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Jiang C, Liu S, Yang Y, Cui W, Xu S, Rasoamananto I, Lavitra T, Zhang L, Sun L. Population genomic analysis reveals a polygenic sex determination system in Apostichopus japonicus. iScience 2024; 27:110852. [PMID: 39381746 PMCID: PMC11458978 DOI: 10.1016/j.isci.2024.110852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 08/16/2024] [Accepted: 08/28/2024] [Indexed: 10/10/2024] Open
Abstract
The sea cucumber Apostichopus japonicus, a key species in Chinese aquaculture, plays a significant evolutionary role within the Echinodermata phylum. However, the sex determination mechanism in this species remains poorly understood. Here, we conducted extensive sex surveys and sampling of eight wild populations, investigating the sex-related SNPs and insertion or deletions (indels) through bulk segregation analysis (BSA) and genome-wide association study (GWAS) analysis. Our findings suggest that A. japonicus employs a polygenic sex determination (PSD) system, with solute carrier family 8 (SLC8A) being the candidate gene for sex determination, encoding sodium-calcium exchanger (NCX1). The analysis of normalized sequencing depth reveals variations across chromosomes 6, 13, 14, 16, and 18, supporting the PSD system. We also identified 541.656 kb of male-specific sequences and screened five markers (C77185, C98086, C64977, C125, and C876) for molecular sex identification. Overall, this study provides new insights into A. japonicus sex determination, highlighting a complex multi-gene mechanism rather than a simple XX/XY system.
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Affiliation(s)
- Chunxi Jiang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujia Yang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Wei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Irène Rasoamananto
- Institut Halieutique et des Sciences Marines (IH.SM), University of Toliara, Toliara, Madagascar
| | - Thierry Lavitra
- Institut Halieutique et des Sciences Marines (IH.SM), University of Toliara, Toliara, Madagascar
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Schiebelhut LM, DeBiasse MB, Gabriel L, Hoff KJ, Dawson MN. A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides. J Hered 2024; 115:86-93. [PMID: 37738158 PMCID: PMC10838127 DOI: 10.1093/jhered/esad054] [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: 06/10/2023] [Revised: 07/29/2023] [Accepted: 09/29/2023] [Indexed: 09/24/2023] Open
Abstract
Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score of 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genus Pisaster. These novel genomic resources for P. helianthoides will underwrite population genomic, comparative genomic, and phylogenomic analyses-as well as their integration across scales-of SSW and environmental stressors.
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Affiliation(s)
- Lauren M Schiebelhut
- Life & Environmental Sciences, University of California, Merced, CA, United States
| | - Melissa B DeBiasse
- Life & Environmental Sciences, University of California, Merced, CA, United States
- Department of Biology, Radford University, Radford, VA, United States
| | - Lars Gabriel
- Institute for Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Katharina J Hoff
- Institute for Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Michael N Dawson
- Life & Environmental Sciences, University of California, Merced, CA, United States
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Wang Y, Wang Y, Yang Y, Ni G, Li Y, Chen M. Chromosome-level genome assembly of the northern Pacific seastar Asterias amurensis. Sci Data 2023; 10:767. [PMID: 37925473 PMCID: PMC10625585 DOI: 10.1038/s41597-023-02688-w] [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: 07/06/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
Asterias amurensis has attracted widespread concern because of its population outbreaks, which has impacted fisheries and aquaculture, as well as disrupting local ecosystems. A high-quality reference genome is necessary to better investigate mechanisms of outbreak and adaptive changes. Combining PacBio HiFi and Hi-C sequencing data, we generated a chromosome-level A. amurensis genome with a size of 491.53 Mb. The contig N50 and scaffold N50 were 8.05 and 23.75 Mb, respectively. The result of BUSCO analysis revealed a completeness score of 98.85%. A total of 16,531 protein-coding genes were predicted in the genome, of which 94.63% were functionally annotated. The high-quality genome assembly resulting from this study will provide a valuable genetic resource for future research on the mechanism of population outbreaks and invasion ecology.
