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Law STS, Yu Y, Nong W, So WL, Li Y, Swale T, Ferrier DEK, Qiu J, Qian P, Hui JHL. The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes. Proc Biol Sci 2023; 290:20231563. [PMID: 37876192 PMCID: PMC10598428 DOI: 10.1098/rspb.2023.1563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Members of the phylum Cnidaria include sea anemones, corals and jellyfish, and have successfully colonized both marine and freshwater habitats throughout the world. The understanding of how cnidarians adapt to extreme environments such as the dark, high-pressure deep-sea habitat has been hindered by the lack of genomic information. Here, we report the first chromosome-level deep-sea cnidarian genome, of the anemone Actinernus sp., which was 1.39 Gbp in length and contained 44 970 gene models including 14 806 tRNA genes and 30 164 protein-coding genes. Analyses of homeobox genes revealed the longest chromosome hosts a mega-array of Hox cluster, HoxL, NK cluster and NKL homeobox genes; until now, such an array has only been hypothesized to have existed in ancient ancestral genomes. In addition to this striking arrangement of homeobox genes, analyses of microRNAs revealed cnidarian-specific complements that are distinctive for nested clades of these animals, presumably reflecting the progressive evolution of the gene regulatory networks in which they are embedded. Also, compared with other sea anemones, circadian rhythm genes were lost in Actinernus sp., which likely reflects adaptation to living in the dark. This high-quality genome of a deep-sea cnidarian thus reveals some of the likely molecular adaptations of this ecologically important group of metazoans to the extreme deep-sea environment. It also deepens our understanding of the evolution of genome content and organization of animals in general and cnidarians in particular, specifically from the viewpoint of key developmental control genes like the homeobox-encoding genes, where we find an array of genes that until now has only been hypothesized to have existed in the ancient ancestor that pre-dated both the cnidarians and bilaterians.
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Affiliation(s)
- Sean Tsz Sum Law
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yifei Yu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Thomas Swale
- Dovetail Genomics, LLC, Scotts Valley, CA 95066, USA
| | - David E. K. Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Jianwen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China
- Department of Biology, Hong Kong Baptist University, Hong Kong, People's Republic of China
| | - Peiyuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Jerome Ho Lam Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
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2
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Fridrich A, Salinas-Saaverda M, Kozlolvski I, Surm JM, Chrysostomou E, Tripathi AM, Frank U, Moran Y. An ancient pan-cnidarian microRNA regulates stinging capsule biogenesis in Nematostella vectensis. Cell Rep 2023; 42:113072. [PMID: 37676763 PMCID: PMC10548089 DOI: 10.1016/j.celrep.2023.113072] [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: 12/16/2022] [Revised: 07/12/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
An ancient evolutionary innovation of a novel cell type, the stinging cell (cnidocyte), appeared >600 million years ago in the phylum Cnidaria (sea anemones, corals, hydroids, and jellyfish). A complex bursting nano-injector of venom, the cnidocyst, is embedded in cnidocytes and enables cnidarians to paralyze their prey and predators, contributing to this phylum's evolutionary success. In this work, we show that post-transcriptional regulation by a pan-cnidarian microRNA, miR-2022, is essential for biogenesis of these cells in the sea anemone Nematostella vectensis. By manipulation of miR-2022 levels in a transgenic reporter line of cnidocytes, followed by transcriptomics, single-cell data analysis, prey paralysis assays, and cell sorting of transgenic cnidocytes, we reveal that miR-2022 enables cnidocyte biogenesis in Nematostella, while exhibiting a conserved expression domain with its targets in cnidocytes of other cnidarian species. Thus, here we revealed a functional basis to the conservation of one of nature's most ancient microRNAs.
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Affiliation(s)
- Arie Fridrich
- Department of Ecology Evolution and Behavior, Faculty of Science, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel; Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria.
| | | | - Itamar Kozlolvski
- Department of Ecology Evolution and Behavior, Faculty of Science, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joachim M Surm
- Department of Ecology Evolution and Behavior, Faculty of Science, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Abhinandan M Tripathi
- Department of Ecology Evolution and Behavior, Faculty of Science, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uri Frank
- Centre for Chromosome Biology, University of Galway, Galway, Ireland
| | - Yehu Moran
- Department of Ecology Evolution and Behavior, Faculty of Science, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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3
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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4
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Li Y, Hui JHL. Small RNAs in Cnidaria: A review. Evol Appl 2023; 16:354-364. [PMID: 36793685 PMCID: PMC9923473 DOI: 10.1111/eva.13445] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/18/2022] [Accepted: 06/17/2022] [Indexed: 11/30/2022] Open
Abstract
As fundamental components of RNA silencing, small RNA (sRNA) molecules ranging from 20 to 32 nucleotides in length have been found as potent regulators of gene expression and genome stability in many biological processes of eukaryotes. Three major small RNAs are active in animals, including the microRNA (miRNA), short interfering RNA (siRNA), and PIWI-interacting RNA (piRNA). Cnidarians, the sister group to bilaterians, are at a critical phylogenetic node to better model eukaryotic small RNA pathway evolution. To date, most of our understanding of sRNA regulation and its potential contribution to evolution has been limited to a few triploblastic bilaterian and plant models. The diploblastic nonbilaterians, including the cnidarians, are understudied in this regard. Therefore, this review will present the current-known small RNA information in cnidarians to enhance our understanding of the development of the small RNA pathways in early branch animals.
