recovered within this clade. Differences in features of the skeleton of "true" caryophylliids in comparison to traditional members of the family were observed and offer further support that the gene rearrangement might be seen as a synapomorphy of family Caryophylliidae.
Collapse
Affiliation(s)
- I G L Seiblitz
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil.
| | - C F Vaga
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - K C C Capel
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Marine Science, Federal University of São Paulo, 11070-100 Santos, Brazil
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163 United States of America
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, PL-00-818 Warsaw, Poland
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163 United States of America
| | - M V Kitahara
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Marine Science, Federal University of São Paulo, 11070-100 Santos, Brazil.
| |
Collapse
|
7
|
Xiao J, Tian P, Guo F, Yu S, Wang W, Wang X, Niu W. Characterization of the complete mitochondrial genome of Diploastrea heliopora and phylogeny of the scleractinia species which have group I introns in their COI genes. Saudi J Biol Sci 2021; 28:7054-7060. [PMID: 34867006 PMCID: PMC8626255 DOI: 10.1016/j.sjbs.2021.07.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/04/2022] Open
Abstract
Mitochondrial genome DNA is a powerful marker for resolving phylogenetic relationships among scleractinian corals. Here, we decode the complete mitochondrial genome of Diploastrea heliopora (Lamarck, 1816) for the first time. The general features are 18 363 bp in length, and conventionally, with 13 protein coding genes, two ribosomal RNAs, and two transfer RNAs. Gene arrangement and distribution are similar to other scleractinian corals. Moreover, the COI gene of D. heliopora is broken up into two parts by a complex group I intron. This intron is 1076 bases in length and contains helical structures (P1-P10, except P2) and four conserved regions (P, Q, R, and S). The mitochondrial genome of D. heliopora has asymmetric base composition (13.03% C, 20.29% G, 25.91% A, and 40.77% for T). Based on concatenated protein coding genes, ML and BI trees show similar phylogenetic relationship: D. heliopora clustered closely with Sclerophyllia maxima and Echinophyllia aspera into the robust branch. The data and conclusion in this study are reference for further phylogenetic studies of corals.
Collapse
Affiliation(s)
- Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Feng Guo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Shuangen Yu
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Wei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiaolei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| |
Collapse
|
8
|
McFadden CS, Quattrini AM, Brugler MR, Cowman PF, Dueñas LF, Kitahara MV, Paz-García DA, Reimer JD, Rodríguez E. Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria). Syst Biol 2021; 70:635-647. [PMID: 33507310 DOI: 10.1093/sysbio/syaa103] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/19/2023] Open
Abstract
Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, analyses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds of ultraconserved elements and exon loci, we explore the evolutionary origins of the major clades of Anthozoa and some of their salient morphological features. The phylogeny supports reciprocally monophyletic Hexacorallia and Octocorallia, with Ceriantharia as the earliest diverging hexacorals; two reciprocally monophyletic clades of Octocorallia; and monophyly of all hexacoral orders with the exception of the enigmatic sea anemone Relicanthus daphneae. Divergence dating analyses place Anthozoa in the Cryogenian to Tonian periods (648-894 Ma), older than has been suggested by previous studies. Ancestral state reconstructions indicate that the ancestral anthozoan was a solitary polyp that had bilateral symmetry and lacked a skeleton. Colonial growth forms and the ability to precipitate calcium carbonate evolved in the Ediacaran (578 Ma) and Cambrian (503 Ma) respectively; these hallmarks of reef-building species have subsequently arisen multiple times independently in different orders. Anthozoans formed associations with photosymbionts by the Devonian (383 Ma), and photosymbioses have been gained and lost repeatedly in all orders. Together, these results have profound implications for the interpretation of the Precambrian environment and the early evolution of metazoans.[Bilateral symmetry; coloniality; coral; early metazoans; exon capture; Hexacorallia; Octocorallia photosymbiosis; sea anemone; ultraconserved elements.].
Collapse
Affiliation(s)
- Catherine S McFadden
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711 USA
| | - Andrea M Quattrini
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711 USA.,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.,Biological Sciences Department, NYC College of Technology, City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA.,Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, SC 29902, USA
| | - Peter F Cowman
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.,Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, QLD 4810, Australia
| | - Luisa F Dueñas
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia-Sede Bogotá, Carrera 30 No.45-03 Edificio 421, Bogotá, D.C., Colombia
| | - Marcelo V Kitahara
- Department of Marine Science, Federal University of São Paulo, Santos, SP 11070-100 Brazil.,Centre for Marine Biology, University of São Paulo, São Sebastião, SP 11612-109 Brazil
| | - David A Paz-García
- CONACyT-Centro de Investigaciones Biológicas del Noroeste (CIBNOR). Laboratorio de Necton y Ecología de Arrecifes. Calle IPN 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, B.C.S., México
| | - James D Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Marine Science, Chemistry, and Biology, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| |
Collapse
|
9
|
Seiblitz IGL, Capel KCC, Stolarski J, Quek ZBR, Huang D, Kitahara MV. The earliest diverging extant scleractinian corals recovered by mitochondrial genomes. Sci Rep 2020; 10:20714. [PMID: 33244171 PMCID: PMC7693180 DOI: 10.1038/s41598-020-77763-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/11/2020] [Indexed: 11/08/2022] Open
Abstract
Evolutionary reconstructions of scleractinian corals have a discrepant proportion of zooxanthellate reef-building species in relation to their azooxanthellate deep-sea counterparts. In particular, the earliest diverging "Basal" lineage remains poorly studied compared to "Robust" and "Complex" corals. The lack of data from corals other than reef-building species impairs a broader understanding of scleractinian evolution. Here, based on complete mitogenomes, the early onset of azooxanthellate corals is explored focusing on one of the most morphologically distinct families, Micrabaciidae. Sequenced on both Illumina and Sanger platforms, mitogenomes of four micrabaciids range from 19,048 to 19,542 bp and have gene content and order similar to the majority of scleractinians. Phylogenies containing all mitochondrial genes confirm the monophyly of Micrabaciidae as a sister group to the rest of Scleractinia. This topology not only corroborates the hypothesis of a solitary and azooxanthellate ancestor for the order, but also agrees with the unique skeletal microstructure previously found in the family. Moreover, the early-diverging position of micrabaciids followed by gardineriids reinforces the previously observed macromorphological similarities between micrabaciids and Corallimorpharia as well as its microstructural differences with Gardineriidae. The fact that both families share features with family Kilbuchophylliidae ultimately points towards a Middle Ordovician origin for Scleractinia.