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Affiliation(s)
- Yanlin Wang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yixin Wang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yujia Yang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Gang Ni
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yulong Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Muyan Chen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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Jung J, Jhang SY, Kim B, Koh B, Ban C, Seo H, Park T, Chi WJ, Kim S, Kim H, Yu J. The first high-quality genome assembly and annotation of Patiria pectinifera. Sci Data 2023; 10:642. [PMID: 37730712 PMCID: PMC10511450 DOI: 10.1038/s41597-023-02508-1] [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: 05/24/2023] [Accepted: 08/29/2023] [Indexed: 09/22/2023] Open
Abstract
The blue bat star, a highly adaptive species in the East Sea of Korea, has displayed remarkable success in adapting to recent climate change. The genetic mechanisms behind this success were not well-understood, prompting our report on the first chromosome-level assembly of the Patiria genus. We assembled the genome using Nanopore and Illumina sequences, yielding a total length of 615 Mb and a scaffold N50 of 24,204,423 bp. Hi-C analysis allowed us to anchor the scaffold sequences onto 22 pseudochromosomes. K-mer based analysis revealed 5.16% heterozygosity rate of the genome, higher than any previously reported echinoderm species. Our transposable element analysis exposed a substantial number of genome-wide retrotransposons and DNA transposons. These results offer valuable resources for understanding the evolutionary mechanisms behind P. pectinifera's successful adaptation in fluctuating environments.
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Affiliation(s)
- Jaehoon Jung
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea
- Department of Agricultural and Life Sciences and Research Institute of Population Genomics, Seoul National University, Seoul, Republic of Korea
| | - So Yun Jhang
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Bongsang Kim
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea
- Department of Agricultural and Life Sciences and Research Institute of Population Genomics, Seoul National University, Seoul, Republic of Korea
| | - Bomin Koh
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea
- Department of Agricultural and Life Sciences and Research Institute of Population Genomics, Seoul National University, Seoul, Republic of Korea
| | - Chaeyoung Ban
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea
| | - Hyojung Seo
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea
| | - Taeseo Park
- Animal Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Won-Jae Chi
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Soonok Kim
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Heebal Kim
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea
- Department of Agricultural and Life Sciences and Research Institute of Population Genomics, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Jaewoong Yu
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea.
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Liu J, Zhou Y, Pu Y, Zhang H. A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis). Sci Data 2023; 10:506. [PMID: 37528102 PMCID: PMC10394057 DOI: 10.1038/s41597-023-02397-4] [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: 02/03/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
Understanding of adaptation and evolution of organisms in the deep sea requires more genomic resources. Zoroaster cf. ophiactis is a sea star in the family Zoroasteridae occurring exclusively in the deep sea. In this study, a chromosome-level genome assembly for Z. cf. ophiactis was generated by combining Nanopore long-read, Illumina short-read, and Hi-C sequencing data. The final assembly was 1,002.0 Mb in length, with a contig N50 of 376 Kb and a scaffold N50 of 40.4 Mb, and included 22 pseudo-chromosomes, covering 92.3% of the assembly. Completeness analysis evaluated with BUSCO revealed that 95.91% of the metazoan conserved genes were complete. Additionally, 39,426 protein-coding genes were annotated for this assembly. This chromosome-level genome assembly represents the first high-quality genome for the deep-sea Asteroidea, and will provide a valuable resource for future studies on evolution and adaptation of deep-sea echinoderms.