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Affiliation(s)
- Yiqian Li
- Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life Sciences The Chinese University of Hong Kong Hong Kong City Hong Kong
| | - Jerome H L Hui
- Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life Sciences The Chinese University of Hong Kong Hong Kong City Hong Kong
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5
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Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ 2023; 11:e15023. [PMID: 37151292 PMCID: PMC10162043 DOI: 10.7717/peerj.15023] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 05/09/2023] Open
Abstract
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, MA, United States
| | - Matthew H. Gamache
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
| | | | | | - Andrew C. Baker
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Anastazia T. Banaszak
- Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Line Kolind Bay
- Australian Institute of Marine Science, Townsville, Australia
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danielle C. Claar
- Nearshore Habitat Program, Washington State Department of Natural Resources, Olympia, WA, USA
| | | | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, United States
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Javier del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Jörg C. Frommlet
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Raúl A. González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Department of Biology, Pennsylvania State University, State College, PA, United States
| | - Tamar L. Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Kenneth D. Hoadley
- Department of Biological Sciences, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Emily J. Howells
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | | | - Dustin W. Kemp
- Department of Biology, University of Alabama—Birmingham, Birmingham, Al, United States
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Todd C. LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Mansfield, CT, United States
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ryan McMinds
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, United States
| | | | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raquel S. Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | | | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - James Davis Reimer
- Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | - Stephanie M. Rosales
- The Cooperative Institute For Marine and Atmospheric Studies, Miami, FL, United States
| | - Osama S. Saad
- Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Eugenia M. Sampayo
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott R. Santos
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Edward G. Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Marie E. Strader
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - David J. Suggett
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy D. Swain
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, United States
| | - Cawa Tran
- Department of Biology, University of San Diego, San Diego, CA, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | | | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Rachel M. Wright
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, United States
| | - Tingting Xiang
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen (Germany), Giessen, Germany
| | | | - John Everett Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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6
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Puntin G, Sweet M, Fraune S, Medina M, Sharp K, Weis VM, Ziegler M. Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont. Microbiol Mol Biol Rev 2022; 86:e0005322. [PMID: 36287022 PMCID: PMC9769930 DOI: 10.1128/mmbr.00053-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.
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Affiliation(s)
- Giulia Puntin
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Sebastian Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Koty Sharp
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, Rhode Island, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
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7
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Shum CW, Nong W, So WL, Li Y, Qu Z, Yip HY, Swale T, Ang PO, Chan KM, Chan TF, Chu KH, Chui AP, Lau KF, Ngai SM, Xu F, Hui JH. Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration. Front Cell Dev Biol 2022; 10:900321. [PMID: 36072338 PMCID: PMC9444052 DOI: 10.3389/fcell.2022.900321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/08/2022] [Indexed: 12/19/2022] Open
Abstract
Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how non-coding RNAs such as microRNAs (also known as miRNAs) contribute to cnidarian tissue regeneration is poorly understood. Here, we sequenced and assembled the genome of the sea anemone Exaiptasia pallida collected in Hong Kong waters. The assembled genome size of E. pallida is 229.21 Mb with a scaffold N50 of 10.58 Mb and BUSCO completeness of 91.1%, representing a significantly improved genome assembly of this species. The organization of ANTP-class homeobox genes in this anthozoan further supported the previous findings in jellyfishes, where most of these genes are mainly located on three scaffolds. Tentacles of E. pallida were excised, and both mRNA and miRNA were sequenced at 9 time points (0 h, 6 h, 12 h, 18 h, 1 day, 2, 3, 6, and 8 days) from regenerating tentacles. In addition to the Wnt signaling pathway and homeobox genes that are shown to be likely involved in tissue regeneration as in other cnidarians, we have shown that GLWamide neuropeptides, and for the first time sesquiterpenoid pathway genes could potentially be involved in the late phase of cnidarian tissue regeneration. The established sea anemone model will be useful for further investigation of biology and evolution in, and the effect of climate change on this important group of animals.