Collapse
Affiliation(s)
- Isabela G L Seiblitz
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil.
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil.
| | - Kátia C C Capel
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | | | | | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Marcelo V Kitahara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| |
Collapse
|
10
|
Goremykin V. A Novel Test for Absolute Fit of Evolutionary Models Provides a Means to Correctly Identify the Substitution Model and the Model Tree. Genome Biol Evol 2020; 11:2403-2419. [PMID: 31368483 PMCID: PMC6736042 DOI: 10.1093/gbe/evz167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2019] [Indexed: 02/07/2023] Open
Abstract
A novel test is described that visualizes the absolute model-data fit of the substitution and tree components of an evolutionary model. The test utilizes statistics based on counts of character state matches and mismatches in alignments of observed and simulated sequences. This comparison is used to assess model-data fit. In simulations conducted to evaluate the performance of the test, the test estimator was able to identify both the correct tree topology and substitution model under conditions where the Goldman-Cox test-which tests the fit of a substitution model to sequence data and is also based on comparing simulated replicates with observed data-showed high error rates. The novel test was found to identify the correct tree topology within a wide range of DNA substitution model misspecifications, indicating the high discriminatory power of the test. Use of this test provides a practical approach for assessing absolute model-data fit when testing phylogenetic hypotheses.
Collapse
Affiliation(s)
- Vadim Goremykin
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trentino, Italy
| |
Collapse
|
11
|
Niu W, Xiao J, Tian P, Yu S, Guo F, Wang J, Huang D. Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics. PeerJ 2020; 8:e8455. [PMID: 32002337 PMCID: PMC6984341 DOI: 10.7717/peerj.8455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 12/24/2019] [Indexed: 11/20/2022] Open
Abstract
Over the past few decades, modern coral taxonomy, combining morphology and molecular sequence data, has resolved many long-standing questions about scleractinian corals. In this study, we sequenced the complete mitochondrial genomes of three Merulinidae corals (Dipsastraea rotumana, Favites pentagona, and Hydnophora exesa) for the first time using next-generation sequencing. The obtained mitogenome sequences ranged from 16,466 bp (D. rotumana) to 18,006 bp (F. pentagona) in length, and included 13 unique protein-coding genes (PCGs), two transfer RNA genes, and two ribosomal RNA genes . Gene arrangement, nucleotide composition, and nucleotide bias of the three Merulinidae corals were canonically identical to each other and consistent with other scleractinian corals. We performed a Bayesian phylogenetic reconstruction based on 13 protein-coding sequences of 86 Scleractinia species. The results showed that the family Merulinidae was conventionally nested within the robust branch, with H. exesa clustered closely with F. pentagona and D. rotumana clustered closely with Favites abdita. This study provides novel insight into the phylogenetics of species within the family Merulinidae and the evolutionary relationships among different Scleractinia genera.
Collapse
Affiliation(s)
- Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Shuangen Yu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Feng Guo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Jianjia Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Dingyong Huang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| |
Collapse
|
12
|
Silvestri S, Figueroa DF, Hicks D, Figueroa NJ. Mitogenomic phylogenetic analyses of Leptogorgia virgulata and Leptogorgia hebes (Anthozoa: Octocorallia) from the Gulf of Mexico provides insight on Gorgoniidae divergence between Pacific and Atlantic lineages. Ecol Evol 2019; 9:14114-14129. [PMID: 31938507 PMCID: PMC6953674 DOI: 10.1002/ece3.5847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 11/28/2022] Open
Abstract
The use of genetics in recent years has brought to light the need to reevaluate the classification of many gorgonian octocorals. This study focuses on two Leptogorgia species-Leptogorgia virgulata and Leptogorgia hebes-from the northwestern Gulf of Mexico (GOM). We target complete mitochondrial genomes and mtMutS sequences, and integrate this data with previous genetic research of gorgonian corals to resolve phylogenetic relationships and estimate divergence times. This study contributes the first complete mitochondrial genomes for L. ptogorgia virgulata and L. hebes. Our resulting phylogenies stress the need to redefine the taxonomy of the genus Leptogorgia in its entirety. The fossil-calibrated divergence times for Eastern Pacific and Western Atlantic Leptogorgia species based on complete mitochondrial genomes shows that the use of multiple genes results in estimates of more recent speciation events than previous research based on single genes. These more recent divergence times are in agreement with geologic data pertaining to the formation of the Isthmus of Panama.
Collapse
Affiliation(s)
- Samantha Silvestri
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
| | - Diego F. Figueroa
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
| | - David Hicks
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
| | - Nicole J. Figueroa
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
| |
Collapse
|
13
|
Richards ZT, Carvajal JI, Wallace CC, Wilson NG. Phylotranscriptomics confirms Alveopora is sister to Montipora within the family Acroporidae. Mar Genomics 2019; 50:100703. [PMID: 31466869 DOI: 10.1016/j.margen.2019.100703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 01/17/2023]
Abstract
The genus Alveopora is a scleractinian coral taxon whose phylogenetic classification has recently changed from the family Poritidae to Acroporidae. This change, which was made based on single-locus genetic data, has led to uncertainty about the placement of Alveopora and the ability for deep evolutionary relationships in these groups to be accurately recovered and represented by limited genetic datasets. We sought to characterize the higher-level position of Alveopora using newly available transcriptome data to confirm its placement within Acroporidae and resolve its closest ancestor. Here we present an analysis of a new 2031 gene dataset that confirms the placement of Alveopora within Acroporidae corroborating other single-locus (COI, 16S and ITS) analyses and a mitogenome dataset. We also resolve the position of Alveopora as sister to the genus Montipora. This has allowed the re-interpretation of morphology, and a rediagnosis of the family Acroporidae and the genus Alveopora.
