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Whitney JL, Coleman RR, Deakos MH. The complete mitochondrial genome of the Reef Manta Ray, Mobula alfredi, from Hawaii. Mitochondrial DNA B Resour 2023; 8:197-203. [PMID: 36755876 PMCID: PMC9901431 DOI: 10.1080/23802359.2023.2167475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We provide the complete mitochondrial genome of the reef manta ray, Mobula alfredi, using an ezRAD approach. The total length of the mitogenome was 18,166 bp and contained 13 protein-coding genes, 22 transfer RNAs genes, two ribosomal RNA genes, and one non-coding control region. The gene organization and length are similar to other Mobula species. This reference mitogenome that includes the control region is expected to be a valuable resource for molecular-based species identification, population genomics, and phylogeography.
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Affiliation(s)
- Jonathan L. Whitney
- Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, HI, USA,CONTACT Jonathan L. Whitney Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, HI, USA
| | - Richard R. Coleman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA,Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Mark H. Deakos
- Hawaiʻi Association for Marine Education and Research, Lahaina, HI, USA
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2
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Laczkó L, Jordán S, Sramkó G. The
RadOrgMiner
pipeline: Automated genotyping of organellar loci from
RADseq
data. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Levente Laczkó
- MTA‐DE “Lendület” Evolutionary Phylogenomics Research Group, Egyetem tér 1 H‐4032 Debrecen Hungary
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- ELKH‐ DE Conservation Biology Research Group, Egyetem tér 1, Debrecen, H‐4032 Hungary
- Department of Metagenomics University of Debrecen Nagyerdei körút 98., Debrecen, H‐4032 Hungary
| | - Sándor Jordán
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- Juhász‐Nagy Pál Doctoral School University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
| | - Gábor Sramkó
- MTA‐DE “Lendület” Evolutionary Phylogenomics Research Group, Egyetem tér 1 H‐4032 Debrecen Hungary
- Department of Botany University of Debrecen Egyetem tér 1, Debrecen, H‐4032 Hungary
- ELKH‐ DE Conservation Biology Research Group, Egyetem tér 1, Debrecen, H‐4032 Hungary
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3
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Terraneo TI, Arrigoni R, Marchese F, Chimienti G, Eweida AA, Rodrigue M, Benzoni F. The complete mitochondrial genome of Dendrophyllia minuscula (Cnidaria: Scleractinia) from the NEOM region of the Northern Red Sea. Mitochondrial DNA B Resour 2022; 7:848-850. [PMID: 35573591 PMCID: PMC9103361 DOI: 10.1080/23802359.2022.2074803] [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: 02/08/2022] [Accepted: 05/02/2022] [Indexed: 11/05/2022] Open
Abstract
The scleractinian coral family Dendrophylliidae is a major component of shallow and deep-water coral ecosystems worldwide, but our knowledge on the evolutionary history of the family remains scarce. Here, we used ezRAD coupled with Illumina sequencing technology and reconstructed the complete mitochondrial genome of Dendrophyllia minuscula (GenBank accession number OL634845), from mesophotic depths in the Red Sea NEOM area. The mitochondrial genome of D. minuscula consisted of 19,054 bp, organized in 13 protein-coding genes, 2 rRNA genes, and 2 tRNA genes, in agreement with the Scleractinia typical mitogenome organization. This complete mitochondrial genome contributes toward a better knowledge of mesophotic and deep-water coral diversity and evolutionary history.
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Affiliation(s)
- Tullia I. Terraneo
- Red Sea Research Center, King Abdullah University of Science and Technology, (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms (BEOM), Genoa Marine Centre (GMC), Stazione Zoologica Anton Dohrn–National Institute of Marine Biology, Ecology and Biotechnology, Villa del Principe, Genoa, Italy
| | - Fabio Marchese
- Red Sea Research Center, King Abdullah University of Science and Technology, (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Giovanni Chimienti
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
- CoNISMa, Rome, Italy
| | - Ameer Abdulla Eweida
- Marine Conservation Division, Nature Conservation Authority, Neom, Saudi Arabia
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida, USA
| | | | - Francesca Benzoni
- Red Sea Research Center, King Abdullah University of Science and Technology, (KAUST), Thuwal, Kingdom of Saudi Arabia
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4
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Terraneo TI, Mariappan KG, Forsman Z, Arrigoni R. Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS). Methods Mol Biol 2022; 2498:1-18. [PMID: 35727537 DOI: 10.1007/978-1-0716-2313-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mitochondrial genomes (mtgenome) represent an important source of information for addressing fundamental evolutionary, phylogeographic, systematic, and ecological questions in marine organisms. In the last two decades the advent of high-throughput next-generation sequencing (NGS) has provided an unprecedented possibility to access large amount of genomic data and, as such, there has been a rapid growth in mtgenome resources and studies. In particular, NGS strategies represent a great advantage for investigating nonmodel marine organisms for which no or limited genomic resources are available. Here, we describe a routinely used standardized protocol to obtain mtgenome of nonmodel marine organisms by NGS. The protocol is composed of five main steps, including DNA extraction, DNA fragmentation, library preparation, high-throughput sequencing, and bioinformatic analyses. Each of the first three steps is followed by size/quality and concentration validations. The advantages of the described protocol rely on the assumption that no a priori information on mtgenome of the studied organism is needed and on its versatility as researchers may choose several kits for DNA extraction and library preparation and adopt different methods for DNA fragmentation depending on their needs, experience, and suppliers.
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Affiliation(s)
- Tullia I Terraneo
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zac Forsman
- Hawaii Institute of Marine Biology, Kaneohe, HI, USA
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy.