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Affiliation(s)
- Cheryl W.Y. Shum
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Thomas Swale
- Dovetail Genomics, Scotts Valley, CA, United States
| | - Put O. Ang
- Institute of Space and Earth Information Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - King Ming Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Apple P.Y. Chui
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwok Fai Lau
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Sai Ming Ngai
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Fei Xu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jerome H.L. Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- *Correspondence: Jerome H.L. Hui,
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8
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Zhu Y, Liao X, Han T, Chen JY, He C, Lu Z. Symbiodiniaceae microRNAs and their targeting sites in coral holobionts: A transcriptomics-based exploration. Genomics 2022; 114:110404. [PMID: 35714829 DOI: 10.1016/j.ygeno.2022.110404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/30/2022] [Accepted: 06/09/2022] [Indexed: 01/23/2023]
Abstract
Corals should make excellent models for cross-kingdom research because of their natural animal-photobiont holobiont composition, yet a lack of studies and experimental data restricts their use. Here we integrate new full-length transcriptomes and small RNAs of four common reef-building corals with the published Cladocopium genomes to gain deeper insight into gene regulation in coral-Symbiodiniaceae holobionts. Eleven novel Symbiodiniaceae miRNAs get identified, and enrichment results of their target genes show that they might play a role in downregulating rejection from host coral cells, protecting symbiont from autophagy and apoptosis in parallel. This work provides evidence for the early origin of cross-kingdom regulation as a mechanism of self-defense autotrophs can use against heterotrophs, sheds more light on coral-Symbiodiniaceae holobionts, and contributes valuable data for further coral research.
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Affiliation(s)
- Yunchi Zhu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China
| | - Xin Liao
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai, Guangxi, China
| | - Tingyu Han
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China
| | - J-Y Chen
- Nanjing Institute of Paleontology and Geology, Nanjing, China
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China.
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China.
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9
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Symbiosis with Dinoflagellates Alters Cnidarian Cell-Cycle Gene Expression. Cell Microbiol 2022. [DOI: 10.1155/2022/3330160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the cnidarian-dinoflagellate symbiosis, hosts show altered expression of genes involved in growth and proliferation when in the symbiotic state, but little is known about the molecular mechanisms that underlie the host’s altered growth rate. Using tissue-specific transcriptomics, we determined how symbiosis affects expression of cell cycle-associated genes, in the model symbiotic cnidarian Exaiptasia diaphana (Aiptasia). The presence of symbionts within the gastrodermis elicited cell-cycle arrest in the G1 phase in a larger proportion of host cells compared with the aposymbiotic gastrodermis. The symbiotic gastrodermis also showed a reduction in the amount of cells synthesizing their DNA and progressing through mitosis when compared with the aposymbiotic gastrodermis. Host apoptotic inhibitors (Mdm2) were elevated, while host apoptotic sensitizers (c-Myc) were depressed, in the symbiotic gastrodermis when compared with the aposymbiotic gastrodermis and epidermis of symbiotic anemones, respectively. This indicates that the presence of symbionts negatively regulates host apoptosis, possibly contributing to their persistence within the host. Transcripts (ATM/ATR) associated with DNA damage were also downregulated in symbiotic gastrodermal tissues. In epidermal cells, a single gene (Mob1) required for mitotic completion was upregulated in symbiotic compared with aposymbiotic anemones, suggesting that the presence of symbionts in the gastrodermis stimulates host cell division in the epidermis. To further corroborate this hypothesis, we performed microscopic analysis using an S-phase indicator (EdU), allowing us to evaluate cell cycling in host cells. Our results confirmed that there were significantly more proliferating host cells in both the gastrodermis and epidermis in the symbiotic state compared with the aposymbiotic state. Furthermore, when comparing between tissue layers in the presence of symbionts, the epidermis had significantly more proliferating host cells than the symbiont-containing gastrodermis. These results contribute to our understanding of the influence of symbionts on the mechanisms of cnidarian cell proliferation and mechanisms associated with symbiont maintenance.
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10
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Dimond JL, Nguyen N, Roberts SB. DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING. G3-GENES GENOMES GENETICS 2021; 11:6275752. [PMID: 33989381 PMCID: PMC8496274 DOI: 10.1093/g3journal/jkab148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/15/2021] [Indexed: 11/20/2022]
Abstract
Symbiosis with protists is common among cnidarians such as corals and sea anemones and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species.