Collapse
Affiliation(s)
- Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6012, Australia; Department of Aquatic Zoology, Western Australian Museum, Kew Street, Welshpool, WA, 6106, Australia.
| | - Jose I Carvajal
- Molecular Systematics Unit, Western Australian Museum, Kew Street, Welshpool, WA 6106, Australia
| | - Carden C Wallace
- Biodiversity and Geosciences Program, Queensland Museum, Brisbane, Queensland 4101, Australia
| | - Nerida G Wilson
- Molecular Systematics Unit, Western Australian Museum, Kew Street, Welshpool, WA 6106, Australia; School of Biological Sciences, University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
| |
Collapse
|
14
|
Cunha RL, Forsman ZH, Belderok R, Knapp ISS, Castilho R, Toonen RJ. Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora. BMC Evol Biol 2019; 19:153. [PMID: 31340762 PMCID: PMC6657087 DOI: 10.1186/s12862-019-1476-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary patterns of scleractinian (stony) corals are difficult to infer given the existence of few diagnostic characters and pervasive phenotypic plasticity. A previous study of Hawaiian Montipora (Scleractinia: Acroporidae) based on five partial mitochondrial and two nuclear genes revealed the existence of a species complex, grouping one of the rarest known species (M. dilatata, which is listed as Endangered by the International Union for Conservation of Nature - IUCN) with widespread corals of very different colony growth forms (M. flabellata and M. cf. turgescens). These previous results could result from a lack of resolution due to a limited number of markers, compositional heterogeneity or reflect biological processes such as incomplete lineage sorting (ILS) or introgression. Results All 13 mitochondrial protein-coding genes from 55 scleractinians (14 lineages from this study) were used to evaluate if a recent origin of the M. dilatata species complex or rate heterogeneity could be compromising phylogenetic inference. Rate heterogeneity detected in the mitochondrial data set seems to have no significant impacts on the phylogenies but clearly affects age estimates. Dating analyses show different estimations for the speciation of M. dilatata species complex depending on whether taking compositional heterogeneity into account (0.8 [0.05–2.6] Myr) or assuming rate homogeneity (0.4 [0.14–0.75] Myr). Genomic data also provided evidence of introgression among all analysed samples of the complex. RADseq data indicated that M. capitata colour morphs may have a genetic basis. Conclusions Despite the volume of data (over 60,000 SNPs), phylogenetic relationships within the M. dilatata species complex remain unresolved most likely due to a recent origin and ongoing introgression. Species delimitation with genomic data is not concordant with the current taxonomy, which does not reflect the true diversity of this group. Nominal species within the complex are either undergoing a speciation process or represent ecomorphs exhibiting phenotypic polymorphisms. Electronic supplementary material The online version of this article (10.1186/s12862-019-1476-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Regina L Cunha
- University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal. .,Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Roy Belderok
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Ingrid S S Knapp
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Rita Castilho
- University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| |
Collapse
|
15
|
Chi SI, Dahl M, Emblem Å, Johansen SD. Giant group I intron in a mitochondrial genome is removed by RNA back-splicing. BMC Mol Biol 2019; 20:16. [PMID: 31153363 PMCID: PMC6545197 DOI: 10.1186/s12867-019-0134-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 05/23/2019] [Indexed: 01/29/2023] Open
Abstract
Background The mitochondrial genomes of mushroom corals (Corallimorpharia) are remarkable for harboring two complex group I introns; ND5-717 and COI-884. How these autocatalytic RNA elements interfere with mitochondrial RNA processing is currently not known. Here, we report experimental support for unconventional processing events of ND5-717 containing RNA. Results We obtained the complete mitochondrial genome sequences and corresponding mitochondrial transcriptomes of the two distantly related corallimorpharian species Ricordea yuma and Amplexidiscus fenestrafer. All mitochondrial genes were found to be expressed at the RNA-level. Both introns were perfectly removed by autocatalytic splicing, but COI-884 excision appeared more efficient than ND5-717. ND5-717 was organized into giant group I intron elements of 18.1 kb and 19.3 kb in A. fenestrafer and R. yuma, respectively. The intron harbored almost the entire mitochondrial genome embedded within the P8 peripheral segment. Conclusion ND5-717 was removed by group I intron splicing from a small primary transcript that contained a permutated intron–exon arrangement. The splicing pathway involved a circular exon-containing RNA intermediate, which is a hallmark of RNA back-splicing. ND5-717 represents the first reported natural group I intron that becomes excised by back-splicing from a permuted precursor RNA. Back-splicing may explain why Corallimorpharia mitochondrial genomes tolerate giant group I introns. Electronic supplementary material The online version of this article (10.1186/s12867-019-0134-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sylvia Ighem Chi
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Mikael Dahl
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Åse Emblem
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Steinar D Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway. .,Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
| |
Collapse
|
16
|
Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia). Mol Phylogenet Evol 2019; 134:12-23. [DOI: 10.1016/j.ympev.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/28/2023]
|
17
|
Stampar SN, Broe MB, Macrander J, Reitzel AM, Brugler MR, Daly M. Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia. Sci Rep 2019; 9:6094. [PMID: 30988357 PMCID: PMC6465557 DOI: 10.1038/s41598-019-42621-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/04/2019] [Indexed: 01/10/2023] Open
Abstract
Sequences and structural attributes of mitochondrial genomes have played a critical role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia (“tube anemones”) remains one of the most enigmatic in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both Isarachnanthus nocturnus and Pachycerianthus magnus, the mitochondrial gene sequences could not be assembled into a single circular genome. Instead, our analyses suggest that both species have mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The inferred number of fragments and variation in gene order between species is much greater within Ceriantharia than among the lineages of Medusozoa. We identify origins of replication for each of the five putative chromosomes of the Isarachnanthus nocturnus mitogenome and for each of the eight putative chromosomes of the Pachycerianthus magnus mitogenome. At 80,923 bp, I. nocturnus now holds the record for the largest animal mitochondrial genome reported to date. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other Anthozoa. The presence of tRNAMet and tRNATrp in both ceriantharian mitogenomes supports a closer relationship between Ceriantharia and Hexacorallia than between Ceriantharia and any other cnidarian lineage, but phylogenetic analysis of the genes contained in the mitogenomes suggests that Ceriantharia is sister to a clade containing Octocorallia + Hexacorallia indicating a possible suppression of tRNATrp in Octocorallia.
