1
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Munley KM, Hoadley AP, Alward BA. A phylogenetics-based nomenclature system for steroid receptors in teleost fishes. Gen Comp Endocrinol 2024; 347:114436. [PMID: 38141859 DOI: 10.1016/j.ygcen.2023.114436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 12/25/2023]
Abstract
Teleost fishes have emerged as tractable models for studying the neuroendocrine regulation of social behavior via molecular genetic techniques, such as CRISPR/Cas9 gene editing. Moreover, teleosts provide an opportunity to investigate the evolution of steroid receptors and their functions, as species within this lineage possess novel steroid receptor paralogs that resulted from a teleost-specific whole genome duplication. Although teleost fishes have grown in popularity as models for behavioral neuroendocrinology, there is not a consistent nomenclature system for steroid receptors and their genes, which may impede a clear understanding of steroid receptor paralogs and their functions. Here, we used a phylogenetic approach to assess the relatedness of protein sequences encoding steroid receptor paralogs in 18 species from 12 different orders of the Infraclass Teleostei. While most similarly named sequences grouped based on the established phylogeny of the teleost lineage, our analysis revealed several inconsistencies in the nomenclature of steroid receptor paralogs, particularly for sequences encoding estrogen receptor beta (ERβ). Based on our results, we propose a nomenclature system for teleosts in which Greek symbols refer to proteins and numbers refer to genes encoding different subtypes of steroid receptors within the five major groups of this nuclear receptor subfamily. Collectively, our results bridge a critical gap by providing a cohesive naming system for steroid receptors in teleost fishes, which will serve to improve communication, promote collaboration, and enhance our understanding of the evolution and function of steroid receptors across vertebrates.
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Affiliation(s)
| | - Andrew P Hoadley
- Department of Psychology, University of Houston, Houston, TX, USA
| | - Beau A Alward
- Department of Psychology, University of Houston, Houston, TX, USA; Department of Biology and Biochemistry, University of Houston, Houston, TX, USA.
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2
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Gendron ME, Buston PM. Review of housing and husbandry of anemonefishes for use in research. JOURNAL OF FISH BIOLOGY 2023; 103:924-938. [PMID: 37354451 DOI: 10.1111/jfb.15492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/23/2023] [Indexed: 06/26/2023]
Abstract
Anemonefishes of the genus Amphiprion are emerging as a model organism for marine science, so there is potentially a lot for the research community to gain by optimizing and standardizing housing and husbandry protocols. Here, we conducted a literature review and a questionnaire survey regarding the housing and husbandry of anemonefishes for use in research. The questionnaire survey was completed by 27 laboratories, with a 45% response rate, across 11 different countries in Europe, North America, Asia and Australia. Results from the literature review identified that housing and husbandry protocols varied widely in terms of tank volume, diet composition and lighting type for the housing of broodstock pairs. These results also emphasize the significant impacts that variation in housing and husbandry protocols have on fish. Results from the questionnaire survey confirmed this. We identified multiple opportunities for improvement of protocols, including the potential for exchange of larvae between laboratories to create strains and reduce pressure on natural populations. In conclusion, our research suggests that the anemonefish research community should be discussing the optimization and standardization of housing and husbandry or, minimally, recognizing that housing and husbandry influence a wide range of traits and will influence the results and conclusions drawn from experiments.
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Affiliation(s)
- Matthew E Gendron
- Department of Biology and Marine Program, Boston University, Boston, Massachusetts, USA
| | - Peter M Buston
- Department of Biology and Marine Program, Boston University, Boston, Massachusetts, USA
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3
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Herrera M, Ravasi T, Laudet V. Anemonefishes: A model system for evolutionary genomics. F1000Res 2023; 12:204. [PMID: 37928172 PMCID: PMC10624958 DOI: 10.12688/f1000research.130752.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 11/07/2023] Open
Abstract
Anemonefishes are an iconic group of coral reef fish particularly known for their mutualistic relationship with sea anemones. This mutualism is especially intriguing as it likely prompted the rapid diversification of anemonefish. Understanding the genomic architecture underlying this process has indeed become one of the holy grails of evolutionary research in these fishes. Recently, anemonefishes have also been used as a model system to study the molecular basis of highly complex traits such as color patterning, social sex change, larval dispersal and life span. Extensive genomic resources including several high-quality reference genomes, a linkage map, and various genetic tools have indeed enabled the identification of genomic features controlling some of these fascinating attributes, but also provided insights into the molecular mechanisms underlying adaptive responses to changing environments. Here, we review the latest findings and new avenues of research that have led to this group of fish being regarded as a model for evolutionary genomics.
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Affiliation(s)
- Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, 4811, Australia
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Marine Research Station, Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, 23-10, Dah-Uen Rd, Jiau Shi I-Lan 262, Taiwan
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4
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Roux N, Miura S, Dussenne M, Tara Y, Lee SH, de Bernard S, Reynaud M, Salis P, Barua A, Boulahtouf A, Balaguer P, Gauthier K, Lecchini D, Gibert Y, Besseau L, Laudet V. The multi-level regulation of clownfish metamorphosis by thyroid hormones. Cell Rep 2023; 42:112661. [PMID: 37347665 PMCID: PMC10467156 DOI: 10.1016/j.celrep.2023.112661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023] Open
Abstract
Most marine organisms have a biphasic life cycle during which pelagic larvae transform into radically different juveniles. In vertebrates, the role of thyroid hormones (THs) in triggering this transition is well known, but how the morphological and physiological changes are integrated in a coherent way with the ecological transition remains poorly explored. To gain insight into this question, we performed an integrated analysis of metamorphosis of a marine teleost, the false clownfish (Amphiprion ocellaris). We show how THs coordinate a change in color vision as well as a major metabolic shift in energy production, highlighting how it orchestrates this transformation. By manipulating the activity of liver X regulator (LXR), a major regulator of metabolism, we also identify a tight link between metabolic changes and metamorphosis progression. Strikingly, we observed that these regulations are at play in the wild, explaining how hormones coordinate energy needs with available resources during the life cycle.