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Affiliation(s)
- James L Dimond
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98195 USA.,Western Washington University, Shannon Point Marine Center, 1900 Shannon Point Rd., Anacortes, WA 98221 USA
| | - Nhung Nguyen
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY 14456 USA.,South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98195 USA
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11
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Abstract
One of the most important events in an animal's life history is the initial colonization by its microbial symbionts, yet little is known about this event's immediate impacts on the extent of host gene expression or the molecular mechanisms controlling it. MicroRNAs (miRNAs) are short, noncoding RNAs that bind to target mRNAs, rapidly shaping gene expression by posttranscriptional control of mRNA translation and decay. Here, we show that, in the experimentally tractable binary squid-vibrio symbiosis, colonization of the light organ induces extensive changes in the miRNA transcriptome. Examination of the squid genome revealed the presence of evolutionarily conserved genes encoding elements essential for the production and processing of miRNAs. At 24 h postcolonization, 215 host miRNAs were detected in the light organ, 26 of which were differentially expressed in response to the symbionts. A functional enrichment analysis of genes potentially targeted by downregulation of certain miRNAs at the initiation of symbiosis revealed two major gene ontology (GO) term categories, neurodevelopment and tissue remodeling. This symbiont-induced downregulation is predicted to promote these activities in host tissues and is consistent with the well-described tissue remodeling that occurs at the onset of the association. Conversely, predicted targets of upregulated miRNAs, including the production of mucus, are consistent with attenuation of immune responses by symbiosis. Taken together, our data provide evidence that, at the onset of symbiosis, host miRNAs in the light organ drive alterations in gene expression that (i) orchestrate the symbiont-induced development of host tissues, and (ii) facilitate the partnership by dampening the immune response.IMPORTANCE Animals often acquire their microbiome from the environment at each generation, making the initial interaction of the partners a critical event in the establishment and development of a stable, healthy symbiosis. However, the molecular nature of these earliest interactions is generally difficult to study and poorly understood. We report that, during the initial 24 h of the squid-vibrio association, a differential expression of host miRNAs is triggered by the presence of the microbial partner. Predicted mRNA targets of these miRNAs were associated with regulatory networks that drive tissue remodeling and immune suppression, two major symbiosis-induced developmental outcomes in this and many other associations. These results implicate regulation by miRNAs as key to orchestrating the critical transcriptional responses that occur very early during the establishment of a symbiosis. Animals with more complex microbiota may have similar miRNA-driven responses as their association is initiated, supporting an evolutionary conservation of symbiosis-induced developmental mechanisms.
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12
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Pillai A, Gungi A, Reddy PC, Galande S. Epigenetic Regulation in Hydra: Conserved and Divergent Roles. Front Cell Dev Biol 2021; 9:663208. [PMID: 34041242 PMCID: PMC8141815 DOI: 10.3389/fcell.2021.663208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Transitions in gene regulatory processes responsible for the emergence of specialized cell types and spatiotemporal regulation of developmental signaling prior to the divergence of Cnidaria and Bilateria are poorly understood. As a sister group of Bilateria, the phylum Cnidaria can provide significant insights into these processes. Among the cnidarians, hydrae have been studied for >250 years to comprehend the mechanisms underlying their unique immortality and robust regenerative capacity. Studies on Hydra spp. and other pre-bilaterians alike have advanced our understanding of the evolutionary underpinnings governing eumetazoan tissue development, homeostasis, and regeneration. In addition to its regenerative potential, Hydra exhibits continuously active axial patterning due to its peculiar tissue dynamics. These distinctive physiological processes necessitate large scale gene expression changes that are governed by the multitude of epigenetic mechanisms operating in cells. This review highlights the contemporary knowledge of epigenetic regulation in Hydra with contemporary studies from other members of Cnidaria, as well as the interplay between regulatory mechanisms wherever demonstrated. The studies covered in the scope of this review reveal both ancestral and divergent roles played by conserved epigenetic mechanisms with emphasis on transcriptional regulation. Additionally, single-cell transcriptomics data was mined to predict the physiological relevance of putative gene regulatory components, which is in agreement with published findings and yielded insights into the possible functions of the gene regulatory mechanisms that are yet to be deciphered in Hydra, such as DNA methylation. Finally, we delineate potentially rewarding epigenetics research avenues that can further leverage the unique biology of Hydra.
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Affiliation(s)
| | | | - Puli Chandramouli Reddy
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, India
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13
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Praher D, Zimmermann B, Dnyansagar R, Miller DJ, Moya A, Modepalli V, Fridrich A, Sher D, Friis-Møller L, Sundberg P, Fôret S, Ashby R, Moran Y, Technau U. Conservation and turnover of miRNAs and their highly complementary targets in early branching animals. Proc Biol Sci 2021; 288:20203169. [PMID: 33622129 PMCID: PMC7935066 DOI: 10.1098/rspb.2020.3169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/25/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) are crucial post-transcriptional regulators that have been extensively studied in Bilateria, a group comprising the majority of extant animals, where more than 30 conserved miRNA families have been identified. By contrast, bilaterian miRNA targets are largely not conserved. Cnidaria is the sister group to Bilateria and thus provides a unique opportunity for comparative studies. Strikingly, like their plant counterparts, cnidarian miRNAs have been shown to predominantly have highly complementary targets leading to transcript cleavage by Argonaute proteins. Here, we assess the conservation of miRNAs and their targets by small RNA sequencing followed by miRNA target prediction in eight species of Anthozoa (sea anemones and corals), the earliest-branching cnidarian class. We uncover dozens of novel miRNAs but only a few conserved ones. Further, given their high complementarity, we were able to computationally identify miRNA targets in each species. Besides evidence for conservation of specific miRNA target sites, which are maintained between sea anemones and stony corals across 500 Myr of evolution, we also find indications for convergent evolution of target regulation by different miRNAs. Our data indicate that cnidarians have only few conserved miRNAs and corresponding targets, despite their high complementarity, suggesting a high evolutionary turnover.