Collapse
Affiliation(s)
- Sérgio N Stampar
- Departamento de Ciências Biológicas, Faculdade de Ciências e Letras, UNESP - Universidade Estadual Paulista, Assis, SP, Brazil.
| | - Michael B Broe
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Jason Macrander
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.,Department of Biology, Florida Southern College, Lakeland, FL, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Mercer R Brugler
- Biological Sciences Department, NYC College of Technology, City University of New York, 285 Jay Street, Brooklyn, New York, 11201, USA.,Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, USA
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
18
|
Ying H, Cooke I, Sprungala S, Wang W, Hayward DC, Tang Y, Huttley G, Ball EE, Forêt S, Miller DJ. Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages. Genome Biol 2018; 19:175. [PMID: 30384840 PMCID: PMC6214176 DOI: 10.1186/s13059-018-1552-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/28/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there are two major clades, Complexa and Robusta, but the genomic bases of significant differences between them remain unclear. RESULTS Draft genome assemblies and annotations were generated for three coral species: Galaxea fascicularis (Complexa), Fungia sp., and Goniastrea aspera (Robusta). Whilst phylogenetic analyses strongly support a deep split between Complexa and Robusta, synteny analyses reveal a high level of gene order conservation between all corals, but not between corals and sea anemones or between sea anemones. HOX-related gene clusters are, however, well preserved across all of these combinations. Differences between species are apparent in the distribution and numbers of protein domains and an apparent correlation between number of HSP20 proteins and stress tolerance. Uniquely amongst animals, a complete histidine biosynthesis pathway is present in robust corals but not in complex corals or sea anemones. This pathway appears to be ancestral, and its retention in the robust coral lineage has important implications for coral nutrition and symbiosis. CONCLUSIONS The availability of three new coral genomes enabled recognition of a de novo histidine biosynthesis pathway in robust corals which is only the second identified biosynthetic difference between corals. These datasets provide a platform for understanding many aspects of coral biology, particularly the interactions of corals with their endosymbionts.
Collapse
Affiliation(s)
- Hua Ying
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Ira Cooke
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811 Australia
| | - Susanne Sprungala
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811 Australia
| | - Weiwen Wang
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - David C. Hayward
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Yurong Tang
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- Computational Biology and Bioinformatics Unit, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gavin Huttley
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- Computational Biology and Bioinformatics Unit, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Eldon E. Ball
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Sylvain Forêt
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - David J. Miller
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811 Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| |
Collapse
|
19
|
Wang X, Drillon G, Ryu T, Voolstra CR, Aranda M. Genome-Based Analyses of Six Hexacorallian Species Reject the "Naked Coral" Hypothesis. Genome Biol Evol 2018; 9:2626-2634. [PMID: 29048525 PMCID: PMC5737686 DOI: 10.1093/gbe/evx196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2017] [Indexed: 12/24/2022] Open
Abstract
Scleractinian corals are the foundation species of the coral-reef ecosystem. Their calcium carbonate skeletons form extensive structures that are home to millions of species, making coral reefs one of the most diverse ecosystems of our planet. However, our understanding of how reef-building corals have evolved the ability to calcify and become the ecosystem builders they are today is hampered by uncertain relationships within their subclass Hexacorallia. Corallimorpharians have been proposed to originate from a complex scleractinian ancestor that lost the ability to calcify in response to increasing ocean acidification, suggesting the possibility for corals to lose and gain the ability to calcify in response to increasing ocean acidification. Here, we employed a phylogenomic approach using whole-genome data from six hexacorallian species to resolve the evolutionary relationship between reef-building corals and their noncalcifying relatives. Phylogenetic analysis based on 1,421 single-copy orthologs, as well as gene presence/absence and synteny information, converged on the same topologies, showing strong support for scleractinian monophyly and a corallimorpharian sister clade. Our broad phylogenomic approach using sequence-based and sequence-independent analyses provides unambiguous evidence for the monophyly of scleractinian corals and the rejection of corallimorpharians as descendants of a complex coral ancestor.
Collapse
Affiliation(s)
- Xin Wang
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Guénola Drillon
- Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne Universités, UPMC-Univ P6, CNRS, IBPS, - UMR 7238, 4 Place Jussieu, Paris, 75005, France
| | | | - Christian R Voolstra
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manuel Aranda
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| |
Collapse
|
20
|
Enríquez S, Méndez ER, Hoegh-Guldberg O, Iglesias-Prieto R. Key functional role of the optical properties of coral skeletons in coral ecology and evolution. Proc Biol Sci 2018; 284:rspb.2016.1667. [PMID: 28446691 DOI: 10.1098/rspb.2016.1667] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 03/21/2017] [Indexed: 11/12/2022] Open
Abstract
Multiple scattering of light on coral skeleton enhances light absorption efficiency of coral symbionts and plays a key role in the regulation of their internal diffuse light field. To understand the dependence of this enhancement on skeleton meso- and macrostructure, we analysed the scattering abilities of naked coral skeletons for 74 Indo-Pacific species. Sensitive morphotypes to thermal and light stress, flat-extraplanate and branching corals, showed the most efficient structures, while massive-robust species were less efficient. The lowest light-enhancing scattering abilities were found for the most primitive colonial growth form: phaceloid. Accordingly, the development of highly efficient light-collecting structures versus the selection of less efficient but more robust holobionts to cope with light stress may constitute a trade-off in the evolution of modern symbiotic scleractinian corals, characterizing two successful adaptive solutions. The coincidence of the most important structural modifications with epitheca decline supports the importance of the enhancement of light transmission across coral skeleton in modern scleractinian diversification, and the central role of these symbioses in the design and optimization of coral skeleton. Furthermore, the same ability that lies at the heart of the success of symbiotic corals as coral-reef-builders can also explain the 'Achilles's heel' of these symbioses in a warming ocean.