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Affiliation(s)
- Natacha Roux
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan
| | - Saori Miura
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan
| | - Mélanie Dussenne
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Yuki Tara
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan
| | - Shu-Hua Lee
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10, Dah-Uen Rd., Jiau Shi, I-Lan 262, Taiwan
| | | | - Mathieu Reynaud
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan
| | - Pauline Salis
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Agneesh Barua
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan
| | - Abdelhay Boulahtouf
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, University of Montpellier, 34090 Montpellier, France
| | - Patrick Balaguer
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, University of Montpellier, 34090 Montpellier, France
| | - Karine Gauthier
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, INRAE USC 1370 École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie, 69007 Lyon, France
| | - David Lecchini
- PSL Research University, EPHE-UPVD-CNRS-UAR 3278 CRIOBE BP 1013, 98729 Papetoai, Moorea, French Polynesia; Laboratoire d'Excellence "CORAIL," 66100 Perpignan, France
| | - Yann Gibert
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
| | - Laurence Besseau
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France.
| | - Vincent Laudet
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa 904-0495, Japan; Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10, Dah-Uen Rd., Jiau Shi, I-Lan 262, Taiwan.
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5
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Roberts MB, Schultz DT, Gatins R, Escalona M, Bernardi G. Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus. G3 (BETHESDA, MD.) 2023; 13:jkac339. [PMID: 36905099 PMCID: PMC10085752 DOI: 10.1093/g3journal/jkac339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/14/2022] [Indexed: 04/12/2023]
Abstract
Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure, and speciation (Dascyllus). The genus Dascyllus includes a group of small-bodied species, and a complex of relatively larger bodied species, the Dascyllus trimaculatus species complex that is comprised of several species including D. trimaculatus itself. The three-spot damselfish, D. trimaculatus, is a widespread and common coral reef fish species found across the tropical Indo-Pacific. Here, we present the first-genome assembly of this species. This assembly contains 910 Mb, 90% of the bases are in 24 chromosome-scale scaffolds, and the Benchmarking Universal Single-Copy Orthologs score of the assembly is 97.9%. Our findings confirm previous reports of a karyotype of 2n = 47 in D. trimaculatus in which one parent contributes 24 chromosomes and the other 23. We find evidence that this karyotype is the result of a heterozygous Robertsonian fusion. We also find that the D. trimaculatus chromosomes are each homologous with single chromosomes of the closely related clownfish species, Amphiprion percula. This assembly will be a valuable resource in the population genomics and conservation of Damselfishes, and continued studies of the karyotypic diversity in this clade.
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Affiliation(s)
- May B Roberts
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Darrin T Schultz
- Department of Molecular Evolution and Development, University of Vienna, Vienna 1010, Austria
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Remy Gatins
- Department of Marine Sciences, Northeastern University, Boston, MA 02115, USA
| | - Merly Escalona
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
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6
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Moore B, Herrera M, Gairin E, Li C, Miura S, Jolly J, Mercader M, Izumiyama M, Kawai E, Ravasi T, Laudet V, Ryu T. The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish. G3 (BETHESDA, MD.) 2023; 13:6982751. [PMID: 36626199 PMCID: PMC9997566 DOI: 10.1093/g3journal/jkad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023]
Abstract
Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0% of conserved actinopterygian genes, making the quality and completeness of this genome the highest among all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanocyte development) in A. clarkii compared with other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.
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Affiliation(s)
- Billy Moore
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Emma Gairin
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Chengze Li
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Saori Miura
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Jeffrey Jolly
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Manon Mercader
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Michael Izumiyama
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Erina Kawai
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan.,Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan 262, Taiwan
| | - Taewoo Ryu
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
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7
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Yepes-Blandón JA, Bian C, Benítez-Galeano MJ, Aristizabal-Regino JL, Estrada-Posada AL, Mir D, Vásquez-Machado G, Atencio-García VJ, Shi Q, Rodríguez-Osorio N. Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae. Front Genet 2023; 13:989788. [PMID: 36744175 PMCID: PMC9893009 DOI: 10.3389/fgene.2022.989788] [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] [Received: 07/08/2022] [Accepted: 12/13/2022] [Indexed: 01/21/2023] Open
Abstract
We report the first draft genome assembly for Prochilodus magdalenae, the leading representative species of the Prochilodontidae family in Colombia. This 1.2-Gb assembly, with a GC content of 42.0% and a repetitive content of around 31.0%, is in the range of previously reported characid species genomes. Annotation identified 34,725 nuclear genes, and BUSCO completeness value was 94.9%. Gene ontology and primary metabolic pathway annotations indicate similar gene profiles for P. magdalenae and the closest species with annotated genomes: blind cave fish (Astyanax mexicanus) and red piranha (Pygocentrus nattereri). A comparative analysis showed similar genome traits to other characid species. The fully sequenced and annotated mitochondrial genome reproduces the taxonomic classification of P. magdalenae and confirms the low mitochondrial genetic divergence inside the Prochilodus genus. Phylogenomic analysis, using nuclear single-copy orthologous genes, also confirmed the evolutionary position of the species. This genome assembly provides a high-resolution genetic resource for sustainable P. magdalenae management in Colombia and, as the first genome assembly for the Prochilodontidae family, will contribute to fish genomics throughout South America.