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Affiliation(s)
- Daniela Praher
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Rohit Dnyansagar
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - David J. Miller
- Department of Molecular and Cell Biology, Comparative Genomics Centre, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Aurelie Moya
- Department of Molecular and Cell Biology, Comparative Genomics Centre, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, UK
| | - Arie Fridrich
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Lene Friis-Møller
- Danish Shellfish Centre, DTU Aqua, Technical University of Denmark, Lyngby, Denmark
| | - Per Sundberg
- Department of Zoology, University of Gothenburg, Gothenburg, Sweden
| | - Sylvain Fôret
- Health Research Institute, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, Australia
| | - Regan Ashby
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ulrich Technau
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
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14
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Cleves PA, Krediet CJ, Lehnert EM, Onishi M, Pringle JR. Insights into coral bleaching under heat stress from analysis of gene expression in a sea anemone model system. Proc Natl Acad Sci U S A 2020; 117:28906-28917. [PMID: 33168733 PMCID: PMC7682557 DOI: 10.1073/pnas.2015737117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Loss of endosymbiotic algae ("bleaching") under heat stress has become a major problem for reef-building corals worldwide. To identify genes that might be involved in triggering or executing bleaching, or in protecting corals from it, we used RNAseq to analyze gene-expression changes during heat stress in a coral relative, the sea anemone Aiptasia. We identified >500 genes that showed rapid and extensive up-regulation upon temperature increase. These genes fell into two clusters. In both clusters, most genes showed similar expression patterns in symbiotic and aposymbiotic anemones, suggesting that this early stress response is largely independent of the symbiosis. Cluster I was highly enriched for genes involved in innate immunity and apoptosis, and most transcript levels returned to baseline many hours before bleaching was first detected, raising doubts about their possible roles in this process. Cluster II was highly enriched for genes involved in protein folding, and most transcript levels returned more slowly to baseline, so that roles in either promoting or preventing bleaching seem plausible. Many of the genes in clusters I and II appear to be targets of the transcription factors NFκB and HSF1, respectively. We also examined the behavior of 337 genes whose much higher levels of expression in symbiotic than aposymbiotic anemones in the absence of stress suggest that they are important for the symbiosis. Unexpectedly, in many cases, these expression levels declined precipitously long before bleaching itself was evident, suggesting that loss of expression of symbiosis-supporting genes may be involved in triggering bleaching.
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Affiliation(s)
- Phillip A Cleves
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Cory J Krediet
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Department of Marine Science, Eckerd College, St. Petersburg, FL 33711
| | - Erik M Lehnert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Masayuki Onishi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - John R Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305;
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15
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Rosset SL, Oakley CA, Ferrier-Pagès C, Suggett DJ, Weis VM, Davy SK. The Molecular Language of the Cnidarian-Dinoflagellate Symbiosis. Trends Microbiol 2020; 29:320-333. [PMID: 33041180 DOI: 10.1016/j.tim.2020.08.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 12/18/2022]
Abstract
The cnidarian-dinoflagellate symbiosis is of huge importance as it underpins the success of coral reefs, yet we know very little about how the host cnidarian and its dinoflagellate endosymbionts communicate with each other to form a functionally integrated unit. Here, we review the current knowledge of interpartner molecular signaling in this symbiosis, with an emphasis on lipids, glycans, reactive species, biogenic volatiles, and noncoding RNA. We draw upon evidence of these compounds from recent omics-based studies of cnidarian-dinoflagellate symbiosis and discuss the signaling roles that they play in other, better-studied symbioses. We then consider how improved knowledge of interpartner signaling might be used to develop solutions to the coral reef crisis by, for example, engineering more thermally resistant corals.
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Affiliation(s)
- Sabrina L Rosset
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | | | - David J Suggett
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, PO Box 123, Broadway NSW 2007, Australia
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.
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16
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RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res 2020; 47:D221-D229. [PMID: 30395267 PMCID: PMC6324050 DOI: 10.1093/nar/gky1034] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022] Open
Abstract
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org.