Collapse
Affiliation(s)
- Susana Enríquez
- Unidad Académica de Sistemas Arrecifales (Puerto Morelos), Instituto de Ciencias del Mar y Limonología, Universidad Nacional Autónoma de México, Mexico
| | - Eugenio R Méndez
- División de Física Aplicada, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana Number 3918, Ensenada, BC 22860, Mexico
| | - Ove Hoegh-Guldberg
- Global Change Institute, University of Queensland, Queensland, Australia
| | - Roberto Iglesias-Prieto
- Unidad Académica de Sistemas Arrecifales (Puerto Morelos), Instituto de Ciencias del Mar y Limonología, Universidad Nacional Autónoma de México, Mexico
| |
Collapse
|
21
|
Voolstra CR, Li Y, Liew YJ, Baumgarten S, Zoccola D, Flot JF, Tambutté S, Allemand D, Aranda M. Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals. Sci Rep 2017; 7:17583. [PMID: 29242500 PMCID: PMC5730576 DOI: 10.1038/s41598-017-17484-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 11/28/2017] [Indexed: 02/07/2023] Open
Abstract
Stony corals form the foundation of coral reef ecosystems. Their phylogeny is characterized by a deep evolutionary divergence that separates corals into a robust and complex clade dating back to at least 245 mya. However, the genomic consequences and clade-specific evolution remain unexplored. In this study we have produced the genome of a robust coral, Stylophora pistillata, and compared it to the available genome of a complex coral, Acropora digitifera. We conducted a fine-scale gene-based analysis focusing on ortholog groups. Among the core set of conserved proteins, we found an emphasis on processes related to the cnidarian-dinoflagellate symbiosis. Genes associated with the algal symbiosis were also independently expanded in both species, but both corals diverged on the identity of ortholog groups expanded, and we found uneven expansions in genes associated with innate immunity and stress response. Our analyses demonstrate that coral genomes can be surprisingly disparate. Future analyses incorporating more genomic data should be able to determine whether the patterns elucidated here are not only characteristic of the differences between S. pistillata and A. digitifera but also representative of corals from the robust and complex clade at large.
Collapse
Affiliation(s)
- Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Yong Li
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yi Jin Liew
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sebastian Baumgarten
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Biology of Host-Parasite Interactions Unit, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 quai Antoine Ier, 98000, Monaco, Monaco
| | - Jean-François Flot
- Université libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050, Bruxelles, Belgium
| | - Sylvie Tambutté
- Centre Scientifique de Monaco, 8 quai Antoine Ier, 98000, Monaco, Monaco
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 quai Antoine Ier, 98000, Monaco, Monaco
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| |
Collapse
|
22
|
Quattrini AM, Faircloth BC, Dueñas LF, Bridge TCL, Brugler MR, Calixto‐Botía IF, DeLeo DM, Forêt S, Herrera S, Lee SMY, Miller DJ, Prada C, Rádis‐Baptista G, Ramírez‐Portilla C, Sánchez JA, Rodríguez E, McFadden CS. Universal target‐enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long‐standing problems. Mol Ecol Resour 2017; 18:281-295. [DOI: 10.1111/1755-0998.12736] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/28/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA USA
| | - Luisa F. Dueñas
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
| | - Tom C. L. Bridge
- Queensland Museum Network Townsville QLD Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD Australia
| | - Mercer R. Brugler
- Division of Invertebrate Zoology American Museum of Natural History New York NY USA
- Biological Sciences Department NYC College of Technology City University of New York Brooklyn NY USA
| | - Iván F. Calixto‐Botía
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
- Department of Animal Ecology and Systematics Justus Liebig Universität Giessen Germany
| | - Danielle M. DeLeo
- Department of Biological Sciences Florida International University North Miami FL USA
- Biology Department Temple University Philadelphia PA USA
| | - Sylvain Forêt
- Research School of Biology Australian National University Canberra ACT Australia
| | - Santiago Herrera
- Department of Biological Sciences Lehigh University Bethlehem PA USA
| | - Simon M. Y. Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences University of Macau Macao China
| | - David J. Miller
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD Australia
| | - Carlos Prada
- Department of Biological Sciences University of Rhode Island Kingston RI USA
| | | | - Catalina Ramírez‐Portilla
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
- Department of Animal Ecology and Systematics Justus Liebig Universität Giessen Germany
| | - Juan A. Sánchez
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology American Museum of Natural History New York NY USA
| | | |
Collapse
|
23
|
Lin MF, Moya A, Ying H, Chen CA, Cooke I, Ball EE, Forêt S, Miller DJ. Analyses of Corallimorpharian Transcriptomes Provide New Perspectives on the Evolution of Calcification in the Scleractinia (Corals). Genome Biol Evol 2017; 9:150-160. [PMID: 28158437 PMCID: PMC5604590 DOI: 10.1093/gbe/evw297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2016] [Indexed: 12/12/2022] Open
Abstract
Corallimorpharians (coral-like anemones) have a close phylogenetic relationship with scleractinians (hard corals) and can potentially provide novel perspectives on the evolution of biomineralization within the anthozoan subclass Hexacorallia. A survey of the transcriptomes of three representative corallimorpharians led to the identification of homologs of some skeletal organic matrix proteins (SOMPs) previously considered to be restricted to corals. Carbonic anhydrases (CAs), which are ubiquitous proteins involved in CO2 trafficking, are involved in both coral calcification and photosynthesis by endosymbiotic Symbiodinium (zooxanthellae). These multiple roles are assumed to place increased demands on the CA repertoire and have presumably driven the elaboration of the complex CA repertoires typical of corals (note that “corals” are defined here as reef-building Scleractinia). Comparison of the CA inventories of corallimorpharians with those of corals reveals that corals have specifically expanded the secreted and membrane-associated type CAs, whereas similar complexity is observed in the two groups with respect to other CA types. Comparison of the CA complement of the nonsymbiotic corallimorph Corynactis australis with that of Ricordea yuma, a corallimorph which normally hosts Symbiodinium, reveals similar numbers and distribution of CA types and suggests that an expansion of the CA repertoire has been necessary to enable calcification but may not be a requirement to enable symbiosis. Consistent with this idea, preliminary analysis suggests that the CA complexity of zooxanthellate and nonzooxanthellate sea anemones is similar. The comparisons above suggest that although there are relatively few new genes in the skeletal organic matrix of corals (which controls the skeleton deposition process), the evolution of calcification required an expanded repertoire of secreted and membrane-associated CAs.