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5
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Colin L, Yesson C, Head CEI. Complete mitochondrial genomes of three reef forming Acropora corals (Acroporidae, Scleractinia) from Chagos Archipelago, Indian Ocean. Biodivers Data J 2021; 9:e72762. [PMID: 34707458 PMCID: PMC8497460 DOI: 10.3897/bdj.9.e72762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/25/2021] [Indexed: 11/12/2022] Open
Abstract
We present the first mitochondrial genomes from Chagos Archipelago, Indian Ocean, of three putative species of reef forming Acropora (Acropora aff. tenuis, Acroporaaff.cytherea and Acropora aff. orbicularis). The circular genome consists respectively of 18,334 bp, 18,353 bp and 18,584 bp. All mitochondrial genomes recovered comprise 13 protein-coding genes, two transfer RNA genes and two ribosomal RNA genes, with an overall GC content ranging from 37.9% to 38.0%. These new genomic data contribute to our increased understanding of genus Acropora and its species boundaries, ultimately aiding species monitoring and conservation efforts.
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Affiliation(s)
- Luigi Colin
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY, London, United Kingdom Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London United Kingdom
| | - Chris Yesson
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY, London, United Kingdom Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London United Kingdom
| | - Catherine E I Head
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY, London, United Kingdom Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London United Kingdom.,Department of Zoology, University of Oxford, John Krebs Field Station, Wytham, OX2 8JQ, Oxford, United Kingdom Department of Zoology, University of Oxford, John Krebs Field Station, Wytham, OX2 8JQ Oxford United Kingdom.,St Peter's College, New Inn Hall Street, OX1 2DL, Oxford, United Kingdom St Peter's College, New Inn Hall Street, OX1 2DL Oxford United Kingdom
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6
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Quek ZBR, Chang JJM, Ip YCA, Chan YKS, Huang D. Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms. Mol Biol Evol 2021; 38:981-985. [PMID: 33027524 PMCID: PMC7947835 DOI: 10.1093/molbev/msaa262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The mitochondrial genetic code is much more varied than the standard genetic code. The invertebrate mitochondrial code, for instance, comprises six initiation codons, including five alternative start codons. However, only two initiation codons are known in the echinoderm and flatworm mitochondrial code, the canonical ATG and alternative GTG. Here, we analyzed 23 Asteroidea mitogenomes, including ten newly sequenced species and unambiguously identified at least two other start codons, ATT and ATC, both of which also initiate translation of mitochondrial genes in other invertebrates. These findings underscore the diversity of the genetic code and expand upon the suite of initiation codons among echinoderms to avoid erroneous annotations. Our analyses have also uncovered the remarkable conservation of gene order among asteroids, echinoids, and holothuroids, with only an interchange between two gene positions in asteroids over ∼500 Ma of echinoderm evolution.
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Affiliation(s)
| | - Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yong Kit Samuel Chan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
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7
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Terraneo TI, Benzoni F, Arrigoni R, Baird AH, Mariappan KG, Forsman ZH, Wooster MK, Bouwmeester J, Marshell A, Berumen ML. Phylogenomics of Porites from the Arabian Peninsula. Mol Phylogenet Evol 2021; 161:107173. [PMID: 33813021 DOI: 10.1016/j.ympev.2021.107173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the scleractinian coral genus Porites. A total of 126 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 12 nominal and two unknown species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were compared and used to obtain thousands of genome-wide loci and SNPs. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus.
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Affiliation(s)
- Tullia I Terraneo
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, QLD, Australia.
| | - Francesca Benzoni
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Roberto Arrigoni
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; European Commission, Joint Research Centre (JRC), Ispra, Italy; Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, 80121 Napoli, Italy
| | - Andrew H Baird
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, QLD, Australia
| | - Kiruthiga G Mariappan
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Zac H Forsman
- Hawaii Institute of Marine Biology, Kaneohe 96744, HI, USA
| | - Michael K Wooster
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | | | - Alyssa Marshell
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Michael L Berumen
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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8
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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.
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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
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9
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Niu W, Yu S, Tian P, Xiao J. Complete mitochondrial genome of Echinophylliaaspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning. Zookeys 2018; 793:1-14. [PMID: 30405308 PMCID: PMC6218560 DOI: 10.3897/zookeys.793.28977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 11/23/2022] Open
Abstract
Lack of mitochondrial genome data of Scleractinia is hampering progress across genetic, systematic, phylogenetic, and evolutionary studies concerning this taxon. Therefore, in this study, the complete mitogenome sequence of the stony coral Echinophylliaaspera (Ellis & Solander, 1786), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome is 17,697 bp in length, containing 13 protein coding genes (PCGs), two transfer RNAs and two ribosomal RNAs. It has the same gene content and gene arrangement as in other Scleractinia. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND2, which uses ATT as the start codon. The A+T content of the mitochondrial genome is 65.92% (25.35% A, 40.57% T, 20.65% G, and 13.43% for C). Bayesian and maximum likelihood phylogenetic analysis have been performed using PCGs, and the result shows that E.aspera clustered closely with Sclerophylliamaxima (Sheppard & Salm, 1988), both of which belong to Lobophylliidae, when compared with species belonging to Merulinidae and other scleractinian taxa used as outgroups. The complete mitogenome of E.aspera provides essential and important DNA molecular data for further phylogenetic and evolutionary analyses of corals.
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Affiliation(s)
- Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, ChinaLaboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic AdministrationXiamenChina
| | - Shuangen Yu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, ChinaLaboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic AdministrationXiamenChina
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, ChinaLaboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic AdministrationXiamenChina
| | - Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, ChinaLaboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic AdministrationXiamenChina
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