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Affiliation(s)
- The RNAcentral Consortium
http://orcid.org/0000-0002-6497-2883SweeneyBlake Ahttp://orcid.org/0000-0001-7279-2682PetrovAnton IBurkovBorishttp://orcid.org/0000-0001-8626-2148FinnRobert Dhttp://orcid.org/0000-0002-6982-4660BatemanAlexSzymanskiMaciejKarlowskiWojciech MGorodkinJanSeemannStefan ECannoneJamie JGutellRobin RFeyPetraBasuSiddharthaKaySimonhttp://orcid.org/0000-0001-7954-7057CochraneGuyBillisKostantinosEmmertDavidMarygoldSteven Jhttp://orcid.org/0000-0001-6718-3559HuntleyRachael Phttp://orcid.org/0000-0002-9791-0064LoveringRuth CFrankishAdamChanPatricia Phttp://orcid.org/0000-0003-3253-6021LoweTodd Mhttp://orcid.org/0000-0002-8380-5247BrufordElspethSealRuthhttp://orcid.org/0000-0001-6274-0184VandesompeleJohttp://orcid.org/0000-0002-2685-2637VoldersPieter-JanParaskevopoulouMariaMaLinaZhangZhangGriffiths-JonesSamBujnickiJanusz MBoccalettoPietrohttp://orcid.org/0000-0001-8522-334XBlakeJudith ABultCarol JChenRunshengZhaoYiWoodValerieRutherfordKimhttp://orcid.org/0000-0002-2084-269XRivasElenaColeJameshttp://orcid.org/0000-0001-5356-4174LaulederkindStanley J FShimoyamaMaryGillespieMarc EOrlic-MilacicMarijahttp://orcid.org/0000-0001-9424-9197KalvariIoannahttp://orcid.org/0000-0002-2497-3427NawrockiEricEngelStacia Rhttp://orcid.org/0000-0001-9163-5180CherryJ MichaelTeamSILVABerardiniTanya ZHatzigeorgiouArtemisKaragkouniDimitrahttp://orcid.org/0000-0002-1751-9226HoweKevinDavisPaulDingerMarcelhttp://orcid.org/0000-0002-7294-0865HeShunminYoshihamaMakiKenmochiNaoyaStadlerPeter FWilliamsKelly P
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- Institute for Cellular and Molecular Biology, and the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
- dictyBase, Northwestern University, 420 E. Superior St., Chicago, IL 60611, USA
- Department of Molecular and Cellular Biology, Harvard University, Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02140, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
- Institute of Cardiovascular Science, University College London, London, UK
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece
- Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
- Ghent University and Cancer Research Institute Ghent, 9000 Ghent, Belgium
- St Vincent's Clinical School, UNSW Sydney, Sydney, Australia
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609, USA
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
- Cambridge Systems Biology and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, Cambridgeshire CB2 1GA, UK
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- College of Pharmacy and Health Sciences, St John's University, Queens, NY 11439, USA
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
- Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI 53226, USA
- Department of Genetics, Stanford University, Palo Alto, CA 94304 USA
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen
- Jacobs University Bremen, School of Engineering and Science, D-28759 Bremen
- Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
- Phoenix Bioinformatics, Fremont, CA 94538, USA
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstr. 1618, 04107 Leipzig, Germany
- Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universität Leipzig, Ritterstrasse 9–13, 04109 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Insel Strasse 22, 04103 Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, 04103 Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
- Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
- To whom correspondence should be addressed. Tel: +44 1223 492550; Fax: +44 1223 494468;
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17
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Leitão AL, Costa MC, Gabriel AF, Enguita FJ. Interspecies Communication in Holobionts by Non-Coding RNA Exchange. Int J Mol Sci 2020; 21:ijms21072333. [PMID: 32230931 PMCID: PMC7177868 DOI: 10.3390/ijms21072333] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 12/18/2022] Open
Abstract
Complex organisms are associations of different cells that coexist and collaborate creating a living consortium, the holobiont. The relationships between the holobiont members are essential for proper homeostasis of the organisms, and they are founded on the establishment of complex inter-connections between all the cells. Non-coding RNAs are regulatory molecules that can also act as communication signals between cells, being involved in either homeostasis or dysbiosis of the holobionts. Eukaryotic and prokaryotic cells can transmit signals via non-coding RNAs while using specific extracellular conveyors that travel to the target cell and can be translated into a regulatory response by dedicated molecular machinery. Within holobionts, non-coding RNA regulatory signaling is involved in symbiotic and pathogenic relationships among the cells. This review analyzes current knowledge regarding the role of non-coding RNAs in cell-to-cell communication, with a special focus on the signaling between cells in multi-organism consortia.
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Affiliation(s)
- Ana Lúcia Leitão
- Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal;
- MEtRICs, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Marina C. Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.C.); (A.F.G.)
| | - André F. Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.C.); (A.F.G.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.C.); (A.F.G.)
- Correspondence: ; Tel.: +351-217999480
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18
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Cziesielski MJ, Schmidt‐Roach S, Aranda M. The past, present, and future of coral heat stress studies. Ecol Evol 2019; 9:10055-10066. [PMID: 31534713 PMCID: PMC6745681 DOI: 10.1002/ece3.5576] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023] Open
Abstract
The global loss and degradation of coral reefs, as a result of intensified frequency and severity of bleaching events, is a major concern. Evidence of heat stress affecting corals through loss of symbionts and consequent coral bleaching was first reported in the 1930s. However, it was not until the 1998 major global bleaching event that the urgency for heat stress studies became internationally recognized. Current efforts focus not only on examining the consequences of heat stress on corals but also on finding strategies to potentially improve thermal tolerance and aid coral reefs survival in future climate scenarios. Although initial studies were limited in comparison with modern technological tools, they provided the foundation for many of today's research methods and hypotheses. Technological advancements are providing new research prospects at a rapid pace. Understanding how coral heat stress studies have evolved is important for the critical assessment of their progress. This review summarizes the development of the field to date and assesses avenues for future research.