Collapse
Affiliation(s)
- Mei-Fang Lin
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Aurelie Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Hua Ying
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Chaolun Allen Chen
- Biodiversity Research Centre, Academia Sinica, Nangang, Taipei, Taiwan.,Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Nangang, Taipei, Taiwan
| | - Ira Cooke
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia
| | - Eldon E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sylvain Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - David J Miller
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| |
Collapse
|
24
|
Wang X, Liew YJ, Li Y, Zoccola D, Tambutte S, Aranda M. Draft genomes of the corallimorphariansAmplexidiscus fenestraferandDiscosomasp. Mol Ecol Resour 2017; 17:e187-e195. [DOI: 10.1111/1755-0998.12680] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/26/2017] [Accepted: 04/03/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Xin Wang
- Biological and Environmental Sciences & Engineering Division (BESE); Red Sea Research Center (RSRC); King Abdullah University of Science and Technology (KAUST); Thuwal Saudi Arabia
| | - Yi Jin Liew
- Biological and Environmental Sciences & Engineering Division (BESE); Red Sea Research Center (RSRC); King Abdullah University of Science and Technology (KAUST); Thuwal Saudi Arabia
| | - Yong Li
- Biological and Environmental Sciences & Engineering Division (BESE); Red Sea Research Center (RSRC); King Abdullah University of Science and Technology (KAUST); Thuwal Saudi Arabia
| | | | | | - Manuel Aranda
- Biological and Environmental Sciences & Engineering Division (BESE); Red Sea Research Center (RSRC); King Abdullah University of Science and Technology (KAUST); Thuwal Saudi Arabia
| |
Collapse
|
25
|
Loss and Gain of Group I Introns in the Mitochondrial Cox1 Gene of the Scleractinia (Cnidaria; Anthozoa). Zool Stud 2017; 56:e9. [PMID: 31966208 DOI: 10.6620/zs.2017.56-09] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/12/2017] [Indexed: 01/21/2023]
Abstract
Yaoyang Chuang, Marcelo Kitahara, Hironobu Fukami, Dianne Tracey, David J. Miller, and Chaolun Allen Chen (2017) Group I introns encoding a homing endonuclease gene (HEG) that is potentially capable of sponsoring mobility are present in the cytochrome oxidase subunit 1 (cox1) gene of some Hexacorallia, including a number of scleractinians assigned to the "robust" coral clade. In an e ort to infer the evolutionary history of this cox1 group I intron, DNA sequences were determined for 12 representative "basal" and "complex" corals and for 11 members of the Corallimorpharia, a sister order of the Scleractinia. Comparisons of insertion sites, secondary structures, and amino acid sequences of the HEG implied a common origin for cox1 introns of corallimorpharians, and basal and complex corals, but cox1 introns of robust corals were highly divergent, most likely reflecting independent acquisition. Phylogenetic analyses with a calibrated molecular clock suggested that cox1 introns of scleractinians and corallimorpharians have persisted at the same insertion site as that in the common ancestor 552 million years ago (mya). This ancestral intron was probably lost in complex corals around 213 to 190 mya at the junction between the Trassic and Jurassic. The coral cox1 gene remained intronless until new introns, probably from sponges or fungi, reinvaded different positions of the cox1 gene in robust corals around 135 mya in the Cretaceous, and then it subsequently began to lose them around 65.5 mya in some robust coral lineages coincident with the later Maastrichtian extinction at the Cretaceous-Tertiary boundary.
Collapse
|
26
|
Evolutionary and biogeographical implications of degraded LAGLIDADG endonuclease functionality and group I intron occurrence in stony corals (Scleractinia) and mushroom corals (Corallimorpharia). PLoS One 2017; 12:e0173734. [PMID: 28278261 PMCID: PMC5344465 DOI: 10.1371/journal.pone.0173734] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/24/2017] [Indexed: 11/29/2022] Open
Abstract
Group I introns and homing endonuclease genes (HEGs) are mobile genetic elements, capable of invading target sequences in intron-less genomes. LAGLIDADG HEGs are the largest family of endonucleases, playing a key role in the mobility of group I introns in a process known as ‘homing’. Group I introns and HEGs are rare in metazoans, and can be mainly found inserted in the COXI gene of some sponges and cnidarians, including stony corals (Scleractinia) and mushroom corals (Corallimorpharia). Vertical and horizontal intron transfer mechanisms have been proposed as explanations for intron occurrence in cnidarians. However, the central role of LAGLIDADG motifs in intron mobility mechanisms remains poorly understood. To resolve questions regarding the evolutionary origin and distribution of group I introns and HEGs in Scleractinia and Corallimorpharia, we examined intron/HEGs sequences within a comprehensive phylogenetic framework. Analyses of LAGLIDADG motif conservation showed a high degree of degradation in complex Scleractinia and Corallimorpharia. Moreover, the two motifs lack the respective acidic residues necessary for metal-ion binding and catalysis, potentially impairing horizontal intron mobility. In contrast, both motifs are highly conserved within robust Scleractinia, indicating a fully functional endonuclease capable of promoting horizontal intron transference. A higher rate of non-synonymous substitutions (Ka) detected in the HEGs of complex Scleractinia and Corallimorpharia suggests degradation of the HEG, whereas lower Ka rates in robust Scleractinia are consistent with a scenario of purifying selection. Molecular-clock analyses and ancestral inference of intron type indicated an earlier intron insertion in complex Scleractinia and Corallimorpharia in comparison to robust Scleractinia. These findings suggest that the lack of horizontal intron transfers in the former two groups is related to an age-dependent degradation of the endonuclease activity. Moreover, they also explain the peculiar geographical patterns of introns in stony and mushroom corals.