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Affiliation(s)
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - María José Benítez-Galeano
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | | | | | - Daiana Mir
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | | | | | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - Nélida Rodríguez-Osorio
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
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8
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Ryu T, Herrera M, Moore B, Izumiyama M, Kawai E, Laudet V, Ravasi T. A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris. G3 (BETHESDA, MD.) 2022; 12:6555996. [PMID: 35353192 PMCID: PMC9073690 DOI: 10.1093/g3journal/jkac074] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/24/2022] [Indexed: 04/13/2023]
Abstract
The false clownfish Amphiprion ocellaris is a popular fish species and an emerging model organism for studying the ecology, evolution, adaptation, and developmental biology of reef fishes. Despite this, high-quality genomic resources for this species are scarce, hindering advanced genomic analyses. Leveraging the power of PacBio long-read sequencing and Hi-C chromosome conformation capture techniques, we constructed a high-quality chromosome-scale genome assembly for the clownfish A. ocellaris. The initial genome assembly comprised of 1,551 contigs of 861.42 Mb, with an N50 of 863.85 kb. Hi-C scaffolding of the genome resulted in 24 chromosomes containing 856.61 Mb. The genome was annotated with 26,797 protein-coding genes and had 96.62% completeness of conserved actinopterygian genes, making this genome the most complete and high quality among published anemonefish genomes. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further, comparative genomic analysis revealed 91 genome elements conserved only in A. ocellaris and its sister species Amphiprion percula, and not in other anemonefish species. These elements are close to genes that are involved in various nervous system functions and exhibited distinct expression patterns in brain tissue, potentially highlighting the genetic toolkits involved in lineage-specific divergence and behaviors of the clownfish branch. Overall, our study provides the highest quality A. ocellaris genome assembly and annotation to date, whilst also providing a valuable resource for understanding the ecology and evolution of reef fishes.
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Affiliation(s)
- Taewoo Ryu
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
- Corresponding author: Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan. ; *Corresponding author: Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan.
| | - Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
| | - Billy Moore
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
| | - Michael Izumiyama
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
| | - Erina Kawai
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, I‐Lan, Taiwan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
- Corresponding author: Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan. ; *Corresponding author: Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan.
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9
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Guo Q, Atkinson SD, Xiao B, Zhai Y, Bartholomew JL, Gu Z. A myxozoan genome reveals mosaic evolution in a parasitic cnidarian. BMC Biol 2022; 20:51. [PMID: 35177085 PMCID: PMC8855578 DOI: 10.1186/s12915-022-01249-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/07/2022] [Indexed: 12/20/2022] Open
Abstract
Background Parasite evolution has been conceptualized as a process of genetic loss and simplification. Contrary to this model, there is evidence of expansion and conservation of gene families related to essential functions of parasitism in some parasite genomes, reminiscent of widespread mosaic evolution—where subregions of a genome have different rates of evolutionary change. We found evidence of mosaic genome evolution in the cnidarian Myxobolus honghuensis, a myxozoan parasite of fish, with extremely simple morphology. Results We compared M. honghuensis with other myxozoans and free-living cnidarians, and determined that it has a relatively larger myxozoan genome (206 Mb), which is less reduced and less compact due to gene retention, large introns, transposon insertion, but not polyploidy. Relative to other metazoans, the M. honghuensis genome is depleted of neural genes and has only the simplest animal immune components. Conversely, it has relatively more genes involved in stress resistance, tissue invasion, energy metabolism, and cellular processes compared to other myxozoans and free-living cnidarians. We postulate that the expansion of these gene families is the result of evolutionary adaptations to endoparasitism. M. honghuensis retains genes found in free-living Cnidaria, including a reduced nervous system, myogenic components, ANTP class Homeobox genes, and components of the Wnt and Hedgehog pathways. Conclusions Our analyses suggest that the M. honghuensis genome evolved as a mosaic of conservative, divergent, depleted, and enhanced genes and pathways. These findings illustrate that myxozoans are not as genetically simple as previously regarded, and the evolution of some myxozoans is driven by both genomic streamlining and expansion. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01249-8.
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Affiliation(s)
- Qingxiang Guo
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China
| | - Stephen D Atkinson
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Bin Xiao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China
| | - Yanhua Zhai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China
| | - Jerri L Bartholomew
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Zemao Gu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. .,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China.
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10
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Mitchell LJ, Tettamanti V, Rhodes JS, Marshall NJ, Cheney KL, Cortesi F. CRISPR/Cas9-mediated generation of biallelic F0 anemonefish (Amphiprion ocellaris) mutants. PLoS One 2021; 16:e0261331. [PMID: 34910772 PMCID: PMC8673619 DOI: 10.1371/journal.pone.0261331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/29/2021] [Indexed: 12/02/2022] Open
Abstract
Genomic manipulation is a useful approach for elucidating the molecular pathways underlying aspects of development, physiology, and behaviour. However, a lack of gene-editing tools appropriated for use in reef fishes has meant the genetic underpinnings for many of their unique traits remain to be investigated. One iconic group of reef fishes ideal for applying this technique are anemonefishes (Amphiprioninae) as they are widely studied for their symbiosis with anemones, sequential hermaphroditism, complex social hierarchies, skin pattern development, and vision, and are raised relatively easily in aquaria. In this study, we developed a gene-editing protocol for applying the CRISPR/Cas9 system in the false clown anemonefish, Amphiprion ocellaris. Microinjection of zygotes was used to demonstrate the successful use of our CRISPR/Cas9 approach at two separate target sites: the rhodopsin-like 2B opsin encoding gene (RH2B) involved in vision, and Tyrosinase-producing gene (tyr) involved in the production of melanin. Analysis of the sequenced target gene regions in A. ocellaris embryos showed that uptake was as high as 73.3% of injected embryos. Further analysis of the subcloned mutant gene sequences combined with amplicon shotgun sequencing revealed that our approach had a 75% to 100% efficiency in producing biallelic mutations in F0 A. ocellaris embryos. Moreover, we clearly show a loss-of-function in tyr mutant embryos which exhibited typical hypomelanistic phenotypes. This protocol is intended as a useful starting point to further explore the potential application of CRISPR/Cas9 in A. ocellaris, as a platform for studying gene function in anemonefishes and other reef fishes.