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Affiliation(s)
- Maha J. Cziesielski
- Red Sea Research CenterDivision of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Sebastian Schmidt‐Roach
- Red Sea Research CenterDivision of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Manuel Aranda
- Red Sea Research CenterDivision of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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19
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Fridrich A, Hazan Y, Moran Y. Too Many False Targets for MicroRNAs: Challenges and Pitfalls in Prediction of miRNA Targets and Their Gene Ontology in Model and Non-model Organisms. Bioessays 2019; 41:e1800169. [PMID: 30919506 PMCID: PMC6701991 DOI: 10.1002/bies.201800169] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 01/28/2019] [Indexed: 12/20/2022]
Abstract
Short ("seed") or extended base pairing between microRNAs (miRNAs) and their target RNAs enables post-transcriptional silencing in many organisms. These interactions allow the computational prediction of potential targets. In model organisms, predicted targets are frequently validated experimentally; hence meaningful miRNA-regulated processes are reported. However, in non-models, these reports mostly rely on computational prediction alone. Many times, further bioinformatic analyses such as Gene Ontology (GO) enrichment are based on these in silico projections. Here such approaches are reviewed, their caveats are highlighted and the ease of picking false targets from predicted lists is demonstrated. Discoveries that shed new light on how miRNAs evolved to regulate targets in various phyletic groups are discussed, in addition to the pitfalls of target identification in non-model organisms. The goal is to prevent the misuse of bioinformatic tools, as they cannot bypass the biological understanding of miRNA-target regulation.
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Affiliation(s)
- Arie Fridrich
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yael Hazan
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
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20
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Graham AM, Barreto FS. Novel microRNAs are associated with population divergence in transcriptional response to thermal stress in an intertidal copepod. Mol Ecol 2018; 28:584-599. [PMID: 30548575 DOI: 10.1111/mec.14973] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 12/29/2022]
Abstract
The role of gene expression in adaptation to differing thermal environments has been assayed extensively. Yet, in most natural systems, analyses of gene expression reveal only one level of the complexity of regulatory machineries. MicroRNAs (miRNAs) are small noncoding RNAs which are key components of many gene regulatory networks, and they play important roles in a variety of cellular pathways by modulating post-transcriptional quantities of mRNA available for protein synthesis. The characterization of miRNA loci and their regulatory dynamics in nonmodel systems are still largely understudied. In this study, we examine the role of miRNAs in response to high thermal stress in the intertidal copepod Tigriopus californicus. Allopatric populations of this species show varying levels of local adaptation with respect to thermal regimes, and previous studies showed divergence in gene expression between populations from very different thermal environments. We examined the transcriptional response to temperature stress in two populations separated by only 8 km by utilizing RNA-seq to quantify both mRNA and miRNA levels. Using the currently available genome sequence, we first describe the repertoire of miRNAs in T. californicus and assess the degree to which transcriptional response to temperature stress is governed by miRNA activity. The two populations showed large differences in the number of genes involved, the magnitude of change in commonly used genes and in the number of miRNAs involved in transcriptional modulation during stress. Our results suggest that an increased level of regulatory network complexity may underlie improved survivorship under thermal stress in one of the populations.
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Affiliation(s)
- Allie M Graham
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon
| | - Felipe S Barreto
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon
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21
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Calcino AD, Fernandez-Valverde SL, Taft RJ, Degnan BM. Diverse RNA interference strategies in early-branching metazoans. BMC Evol Biol 2018; 18:160. [PMID: 30382896 PMCID: PMC6211395 DOI: 10.1186/s12862-018-1274-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Micro RNAs (miRNAs) and piwi interacting RNAs (piRNAs), along with the more ancient eukaryotic endogenous small interfering RNAs (endo-siRNAs) constitute the principal components of the RNA interference (RNAi) repertoire of most animals. RNAi in non-bilaterians - sponges, ctenophores, placozoans and cnidarians - appears to be more diverse than that of bilaterians, and includes structurally variable miRNAs in sponges, an enormous number of piRNAs in cnidarians and the absence of miRNAs in ctenophores and placozoans. RESULTS Here we identify thousands of endo-siRNAs and piRNAs from the sponge Amphimedon queenslandica, the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis using a computational approach that clusters mapped small RNA sequences and annotates each cluster based on the read length and relative abundance of the constituent reads. This approach was validated on 11 small RNA libraries in Drosophila melanogaster, demonstrating the successful annotation of RNAi-associated loci with properties consistent with previous reports. In the non-bilaterians we uncover seven new miRNAs from Amphimedon and four from Nematostella as well as sub-populations of candidate cis-natural antisense transcript (cis-NAT) endo-siRNAs. We confirmed the absence of miRNAs in Mnemiopsis but detected an abundance of endo-siRNAs in this ctenophore. Analysis of putative piRNA structure suggests that conserved localised secondary structures in primary transcripts may be important for the production of mature piRNAs in Amphimedon and Nematostella, as is also the case for endo-siRNAs. CONCLUSION Together, these findings suggest that the last common ancestor of extant animals did not have the entrained RNAi system that typifies bilaterians. Instead it appears that bilaterians, cnidarians, ctenophores and sponges express unique repertoires and combinations of miRNAs, piRNAs and endo-siRNAs.