Collapse
|
27
|
Lin MF, Chou WH, Kitahara MV, Chen CLA, Miller DJ, Forêt S. Corallimorpharians are not "naked corals": insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses. PeerJ 2016; 4:e2463. [PMID: 27761308 PMCID: PMC5068439 DOI: 10.7717/peerj.2463] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/19/2016] [Indexed: 01/01/2023] Open
Abstract
Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.
Collapse
Affiliation(s)
- Mei Fang Lin
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia; Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, Australia
| | - Wen Hwa Chou
- Biodiversity Research Center, Academia Sinica , Taipei , Taiwan
| | - Marcelo V Kitahara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil; Centro de Biologia Marinha, Universidade Federal de São Paulo, São Sebastião, São Paulo, Brazil
| | | | - David John Miller
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia; Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, Australia
| | - Sylvain Forêt
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia; Research School of Biology, Australian National University, Canberra, ACT, Australia
| |
Collapse
|
28
|
Capel KCC, Migotto AE, Zilberberg C, Lin MF, Forsman Z, Miller DJ, Kitahara MV. Complete mitochondrial genome sequences of Atlantic representatives of the invasive Pacific coral species Tubastraea coccinea and T. tagusensis (Scleractinia, Dendrophylliidae): Implications for species identification. Gene 2016; 590:270-7. [PMID: 27234370 DOI: 10.1016/j.gene.2016.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
Members of the azooxanthellate coral genus Tubastraea are invasive species with particular concern because they have become established and are fierce competitors in the invaded areas in many parts of the world. Pacific Tubastraea species are spreading fast throughout the Atlantic Ocean, occupying over 95% of the available substrate in some areas and out-competing native endemic species. Approximately half of all known coral species are azooxanthellate but these are seriously under-represented compared to zooxanthellate corals in terms of the availability of mitochondrial (mt) genome data. In the present study, the complete mt DNA sequences of Atlantic individuals of the invasive scleractinian species Tubastraea coccinea and Tubastraea tagusensis were determined and compared to the GenBank reference sequence available for a Pacific "T. coccinea" individual. At 19,094bp (compared to 19,070bp for the GenBank specimen), the mt genomes assembled for the Atlantic T. coccinea and T. tagusensis were among the longest sequence determined to date for "Complex" scleractinians. Comparisons of genomes data showed that the "T. coccinea" sequence deposited on GenBank was more closely related to that from Dendrophyllia arbuscula than to the Atlantic Tubastraea spp., in terms of genome length and base pair similarities. This was confirmed by phylogenetic analysis, suggesting that the former was misidentified and might actually be a member from the genus Dendrophyllia. In addition, although in general the COX1 locus has a slow evolutionary rate in Scleractinia, it was the most variable region of the Tubastraea mt genome and can be used as markers for genus or species identification. Given the limited data available for azooxanthellate corals, the results presented here represent an important contribution to our understanding of phylogenetic relationships and the evolutionary history of the Scleractinia.
Collapse
Affiliation(s)
- K C C Capel
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - A E Migotto
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | - C Zilberberg
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M F Lin
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia; Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Z Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i, USA
| | - D J Miller
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - M V Kitahara
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil; Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil.
| |
Collapse
|
29
|
Addamo AM, Vertino A, Stolarski J, García-Jiménez R, Taviani M, Machordom A. Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia. BMC Evol Biol 2016; 16:108. [PMID: 27193263 PMCID: PMC4870751 DOI: 10.1186/s12862-016-0654-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/12/2016] [Indexed: 12/16/2022] Open
Abstract
Background In recent years, several types of molecular markers and new microscale skeletal characters have shown potential as powerful tools for phylogenetic reconstructions and higher-level taxonomy of scleractinian corals. Nonetheless, discrimination of closely related taxa is still highly controversial in scleractinian coral research. Here we used newly sequenced complete mitochondrial genomes and 30 microsatellites to define the genetic divergence between two closely related azooxanthellate taxa of the family Caryophylliidae: solitary Desmophyllum dianthus and colonial Lophelia pertusa. Results In the mitochondrial control region, an astonishing 99.8 % of nucleotides between L. pertusa and D. dianthus were identical. Variability of the mitochondrial genomes of the two species is represented by only 12 non-synonymous out of 19 total nucleotide substitutions. Microsatellite sequence (37 loci) analysis of L. pertusa and D. dianthus showed genetic similarity is about 97 %. Our results also indicated that L. pertusa and D. dianthus show high skeletal plasticity in corallum shape and similarity in skeletal ontogeny, micromorphological (septal and wall granulations) and microstructural characters (arrangement of rapid accretion deposits, thickening deposits). Conclusions Molecularly and morphologically, the solitary Desmophyllum and the dendroid Lophelia appear to be significantly more similar to each other than other unambiguous coral genera analysed to date. This consequently leads to ascribe both taxa under the generic name Desmophyllum (priority by date of publication). Findings of this study demonstrate that coloniality may not be a robust taxonomic character in scleractinian corals. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0654-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Anna Maria Addamo
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Agostina Vertino
- Dipartimento di Scienze dell'Ambiente e del Territorio e di Scienze della Terra, Università di Milano Bicocca (UNIMIB), Piazza della Scienza 4, 20126, Milan, Italy.,Department of Geology Renard Centre of Marine Geology, Universiteit Ghent, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Jaroslaw Stolarski
- Polskiej Akademii Nauk, Instytut Paleobiologii, Twarda 51/55, PL-00-818, Warsaw, Poland
| | - Ricardo García-Jiménez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Marco Taviani
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine (ISMAR), Via Gobetti 101, 40129, Bologna, Italy.,Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, 02543, MA, USA.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Annie Machordom
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| |
Collapse
|
30
|
Lin MF, Kitahara MV, Luo H, Tracey D, Geller J, Fukami H, Miller DJ, Chen CA. Mitochondrial genome rearrangements in the scleractinia/corallimorpharia complex: implications for coral phylogeny. Genome Biol Evol 2016; 6:1086-95. [PMID: 24769753 PMCID: PMC4040992 DOI: 10.1093/gbe/evu084] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Corallimorpharia is a small Order of skeleton-less animals that is closely related to the reef-building corals (Scleractinia) and of fundamental interest in the context of understanding the potential impacts of climate change in the future on coral reefs. The relationship between the nominal Orders Corallimorpharia and Scleractinia is controversial—the former is either the closest outgroup to the Scleractinia or alternatively is derived from corals via skeleton loss. This latter scenario, the “naked coral” hypothesis, is strongly supported by analyses based on mitochondrial (mt) protein sequences, whereas the former is equally strongly supported by analyses of mt nucleotide sequences. The “naked coral” hypothesis seeks to link skeleton loss in the putative ancestor of corallimorpharians with a period of elevated oceanic CO2 during the Cretaceous, leading to the idea that these skeleton-less animals may be harbingers for the fate of coral reefs under global climate change. In an attempt to better understand their evolutionary relationships, we examined mt genome organization in a representative range (12 species, representing 3 of the 4 extant families) of corallimorpharians and compared these patterns with other Hexacorallia. The most surprising finding was that mt genome organization in Corallimorphus profundus, a deep-water species that is the most scleractinian-like of all corallimorpharians on the basis of morphology, was much more similar to the common scleractinian pattern than to those of other corallimorpharians. This finding is consistent with the idea that C. profundus represents a key position in the coral <-> corallimorpharian transition.