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Affiliation(s)
- Laurie J. Mitchell
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
- * E-mail:
| | - Valerio Tettamanti
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Justin S. Rhodes
- Department of Psychology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana, Champaign, Urbana, IL, United States of America
| | - N. Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Karen L. Cheney
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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11
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Yang Y, Wang T, Chen J, Wu L, Wu X, Zhang W, Luo J, Xia J, Meng Z, Liu X. Whole-genome sequencing of brown-marbled grouper (Epinephelus fuscoguttatus) provides insights into adaptive evolution and growth differences. Mol Ecol Resour 2021; 22:711-723. [PMID: 34455708 DOI: 10.1111/1755-0998.13494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 07/29/2021] [Accepted: 08/23/2021] [Indexed: 11/27/2022]
Abstract
The brown-marbled grouper (Epinephelus fuscoguttatus) is an important species of fish in the coral reef ecosystem and marine aquaculture industry. In this study, a high-quality chromosome-level genome of brown-marbled grouper was assembled using Oxford Nanopore technology and Hi-C technology. The GC content and heterozygosity were approximately 42% and 0.35%, respectively. A total of 230 contigs with a total length of 1047 Mb and contig N50 of 13.8 Mb were assembled, and 228 contigs (99.13%) were anchored into 24 chromosomes. A total of 24,005 protein-coding genes were predicted, among which 23,862 (99.4%) predicted genes were annotated. Phylogenetic analysis showed that brown-marbled grouper and humpback grouper were clustered into one clade that separated approximately 11-23 million years ago. Collinearity analyses showed that there was no obvious duplication of large fragments between chromosomes in the brown-marbled grouper. Genomes of the humpback grouper and giant grouper showed a high collinearity with that of the brown-marbled grouper. A total of 305 expanded gene families were detected in the brown-marbled grouper genome, which is mainly involved in disease resistance. In addition, a genetic linkage map with 3061.88 cM was constructed. Based on the physical and genetic map, one growth-related quantitative trait loci was detected in 32,332,447 bp of chromosome 20, and meox1 and etv4 were considered candidate growth-related genes. This study provides pivotal genetic resources for further evolutionary analyses and artificial breeding of groupers.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Tong Wang
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Jingfang Chen
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Lina Wu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Xi Wu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Weiwei Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Key Laboratory of Tropical Biological Resources of Education, Marine Sciences College of Hainan University, Haikou, China
| | - Jian Luo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Key Laboratory of Tropical Biological Resources of Education, Marine Sciences College of Hainan University, Haikou, China
| | - Junhong Xia
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China.,Southern Laboratory of Ocean Science and Engineering, Zhuhai, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China.,Southern Laboratory of Ocean Science and Engineering, Zhuhai, China
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China.,Southern Laboratory of Ocean Science and Engineering, Zhuhai, China
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12
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Schunter C, Jarrold MD, Munday PL, Ravasi T. Diel pCO 2 fluctuations alter the molecular response of coral reef fishes to ocean acidification conditions. Mol Ecol 2021; 30:5105-5118. [PMID: 34402113 DOI: 10.1111/mec.16124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 12/26/2022]
Abstract
Environmental partial pressure of CO2 (pCO2 ) variation can modify the responses of marine organisms to ocean acidification, yet the underlying mechanisms for this effect remain unclear. On coral reefs, environmental pCO2 fluctuates on a regular day-night cycle. Effects of future ocean acidification on coral reef fishes might therefore depend on their response to this diel cycle of pCO2 . To evaluate the effects on the brain molecular response, we exposed two common reef fishes (Acanthochromis polyacanthus and Amphiprion percula) to two projected future pCO2 levels (750 and 1,000 µatm) under both stable and diel fluctuating conditions. We found a common signature to stable elevated pCO2 for both species, which included the downregulation of immediate early genes, indicating lower brain activity. The transcriptional programme was more strongly affected by higher average pCO2 in a stable treatment than for fluctuating treatments, but the largest difference in molecular response was between stable and fluctuating pCO2 treatments. This indicates that a response to a change in environmental pCO2 conditions is different for organisms living in a fluctuating than in stable environments. This differential regulation was related to steroid hormones and circadian rhythm (CR). Both species exhibited a marked difference in the expression of CR genes among pCO2 treatments, possibly accommodating a more flexible adaptive approach in the response to environmental changes. Our results suggest that environmental pCO2 fluctuations might enable reef fishes to phase-shift their clocks and anticipate pCO2 changes, thereby avoiding impairments and more successfully adjust to ocean acidification conditions.
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Affiliation(s)
- Celia Schunter
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Michael D Jarrold
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Philip L Munday
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Timothy Ravasi
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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13
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Mitchell LJ, Cheney KL, Luehrmann M, Marshall NJ, Michie K, Cortesi F. Molecular evolution of ultraviolet visual opsins and spectral tuning of photoreceptors in anemonefishes (Amphiprioninae). Genome Biol Evol 2021; 13:6347585. [PMID: 34375382 PMCID: PMC8511661 DOI: 10.1093/gbe/evab184] [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] [Accepted: 08/05/2021] [Indexed: 11/29/2022] Open
Abstract
Many animals including birds, reptiles, insects, and teleost fishes can see ultraviolet (UV) light (shorter than 400 nm), which has functional importance for foraging and communication. For coral reef fishes, shallow reef environments transmit a broad spectrum of light, rich in UV, driving the evolution of diverse spectral sensitivities. However, the identities and sites of the specific visual genes that underly vision in reef fishes remain elusive and are useful in determining how evolution has tuned vision to suit life on the reef. We investigated the visual systems of 11 anemonefish (Amphiprioninae) species, specifically probing for the molecular pathways that facilitate UV-sensitivity. Searching the genomes of anemonefishes, we identified a total of eight functional opsin genes from all five vertebrate visual opsin subfamilies. We found rare instances of teleost UV-sensitive SWS1 opsin gene duplications that produced two functionally coding paralogs (SWS1α and SWS1β) and a pseudogene. We also found separate green sensitive RH2A opsin gene duplicates not yet reported in the family Pomacentridae. Transcriptome analysis revealed false clown anemonefish (Amphiprion ocellaris) expressed one rod opsin (RH1) and six cone opsins (SWS1β, SWS2B, RH2B, RH2A-1, RH2A-2, LWS) in the retina. Fluorescent in situ hybridization highlighted the (co-)expression of SWS1β with SWS2B in single cones, and either RH2B, RH2A, or RH2A together with LWS in different members of double cone photoreceptors (two single cones fused together). Our study provides the first in-depth characterization of visual opsin genes found in anemonefishes and provides a useful basis for the further study of UV-vision in reef fishes.