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Affiliation(s)
- Andrew D Calcino
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: Department of Integrative Zoology, University of Vienna, Althanstraße 1, 4A-1090, Vienna, Austria
| | - Selene L Fernandez-Valverde
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: CONACYT, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio). CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Ryan J Taft
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia.,Illumina Inc, San Diego, California, 92122, USA
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
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22
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Barfield SJ, Aglyamova GV, Bay LK, Matz MV. Contrasting effects of
Symbiodinium
identity on coral host transcriptional profiles across latitudes. Mol Ecol 2018; 27:3103-3115. [DOI: 10.1111/mec.14774] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/29/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Sarah J. Barfield
- Department of Integrative Biology University of Texas at Austin Austin Texas
| | - Galina V. Aglyamova
- Department of Integrative Biology University of Texas at Austin Austin Texas
| | - Line K. Bay
- Australian Institute of Marine Science Townsville QLD Australia
| | - Mikhail V. Matz
- Department of Integrative Biology University of Texas at Austin Austin Texas
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23
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Bellis ES, Edlund RB, Berrios HK, Lessios HA, Denver DR. Molecular signatures of host specificity linked to habitat specialization in Exaiptasia sea anemones. Ecol Evol 2018; 8:5413-5426. [PMID: 29938062 PMCID: PMC6010850 DOI: 10.1002/ece3.4058] [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] [Received: 01/30/2018] [Revised: 02/24/2018] [Accepted: 02/27/2018] [Indexed: 12/17/2022] Open
Abstract
Rising ocean temperatures associated with global climate change induce breakdown of the symbiosis between coelenterates and photosynthetic microalgae of the genus Symbiodinium. Association with more thermotolerant partners could contribute to resilience, but the genetic mechanisms controlling specificity of hosts for particular Symbiodinium types are poorly known. Here, we characterize wild populations of a sea anemone laboratory model system for anthozoan symbiosis, from contrasting environments in Caribbean Panama. Patterns of anemone abundance and symbiont diversity were consistent with specialization of holobionts for particular habitats, with Exaiptasia pallida/S. minutum (ITS2 type B1) abundant on vertical substrate in thermally stable, shaded environments but E. brasiliensis/Symbiodinium sp. (ITS2 clade A) more common in shallow areas subject to high temperature and irradiance. Population genomic sequencing revealed a novel E. pallida population from the Bocas del Toro Archipelago that only harbors S. minutum. Loci most strongly associated with divergence of the Bocas-specific population were enriched in genes with putative roles in cnidarian symbiosis, including activators of the complement pathway of the innate immune system, thrombospondin-type-1 repeat domain proteins, and coordinators of endocytic recycling. Our findings underscore the importance of unmasking cryptic diversity in natural populations and the role of long-term evolutionary history in mediating interactions with Symbiodinium.
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Affiliation(s)
- Emily S. Bellis
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
| | - Reid. B. Edlund
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
| | - Hazel K. Berrios
- Department of Biological SciencesArkansas State UniversityJonesboroArkansas
| | | | - Dee R. Denver
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
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24
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Merselis DG, Lirman D, Rodriguez-Lanetty M. Symbiotic immuno-suppression: is disease susceptibility the price of bleaching resistance? PeerJ 2018; 6:e4494. [PMID: 29682405 PMCID: PMC5909685 DOI: 10.7717/peerj.4494] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/22/2018] [Indexed: 12/11/2022] Open
Abstract
Accelerating anthropogenic climate change threatens to destroy coral reefs worldwide through the processes of bleaching and disease. These major contributors to coral mortality are both closely linked with thermal stress intensified by anthropogenic climate change. Disease outbreaks typically follow bleaching events, but a direct positive linkage between bleaching and disease has been debated. By tracking 152 individual coral ramets through the 2014 mass bleaching in a South Florida coral restoration nursery, we revealed a highly significant negative correlation between bleaching and disease in the Caribbean staghorn coral, Acropora cervicornis. To explain these results, we propose a mechanism for transient immunological protection through coral bleaching: removal of Symbiodinium during bleaching may also temporarily eliminate suppressive symbiont modulation of host immunological function. We contextualize this hypothesis within an ecological perspective in order to generate testable predictions for future investigation.
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Affiliation(s)
- Daniel G Merselis
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Diego Lirman
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, USA
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