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Affiliation(s)
- Jun Liu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yang Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yujin Pu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haibin Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
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DeBiasse MB, Schiebelhut LM, Escalona M, Beraut E, Fairbairn C, Marimuthu MPA, Nguyen O, Sahasrabudhe R, Dawson MN. A chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus, a species severely impacted by wasting. J Hered 2022; 113:689-698. [PMID: 36044245 PMCID: PMC9709977 DOI: 10.1093/jhered/esac044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Efforts to protect the ecologically and economically significant California Current Ecosystem from global change will greatly benefit from data about patterns of local adaptation and population connectivity. To facilitate that work, we present a reference-quality genome for the giant pink sea star, Pisaster brevispinus, a species of ecological importance along the Pacific west coast of North America that has been heavily impacted by environmental change and disease. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly of 550 Mb in length. The assembly contains 127 scaffolds with a contig N50 of 4.6 Mb and a scaffold N50 of 21.4 Mb; the BUSCO completeness score is 98.70%. The P. brevispinus genome assembly is comparable to the genome of the congener species P. ochraceus in size and completeness. Both Pisaster assemblies are consistent with previously published karyotyping results showing sea star genomes are organized into 22 autosomes. The reference genome for P. brevispinus is an important first step toward the goal of producing a comprehensive, population genomics view of ecological and evolutionary processes along the California coast. This resource will help scientists, managers, and policy makers in their task of understanding and protecting critical coastal regions from the impacts of global change.
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Affiliation(s)
- Melissa B DeBiasse
- Department of Life and Environmental Sciences, University of California, Merced, CA, United States
| | - Lauren M Schiebelhut
- Department of Life and Environmental Sciences, University of California, Merced, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Ecology & Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Colin Fairbairn
- Ecology & Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California Davis, Davis, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California Davis, Davis, CA, United States
| | - Michael N Dawson
- Department of Life and Environmental Sciences, University of California, Merced, CA, United States
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Andrade C, Oliveira B, Guatelli S, Martinez P, Simões B, Bispo C, Ferrario C, Bonasoro F, Rino J, Sugni M, Gardner R, Zilhão R, Coelho AV. Characterization of Coelomic Fluid Cell Types in the Starfish Marthasterias glacialis Using a Flow Cytometry/Imaging Combined Approach. Front Immunol 2021; 12:641664. [PMID: 33815394 PMCID: PMC8013778 DOI: 10.3389/fimmu.2021.641664] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/02/2021] [Indexed: 12/22/2022] Open
Abstract
Coelomocytes is the generic name for a collection of cellular morphotypes, present in many coelomate animals, and highly variable among echinoderm classes. The roles attributed to the major types of these free circulating cells present in the coelomic fluid of echinoderms include immune response, phagocytic digestion and clotting. Our main aim in this study was to characterize coelomocytes found in the coelomic fluid of Marthasterias glacialis (class Asteroidea) by using a combination of flow cytometry (FC), imaging flow cytometry (IFC) and fluorescence plus transmission electron microscopy (TEM). Two coelomocyte populations (P1 and P2) identified through flow cytometry were subsequently studied in terms of abundance, morphology, ultrastructure, cell viability and cell cycle profiles. Ultrastructurally, P2 diploid cells were present as two main morphotypes, similar to phagocytes and vertebrate thrombocytes, whereas the smaller P1 cellular population was characterized by low mitotic activity, a relatively undifferentiated cytotype and a high nucleus/cytoplasm ratio. In the present study we could not rule out possible similarities between haploid P1 cells and stem-cell types in other animals. Additionally, we report the presence of two other morphotypes in P2 that could only be detected by fluorescence microscopy, as well as a morphotype revealed via combined microscopy/FC. This integrative experimental workflow combined cells physical separation with different microscopic image capture technologies, enabling us to better tackle the characterization of the heterogeneous composition of coelomocytes populations.