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Affiliation(s)
- Laurie J Mitchell
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Karen L Cheney
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Martin Luehrmann
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - N Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kyle Michie
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.,King's College, Cambridge, CB2 1ST, UK
| | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
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14
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Black AN, Willoughby JR, Brüniche-Olsen A, Pierce BL, DeWoody JA. The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation. Mol Ecol Resour 2021; 21:2520-2532. [PMID: 34137170 DOI: 10.1111/1755-0998.13447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022]
Abstract
The White Sands pupfish (Cyprinodon tularosa), endemic to New Mexico in Southwestern North America, is of conservation concern due in part to invasive species, chemical pollution, and groundwater withdrawal. Herein, we developed a draft reference genome and use it to provide biological insights into the evolution and conservation of C. tularosa. We used our assembly to localize microsatellite markers previously used to demarcate evolutionary significant units (ESU), quantified genomic divergence and transposable element profiles between species, and compared C. tularosa genomic diversity related species. Our de novo assembly of PacBio Sequel II error-corrected reads resulted in a 1.08 Gb draft genome with a contig N50 of 1.4 Mb and 25,260 annotated protein coding genes, including 95% of the expected Actinopterygii conserved complete single-copy orthologues. Many of the C. tularosa microsatellite markers used for conservation assessments fell within, or near, genes and exhibited a pattern of increased heterozygosity near genic areas compared to those in intergenic regions. Nuclear alignments between these two species revealed 193 genes contained in rapidly diverging tracts; transposable element profiles were largely concordant and suggest a shared, rapid expansion of LINE and Gypsy elements. Genome-wide heterozygosity was markedly lower in C. tularosa compared to estimates from other related species, probably because of smaller long-term effective population sizes constrained by their isolated and limited habitat. Overall, these inferences provide new insights into C. tularosa that should help inform future management efforts.
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Affiliation(s)
- Andrew N Black
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
| | - Janna R Willoughby
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA.,School of Forestry and Wildlife Sciences, Auburn University, Auburn, USA
| | - Anna Brüniche-Olsen
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Brian L Pierce
- Natural Resources Institute, Texas A&M University, College Station, Texas, USA
| | - J Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
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15
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Tigano A, Jacobs A, Wilder AP, Nand A, Zhan Y, Dekker J, Therkildsen NO. Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation. Genome Biol Evol 2021; 13:evab098. [PMID: 33964136 PMCID: PMC8214408 DOI: 10.1093/gbe/evab098] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/21/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)-an established ecological model for studying the phenotypic effects of natural and artificial selection-and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ∼23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.
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Affiliation(s)
- Anna Tigano
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Arne Jacobs
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
| | - Aryn P Wilder
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
- Conservation Genetics, San Diego Zoo Global, Escondido, California, USA
| | - Ankita Nand
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ye Zhan
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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16
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Liu D, Wang X, Guo H, Zhang X, Zhang M, Tang W. Chromosome-level genome assembly of the endangered humphead wrasse Cheilinus undulatus: Insight into the expansion of opsin genes in fishes. Mol Ecol Resour 2021; 21:2388-2406. [PMID: 34003602 DOI: 10.1111/1755-0998.13429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 11/26/2022]
Abstract
Wrasses are dominant components of major coral reef systems. Among wrasses, Cheilinus undulatus is an endangered species with high economic and ecological value that exhibits sex reversal of females to males, while sexual selection occurs in breeding aggregations. However, the molecular-associated mechanism underlying this remains unclear. Opsin gene diversification is regarded as a potent force in sexual selection. Here we present a genome assembly of C. undulatus, using Illumina, Nanopore and Hi-C sequencing. The 1.17 Gb genome was generated from 328 contigs with an N50 length of 16.5 Mb and anchored to 24 chromosomes. In total, 22,218 genes were functionally annotated, and 96.36% of BUSCO genes were fully represented. Transcriptomic analyses showed that 96.79% of the predicted genes were expressed. Transposons were most abundant, accounting for 39.88% of the genome, with low divergence, owing to their evolution with close species ~60.53 million years ago. In total, 567/1,826 gene families were expanded and contracted in the reconstructed phylogeny, respectively. Forty-six genes were under positive selection. Comparative genomic analyses with other fish revealed expansion of opsin SWS2B, LWS1 and Rh2. The elevated duplicates of SWS2B were generated by gene conversions via transposition of transposons followed by nonallelic homologous recombination. Amino acid substitutions of opsin paralogues occurred at key tuning sites, causing a spectral shift in maximal absorbance of visual pigment to capture functional changes. Among these opsin genes, SWS2B-3 and 4 and Rh1 are expressed in the retina. The genome sequence of C. undulatus provides valuable resources for future investigation of the conservation, evolution and behaviour of fishes.
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Affiliation(s)
- Dong Liu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xinyang Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Hongyi Guo
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xuguang Zhang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Wenqiao Tang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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17
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Czimer D, Porok K, Csete D, Gyüre Z, Lavró V, Fülöp K, Chen Z, Gyergyák H, Tusnády GE, Burgess SM, Mócsai A, Váradi A, Varga M. A New Zebrafish Model for Pseudoxanthoma Elasticum. Front Cell Dev Biol 2021; 9:628699. [PMID: 33768091 PMCID: PMC7985086 DOI: 10.3389/fcell.2021.628699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/16/2021] [Indexed: 11/30/2022] Open
Abstract
Calcification of various tissues is a significant health issue associated with aging, cancer and autoimmune diseases. There are both environmental and genetic factors behind this phenomenon and understanding them is essential for the development of efficient therapeutic approaches. Pseudoxanthoma elasticum (PXE) is a rare genetic disease, a prototype for calcification disorders, resulting from the dysfunction of ABCC6, a transport protein found in the membranes of cells. It is identified by excess calcification in a variety of tissues (e.g., eyes, skin, arteries) and currently it has no cure, known treatments target the symptoms only. Preclinical studies of PXE have been successful in mice, proving the usefulness of animal models for the study of the disease. Here, we present a new zebrafish (Danio rerio) model for PXE. By resolving some ambiguous assemblies in the zebrafish genome, we show that there are two functional and one non-functional paralogs for ABCC6 in zebrafish (abcc6a, abcc6b.1, and abcc6b.2, respectively). We created single and double mutants for the functional paralogs and characterized their calcification defects with a combination of techniques. Zebrafish deficient in abcc6a show defects in their vertebral calcification and also display ectopic calcification foci in their soft tissues. Our results also suggest that the impairment of abcc6b.1 does not affect this biological process.