Collapse
Affiliation(s)
- Mei-Fang Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Blackall LL, Wilson B, van Oppen MJH. Coral-the world's most diverse symbiotic ecosystem. Mol Ecol 2015; 24:5330-47. [DOI: 10.1111/mec.13400] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 09/21/2015] [Accepted: 09/24/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Linda L. Blackall
- Department of Chemistry and Biotechnology; Faculty of Science, Engineering & Technology; Swinburne University of Technology; Melbourne Vic. 3122 Australia
| | - Bryan Wilson
- Marine Microbiology Research Group; Department of Biology; University of Bergen; Thormøhlensgate 53B 5020 Bergen Norway
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science; PMB No. 3 Townsville MC Qld. 4810 Australia
- School of BioSciences; The University of Melbourne; Parkville Vic. 3010 Australia
| |
Collapse
|
32
|
Luz BLP, Capel KCC, Stampar SN, Kitahara MV. Description of the mitochondrial genome of the tree coral Dendrophyllia arbuscula (Anthozoa, Scleractinia). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2911-2. [PMID: 26119126 DOI: 10.3109/19401736.2015.1060435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Dendrophylliidae is one of the few monophyletic families within the Scleractinia that embraces zooxanthellate and azooxanthellate species represented by both solitary and colonial forms. Among the exclusively azooxanthellate genera, Dendrophyllia is reported worldwide from 1 to 1200 m deep. To date, although three complete mitochondrial (mt) genomes from representatives of the family are available, only that from Turbinaria peltata has been formally published. Here we describe the complete nucleotide sequence of the mt genome from Dendrophyllia arbuscula that is 19 069 bp in length and comprises two rDNAs, two tRNAs, and 13 protein-coding genes arranged in the canonical scleractinian mt gene order. No genes overlap, resulting in the presence of 18 intergenic spacers and one of the longest scleractinian mt genome sequenced to date.
Collapse
Affiliation(s)
- Bruna Louise Pereira Luz
- a Programa de Pós graduação em Sistemas Costeiros e Oceânicos, Centro de Estudos do Mar (CEM), Universidade Federal do Paraná, Pontal do Paraná , Paraná , Brazil
| | - Kátia Cristina Cruz Capel
- b Programa de Pós graduação em Biodiversidade e Biologia Evolutiva, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil
| | - Sérgio Nascimento Stampar
- c Faculdade de Ciências e Letras de Assis , UNESP - Universidade Estadual Paulista , Assis , São Paulo , Brazil
| | - Marcelo Visentini Kitahara
- a Programa de Pós graduação em Sistemas Costeiros e Oceânicos, Centro de Estudos do Mar (CEM), Universidade Federal do Paraná, Pontal do Paraná , Paraná , Brazil .,d Departamento de Ciências do Mar , Universidade Federal de São Paulo , Campus Baixada Santista , Santos , São Paulo , Brazil , and.,e Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo , São Sebastião , São Paulo , Brazil
| |
Collapse
|
33
|
Chuang Y, Chen CA. The complete mitochondrial genomes of Pseudosiderastrea spp (Cnidaria, Scleractinia, Siderastreidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4065-4066. [PMID: 25629500 DOI: 10.3109/19401736.2014.1003845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genomes of the Indo-Pacific scleractinians, Pseudosiderastrea formosa and P. tayamai, were sequenced. The mitochondrial genomes are 19,475 bp in length for both P. formosa and P. tayamai, representing the longest mitochondrial genome in the complex corals sequenced to date. The overall GC composition (36.3%) and the gene arrangement are similar to those of the other scleractinian corals, including 13 protein-coding genes, 2 rRNA genes (rnl and rns) and 2 tRNA genes (tRNA-Met and tRNA-Trp). All genes, except tRNA-Trp, tRNA-Met, rnl, cox1, and atp8, are engulfed by a large group I intron in the nad5 gene. The second group I intron (970 bp) encoding a putative homing endonuclease is inserted in the cox1 gene, where insertion site is different from those of robust corals. Genes were separated by intergenic spacer regions for a total of 2593 bp, of which the cytb-nad2 region may correspond to the putative control region.
Collapse
Affiliation(s)
- Yaoyang Chuang
- a Biodiversity Research Centre, Academia Sinica , Nangang , Taipei , Taiwan.,b Institute of Oceanography, National Taiwan University , Taipei , Taiwan , and
| | - Chaolun Allen Chen
- a Biodiversity Research Centre, Academia Sinica , Nangang , Taipei , Taiwan.,b Institute of Oceanography, National Taiwan University , Taipei , Taiwan , and.,c Taiwan International Graduate Program (TIGP) - Biodiversity, Academia Sinica , Nangang , Taipei , Taiwan
| |
Collapse
|