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Affiliation(s)
- Claúdia Andrade
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Medicas, Universidade NOVA de Lisboa, Lisboa, Portugal
- Flow Cytometry SRL, Instituto Gulbenkian Ciencia, Oeiras, Portugal
| | - Bárbara Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Silvia Guatelli
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- ICREA (Institut Català de Recerca i Estudis Avancats), Barcelona, Spain
| | - Beatriz Simões
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Claúdia Bispo
- Flow Cytometry SRL, Instituto Gulbenkian Ciencia, Oeiras, Portugal
| | - Cinzia Ferrario
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
| | - Francesco Bonasoro
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - José Rino
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Michela Sugni
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
| | - Rui Gardner
- Flow Cytometry SRL, Instituto Gulbenkian Ciencia, Oeiras, Portugal
| | - Rita Zilhão
- Departamento de Biologia Vegetal, Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Ruiz-Ramos DV, Schiebelhut LM, Hoff KJ, Wares JP, Dawson MN. An initial comparative genomic autopsy of wasting disease in sea stars. Mol Ecol 2020; 29:1087-1102. [PMID: 32069379 DOI: 10.1111/mec.15386] [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: 06/22/2019] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 12/18/2022]
Abstract
Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as "asteroid idiopathic wasting syndrome" (AIWS) due to its elusive aetiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell-tale symptoms. Here, we take a forensic genomic approach to discover candidate genes that may help explain sea star wasting syndrome. We report the first genome and annotation for Pisaster ochraceus, along with differential gene expression (DGE) analyses in four size classes, three tissue types, and in symptomatic and asymptomatic individuals. We integrate nucleotide polymorphisms associated with survivors of the wasting disease outbreak, DGE associated with temperature treatments in P. ochraceus, and DGE associated with wasting in another asteroid Pycnopodia helianthoides. In P. ochraceus, we found DGE across all tissues, among size classes, and between asymptomatic and symptomatic individuals; the strongest wasting-associated DGE signal was in pyloric caecum. We also found previously identified outlier loci co-occur with differentially expressed genes. In cross-species comparisons of symptomatic and asymptomatic individuals, consistent responses distinguish genes associated with invertebrate innate immunity and chemical defence, consistent with context-dependent stress responses, defensive apoptosis, and tissue degradation. Our analyses thus highlight genomic constituents that may link suspected environmental drivers (elevated temperature) with intrinsic differences among individuals (age/size, alleles associated with susceptibility) that elicit organismal responses (e.g., coelomocyte proliferation) and manifest as sea star wasting mass mortality.
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Affiliation(s)
- Dannise V Ruiz-Ramos
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
| | - Lauren M Schiebelhut
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
| | - Katharina J Hoff
- Institute for Computer Science and Mathematics, University of Greifswald, Greifswald, Germany.,Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - John P Wares
- Department of Genetics and the Odum School of Ecology, University of Georgia, Athens, GA, USA
| | - Michael N Dawson
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
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Kondo M, Akasaka K. Current Status of Echinoderm Genome Analysis - What do we Know? Curr Genomics 2012; 13:134-43. [PMID: 23024605 PMCID: PMC3308324 DOI: 10.2174/138920212799860643] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 09/20/2011] [Accepted: 09/30/2011] [Indexed: 11/22/2022] Open
Abstract
Echinoderms have long served as model organisms for a variety of biological research, especially in the field of developmental biology. Although the genome of the purple sea urchin Strongylocentrotus purpuratus has been sequenced, it is the only echinoderm whose whole genome sequence has been reported. Nevertheless, data is rapidly accumulating on the chromosomes and genomic sequences of all five classes of echinoderms, including the mitochondrial genomes and Hox genes. This blossoming new data will be essential for estimating the phylogenetic relationships among echinoderms, and also to examine the underlying mechanisms by which the diverse morphologies of echinoderms have arisen.
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Affiliation(s)
- Mariko Kondo
- Misaki Marine Biological Station, Graduate School of Science, and Center for Marine Biology, The University of Tokyo, Japan
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DUFFY LISA, SEWELL MARYA, MURRAY BRIANG. Chromosome number and chromosome variation in embryos of Evechinus chloroticus(Echinoidea: Echinometridae): Is there conservation of chromosome number in the Phylum Echinodermata? New findings and a brief review. INVERTEBR REPROD DEV 2007. [DOI: 10.1080/07924259.2007.9652249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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