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Affiliation(s)
- Dávid Czimer
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Klaudia Porok
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Csete
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Zsolt Gyüre
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Viktória Lavró
- Division of Biosciences, University College London, London, United Kingdom
| | - Krisztina Fülöp
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zelin Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hella Gyergyák
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor E Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, United States
| | - Attila Mócsai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - András Váradi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
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18
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Whibley A, Kelley JL, Narum SR. The changing face of genome assemblies: Guidance on achieving high-quality reference genomes. Mol Ecol Resour 2021; 21:641-652. [PMID: 33326691 DOI: 10.1111/1755-0998.13312] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 12/20/2022]
Abstract
The quality of genome assemblies has improved rapidly in recent years due to continual advances in sequencing technology, assembly approaches, and quality control. In the field of molecular ecology, this has led to the development of exceptional quality genome assemblies that will be important long-term resources for broader studies into ecological, conservation, evolutionary, and population genomics of naturally occurring species. Moreover, the extent to which a single reference genome represents the diversity within a species varies: pan-genomes will become increasingly important ecological genomics resources, particularly in systems found to have considerable presence-absence variation in their functional content. Here, we highlight advances in technology that have raised the bar for genome assembly and provide guidance on standards to achieve exceptional quality reference genomes. Key recommendations include the following: (a) Genome assemblies should include long-read sequencing except in rare cases where it is effectively impossible to acquire adequately preserved samples needed for high molecular weight DNA standards. (b) At least one scaffolding approach should be included with genome assembly such as Hi-C or optical mapping. (c) Genome assemblies should be carefully evaluated, this may involve utilising short read data for genome polishing, error correction, k-mer analyses, and estimating the percent of reads that map back to an assembly. Finally, a genome assembly is most valuable if all data and methods are made publicly available and the utility of a genome for further studies is verified through examples. While these recommendations are based on current technology, we anticipate that future advances will push the field further and the molecular ecology community should continue to adopt new approaches that attain the highest quality genome assemblies.
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Affiliation(s)
| | | | - Shawn R Narum
- University of Idaho, Moscow, ID, USA.,Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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19
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Sun C, Li J, Dong J, Niu Y, Hu J, Lian J, Li W, Li J, Tian Y, Shi Q, Ye X. Chromosome-level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water. Mol Ecol Resour 2020; 21:301-315. [PMID: 32985096 DOI: 10.1111/1755-0998.13256] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Abstract
Largemouth bass (LMB; Micropterus salmoides) has been an economically important fish in North America, Europe, and China. This study obtained a chromosome-level genome assembly of LMB using PacBio and Hi-C sequencing. The final assembled genome is 964 Mb, with contig N50 and scaffold N50 values of 1.23 Mb and 36.48 Mb, respectively. Combining with RNA sequencing data, we annotated a total of 23,701 genes. Chromosomal assembly and syntenic analysis proved that, unlike most Perciformes with the popular haploid chromosome number of 24, LMB has only 23 chromosomes (Chr), among which the Chr1 seems to be resulted from a chromosomal fusion event. LMB is phylogenetically closely related to European seabass and spotted seabass, diverging 64.1 million years ago (mya) from the two seabass species. Eight gene families comprising 294 genes associated with ionic regulation were identified through positive selection, transcriptome and genome comparisons. These genes involved in iron facilitated diffusion (such as claudin, aquaporins, sodium channel protein and so on) and others related to ion active transport (such as sodium/potassium-transporting ATPase and sodium/calcium exchanger). The claudin gene family, which is critical for regulating cell tight junctions and osmotic homeostasis, showed a significant expansion in LMB with 27 family members and 68 copies for salinity adaptation. In summary, we reported the first high-quality LMB genome, and provided insights into the molecular mechanisms of LMB adaptation to fresh and brackish water. The chromosome-level LMB genome will also be a valuable genomic resource for in-depth biological and evolutionary studies, germplasm conservation and genetic breeding of LMB.
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Affiliation(s)
- Chengfei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jia Li
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Junjian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | | | - Jie Hu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | | | - Wuhui Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiang Li
- Biozeron Shenzhen Inc., Shenzhen, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Qiong Shi
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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20
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Roux N, Salis P, Lee SH, Besseau L, Laudet V. Anemonefish, a model for Eco-Evo-Devo. EvoDevo 2020; 11:20. [PMID: 33042514 PMCID: PMC7539381 DOI: 10.1186/s13227-020-00166-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/18/2020] [Indexed: 12/20/2022] Open
Abstract
Anemonefish, are a group of about 30 species of damselfish (Pomacentridae) that have long aroused the interest of coral reef fish ecologists. Combining a series of original biological traits and practical features in their breeding that are described in this paper, anemonefish are now emerging as an experimental system of interest for developmental biology, ecology and evolutionary sciences. They are small sized and relatively easy to breed in specific husbandries, unlike the large-sized marine fish used for aquaculture. Because they live in highly structured social groups in sea anemones, anemonefish allow addressing a series of relevant scientific questions such as the social control of growth and sex change, the mechanisms controlling symbiosis, the establishment and variation of complex color patterns, and the regulation of aging. Combined with the use of behavioral experiments, that can be performed in the lab or directly in the wild, as well as functional genetics and genomics, anemonefish provide an attractive experimental system for Eco-Evo-Devo.
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Affiliation(s)
- Natacha Roux
- Sorbonne Université, CNRS, UMR « Biologie Intégrative Des Organismes Marins », BIOM, 1, 66650 Banyuls-sur-Mer, France
| | - Pauline Salis
- Sorbonne Université, CNRS, UMR « Biologie Intégrative Des Organismes Marins », BIOM, 1, 66650 Banyuls-sur-Mer, France
| | - Shu-Hua Lee
- Lab of Marine Eco-Evo-Devo, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Laurence Besseau
- Sorbonne Université, CNRS, UMR « Biologie Intégrative Des Organismes Marins », BIOM, 1, 66650 Banyuls-sur-Mer, France
| | - Vincent Laudet
- Lab of Marine Eco-Evo-Devo, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna son, Okinawa, 904-0495 Japan
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21
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Heras J, Chakraborty M, Emerson JJ, German DP. Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish. Proc Biol Sci 2020; 287:20192327. [PMID: 32070255 PMCID: PMC7062031 DOI: 10.1098/rspb.2019.2327] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/26/2020] [Indexed: 01/30/2023] Open
Abstract
Adopting a new diet is a significant evolutionary change, and can profoundly affect an animal's physiology, biochemistry, ecology and genome. To study this evolutionary transition, we investigated the physiology and genomics of digestion of a derived herbivorous fish, Cebidichthys violaceus. We sequenced and assembled its genome (N50 = 6.7 Mb) and digestive transcriptome, and revealed the molecular changes related to digestive enzymes (carbohydrases, proteases and lipases), finding abundant evidence of molecular adaptation. Specifically, two gene families experienced expansion in copy number and adaptive amino acid substitutions: amylase and carboxyl ester lipase (cel), which are involved in the digestion of carbohydrates and lipids, respectively. Both show elevated levels of gene expression and increased enzyme activity. Because carbohydrates are abundant in the prickleback's diet and lipids are rare, these findings suggest that such dietary specialization involves both exploiting abundant resources and scavenging rare ones, especially essential nutrients, like essential fatty acids.
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Affiliation(s)
- Joseph Heras
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA
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22
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Kang S, Kim JH, Jo E, Lee SJ, Jung J, Kim BM, Lee JH, Oh TJ, Yum S, Rhee JS, Park H. Chromosomal-level assembly of Takifugu obscurus (Abe, 1949) genome using third-generation DNA sequencing and Hi-C analysis. Mol Ecol Resour 2020; 20:520-530. [PMID: 31887246 DOI: 10.1111/1755-0998.13132] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 01/12/2023]
Abstract
The Tetraodontidae family are known to have relatively small and compact genomes compared to other vertebrates. The obscure puffer fish Takifugu obscurus is an anadromous species that migrates to freshwater from the sea for spawning. Thus the euryhaline characteristics of T. obscurus have been investigated to gain understanding of their survival ability, osmoregulation, and other homeostatic mechanisms in both freshwater and seawater. In this study, a high quality chromosome-level reference genome for T. obscurus was constructed using long-read Pacific Biosciences (PacBio) Sequel sequencing and a Hi-C-based chromatin contact map platform. The final genome assembly of T. obscurus is 381 Mb, with a contig N50 length of 3,296 kb and longest length of 10.7 Mb, from a total of 62 Gb of raw reads generated using single-molecule real-time sequencing technology from a PacBio Sequel platform. The PacBio data were further clustered into chromosome-scale scaffolds using a Hi-C approach, resulting in a 373 Mb genome assembly with a contig N50 length of 15.2 Mb and and longest length of 28 Mb. When we directly compared the 22 longest scaffolds of T. obscurus to the 22 chromosomes of the tiger puffer Takifugu rubripes, a clear one-to-one orthologous relationship was observed between the two species, supporting the chromosome-level assembly of T. obscurus. This genome assembly can serve as a valuable genetic resource for exploring fugu-specific compact genome characteristics, and will provide essential genomic information for understanding molecular adaptations to salinity fluctuations and the evolution of osmoregulatory mechanisms.
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Affiliation(s)
- Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, Korea
| | - Jin-Hyoung Kim
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, Korea
| | - Euna Jo
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, Korea.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Seung Jae Lee
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Jihye Jung
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, Korea
| | - Bo-Mi Kim
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, Korea.,Polar Sciences, University of Science & Technology, Daejeon, Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan, Korea.,Genome-based BioIT Convergence Institute, Asan, Korea.,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Korea
| | - Seungshic Yum
- Risk Assessment Research Center, Korea Institute of Ocean Science and Technology (KIOST), Geoje, Korea
| | - Jae-Sung Rhee
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, Korea.,Research Institute of Basic Sciences, Incheon National University, Incheon, Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
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23
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Peñalba JV, Deng Y, Fang Q, Joseph L, Moritz C, Cockburn A. Genome of an iconic Australian bird: High-quality assembly and linkage map of the superb fairy-wren (Malurus cyaneus). Mol Ecol Resour 2020; 20:560-578. [PMID: 31821695 DOI: 10.1111/1755-0998.13124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/09/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022]
Abstract
The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high-quality reference. To rectify that, we present the first high-quality genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07-Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high-quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the fairy-wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high-quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy-wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses.
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Affiliation(s)
- Joshua V Peñalba
- Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Qi Fang
- BGI-Shenzhen, Shenzhen, China
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections, Australia, Canberra, ACT, Australia
| | - Craig Moritz
- Centre for Biodiversity Analysis, Acton, ACT, Australia.,Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
| | - Andrew Cockburn
- Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
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24
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Narum S, Kelley J, Sibbett B. Editorial 2020. Mol Ecol Resour 2020; 20:1-7. [DOI: 10.1111/1755-0998.13125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 11/29/2022]
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25
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Ge H, Lin K, Shen M, Wu S, Wang Y, Zhang Z, Wang Z, Zhang Y, Huang Z, Zhou C, Lin Q, Wu J, Liu L, Hu J, Huang Z, Zheng L. De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C. Mol Ecol Resour 2019; 19:1461-1469. [PMID: 31325912 PMCID: PMC6899872 DOI: 10.1111/1755-0998.13064] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/02/2023]
Abstract
The red‐spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South‐East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome‐level reference genome of E. akaara by taking advantage of long‐read single‐molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi‐C. A red‐spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96‐fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi‐C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA‐seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein‐coding sequences. The high‐quality chromosome‐level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red‐spotted grouper in the future.
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Affiliation(s)
- Hui Ge
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
| | - Kebing Lin
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Mi Shen
- Nextomics Biosciences Institute, Wuhan, China
| | - Shuiqing Wu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
| | - Ziping Zhang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
| | - Yong Zhang
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Normal University, Fuzhou, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Lei Liu
- Nextomics Biosciences Institute, Wuhan, China
| | - Jiang Hu
- Nextomics Biosciences Institute, Wuhan, China
| | - Zhongchi Huang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Leyun Zheng
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
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26
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Hotaling S, Kelley JL. The rising tide of high‐quality genomic resources. Mol Ecol Resour 2019; 19:567-569. [DOI: 10.1111/1755-0998.12964] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/17/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Scott Hotaling
- School of Biological SciencesWashington State University Pullman Washington
| | - Joanna L. Kelley
- School of Biological SciencesWashington State University Pullman Washington
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27
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Guo L, Xu YH, Zhang N, Zhou FL, Huang JH, Liu BS, Jiang SG, Zhang DC. A High-Density Genetic Linkage Map and QTL Mapping for Sex in Black Tiger Shrimp ( Penaeus monodon). Front Genet 2019; 10:326. [PMID: 31024632 PMCID: PMC6465554 DOI: 10.3389/fgene.2019.00326] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/26/2019] [Indexed: 12/20/2022] Open
Abstract
The black tiger shrimp, Penaeus monodon, is important in both fishery and aquaculture and is the second-most widely cultured shrimp species in the world. However, the current strains cannot meet the market needs in various cultural environments, and the genome resources for P. monodon are still lacking. Restriction-site associated DNA sequencing (RADseq) has been widely used in genetic linkage map construction and in quantitative trait loci (QTL) mapping. We constructed a high-density genetic linkage map with RADseq in a full-sib family. This map contained 6524 single nucleotide polymorphisms (SNPs) and 2208 unique loci. The total length was 3275.4 cM, and the genetic distance was estimated to be 1.1 Mb/cM. The sex trait is a dichotomous phenotype, and the same interval was detected as a QTL using QTL mapping and genome-wide association analysis. The most significant locus explained 77.4% of the phenotype variance. The sex locus was speculated to be the same in this species based on the sequence alignments in Mozambique, India, and Hawaii populations. The constructed genetic linkage map provided a valuable resource for QTL mapping, genome assembly, and genome comparison for shrimp. The demonstrated common sex locus is a step closer to locating the underlying gene.
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Affiliation(s)
- Liang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Yu-Hui Xu
- Biomarker Technologies Corporation, Beijing, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Fa-Lin Zhou
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Jian-Hua Huang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
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28
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Marcionetti A, Rossier V, Roux N, Salis P, Laudet V, Salamin N. Insights into the Genomics of Clownfish Adaptive Radiation: Genetic Basis of the Mutualism with Sea Anemones. Genome Biol Evol 2019; 11:869-882. [PMID: 30830203 PMCID: PMC6430985 DOI: 10.1093/gbe/evz042] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2019] [Indexed: 02/06/2023] Open
Abstract
Clownfishes are an iconic group of coral reef fishes, especially known for their mutualism with sea anemones. This mutualism is particularly interesting as it likely acted as the key innovation that triggered clownfish adaptive radiation. Indeed, after the acquisition of the mutualism, clownfishes diversified into multiple ecological niches linked with host and habitat use. However, despite the importance of this mutualism, the genetic mechanisms allowing clownfishes to interact with sea anemones are still unclear. Here, we used a comparative genomics and molecular evolutionary analyses to investigate the genetic basis of clownfish mutualism with sea anemones. We assembled and annotated the genome of nine clownfish species and one closely related outgroup. Orthologous genes inferred between these species and additional publicly available teleost genomes resulted in almost 16,000 genes that were tested for positively selected substitutions potentially involved in the adaptation of clownfishes to live in sea anemones. We identified 17 genes with a signal of positive selection at the origin of clownfish radiation. Two of them (Versican core protein and Protein O-GlcNAse) show particularly interesting functions associated with N-acetylated sugars, which are known to be involved in sea anemone discharge of toxins. This study provides the first insights into the genetic mechanisms of clownfish mutualism with sea anemones. Indeed, we identified the first candidate genes likely to be associated with clownfish protection form sea anemones, and thus the evolution of their mutualism. Additionally, the genomic resources acquired represent a valuable resource for further investigation of the genomic basis of clownfish adaptive radiation.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
| | - Victor Rossier
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
| | - Natacha Roux
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Pauline Salis
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
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29
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Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW. Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish. Mol Ecol 2019; 28:1491-1505. [DOI: 10.1111/mec.14969] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/15/2018] [Accepted: 10/23/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Stefan Dennenmoser
- Institute for Biology and Environmental Sciences Carl von Ossietzky University Oldenburg Oldenburg Germany
| | | | - Michael C. Schatz
- Cold Spring Harbor Laboratory Cold Spring Harbor New York
- Departments of Computer Science and Biology Johns Hopkins University Baltimore Maryland
| | - Janine Altmüller
- Cologne Center for Genomics, and Institute of Human Genetics University of Cologne Cologne Germany
| | | | - Arne W. Nolte
- Institute for Biology and Environmental Sciences Carl von Ossietzky University Oldenburg Oldenburg Germany
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30
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Lehmann R, Lightfoot DJ, Schunter C, Michell CT, Ohyanagi H, Mineta K, Foret S, Berumen ML, Miller DJ, Aranda M, Gojobori T, Munday PL, Ravasi T. Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. Mol Ecol Resour 2018; 19:570-585. [PMID: 30203521 PMCID: PMC7379943 DOI: 10.1111/1755-0998.12939] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 11/29/2022]
Abstract
The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C-based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein-coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.
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Affiliation(s)
- Robert Lehmann
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Damien J Lightfoot
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Celia Schunter
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Craig T Michell
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Hajime Ohyanagi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sylvain Foret
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Philip L Munday
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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