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Arimura S, Wong MKS, Inoue R, Kawano M, Shimoyama K, Fujimori C, Tokunaga K, Takagi W, Hyodo S. Functional characterization of follicle-stimulating hormone and luteinizing hormone receptors in cloudy catshark, Scyliorhinus torazame. Gen Comp Endocrinol 2024; 354:114542. [PMID: 38685391 DOI: 10.1016/j.ygcen.2024.114542] [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: 11/13/2023] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
The follicle-stimulating hormone receptor (FSHR) and luteinizing hormone receptor (LHR) in cloudy catshark were cloned, and recombinant FSHR and LHR were expressed for characterization. Ventral lobe extract (VLE) from the pituitary contains homologous FSH and LH, and it stimulated the cAMP signaling of FSHR and LHR dose-dependently. Two transcript variants of LHR (LHR-L with exon 10 and LHR-S without) were identified, and LHR-S was the dominant form with higher basal cAMP activity without VLE stimulation. Among various developmental stages of follicles, FSHR expression was mainly associated with the pre-vitellogenic and early white follicles. When follicles were recruited into vitellogenesis, the expression of FSHR decreased while of LHR was upregulated reciprocally, suggesting that LHR may also be responsible for the control of vitellogenesis in chondrichthyans. The expression of LHR-L was upregulated among maturing follicles before ovulation, indicating LHR-L could have a specific role in receiving the LH surge signal for final maturation. Plasma LH-like activity was transiently increased prior to the progesterone (P4)-surge and testosterone-drop at the beginning of P4-phase, supporting a pituitary control of follicle-maturation via LH signaling in chondrichthyans. The expression of follicular LHR was downregulated during the P4-phase when LH-like activity was high, indicating that the LH-dependent downregulation of LHR is conserved in chondrichthyans as it is in other vertebrate lineages. (213 words).
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Affiliation(s)
- Shogo Arimura
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Marty Kwok Shing Wong
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Ryotaro Inoue
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Mai Kawano
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Koya Shimoyama
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Chika Fujimori
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
| | - Kotaro Tokunaga
- Ibaraki Prefectural Oarai Aquarium, Oarai, Ibaraki 311-1301, Japan.
| | - Wataru Takagi
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Susumu Hyodo
- Laboratory of Physiology, Department of Marine Biosciences, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
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Wu J, Liu F, Jiao J, Luo H, Fan S, Liu J, Wang H, Cui N, Zhao N, Qu Q, Kuraku S, Huang Z, Xu L. Comparative genomics illuminates karyotype and sex chromosome evolution of sharks. CELL GENOMICS 2024:100607. [PMID: 38996479 DOI: 10.1016/j.xgen.2024.100607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/01/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024]
Abstract
Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow evolutionary rate of chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The chondrichthyan common ancestor had a proto-vertebrate-like karyotype, including the presence of 18 microchromosome pairs. The X chromosome is a conversed microchromosome shared by all sharks, suggesting a likely common origin of the sex chromosome at least 181 million years ago. We characterized the Y chromosomes of two sharks that are highly differentiated from the X except for a small young evolutionary stratum and a small pseudoautosomal region. We found that shark sex chromosomes lack global dosage compensation but that dosage-sensitive genes are locally compensated. Our study on shark chromosome evolution enhances our understanding of shark sex chromosomes and vertebrate chromosome evolution.
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Affiliation(s)
- Jiahong Wu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Fujiang Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jie Jiao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haoran Luo
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Ministry of Education for the Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Shiyu Fan
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiao Liu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hongxiang Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ning Cui
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ning Zhao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qingming Qu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan; Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
| | - Zhen Huang
- Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou 350108, China
| | - Luohao Xu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China.
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3
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Clark AJ, Atkinson SR, Scarponi V, Cane T, Geraldi NR, Hendy IW, Shipway JR, Peck M. Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities. PeerJ 2024; 12:e17091. [PMID: 38708339 PMCID: PMC11067900 DOI: 10.7717/peerj.17091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/20/2024] [Indexed: 05/07/2024] Open
Abstract
Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and conservation monitoring programs around the globe.
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Affiliation(s)
- Alice J. Clark
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sophie R. Atkinson
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Valentina Scarponi
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Tim Cane
- Department of Geography, University of Sussex, Brighton, United Kingdom
| | | | - Ian W. Hendy
- School of Biological Science, University of Portsmouth, Portsmouth, United Kingdom
| | - J. Reuben Shipway
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Mika Peck
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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Torralba Sáez M, Hofreiter M, Straube N. Shark genome size evolution and its relationship with cellular, life-history, ecological, and diversity traits. Sci Rep 2024; 14:8909. [PMID: 38632352 PMCID: PMC11024215 DOI: 10.1038/s41598-024-59202-4] [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: 11/24/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Among vertebrates, sharks exhibit both large and heterogeneous genome sizes ranging from 2.86 to 17.05 pg. Aiming for a better understanding of the patterns and causalities of shark genome size evolution, we applied phylogenetic comparative methods to published genome-size estimates for 71 species representing the main phylogenetic lineages, life-histories and ecological traits. The sixfold range of genome size variation was strongly traceable throughout the phylogeny, with a major expansion preceding shark diversification during the late Paleozoic and an ancestral state (6.33 pg) close to the present-day average (6.72 pg). Subsequent deviations from this average occurred at higher rates in squalomorph than in galeomorph sharks and were unconnected to evolutionary changes in the karyotype architecture, which were dominated by descending disploidy events. Genome size was positively correlated with cell and nucleus sizes and negatively with metabolic rate. The metabolic constraints on increasing genome size also manifested at higher phenotypic scales, with large genomes associated with slow lifestyles and purely marine waters. Moreover, large genome sizes were also linked to non-placental reproductive modes, which may entail metabolically less demanding embryological developments. Contrary to ray-finned fishes, large genome size was associated neither with the taxonomic diversity of affected clades nor with low genetic diversity.
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Affiliation(s)
- Mario Torralba Sáez
- Ichthyology Section, Bavarian State Collection of Zoology (SNSB-ZSM), 81247, Munich, Germany
- Systematic Zoology, Department Biology II, Faculty of Biology, Ludwig Maximilian University of Munich (LMU), 82152, Munich, Germany
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Nicolas Straube
- Department of Natural History, University Museum Bergen, University of Bergen (UiB), 5007, Bergen, Norway.
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Harshan P, Sukumaran S, Gopalakrishnan A. De novo transcriptome for Chiloscyllium griseum, a long-tail carpet shark of the Indian waters. Sci Data 2024; 11:285. [PMID: 38461175 PMCID: PMC10924892 DOI: 10.1038/s41597-024-03093-7] [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: 09/25/2023] [Accepted: 02/27/2024] [Indexed: 03/11/2024] Open
Abstract
Sharks have thrived in the oceans for 400 million years, experienced five extinctions and evolved into today's apex predators. However, enormous genome size, poor karyotyping and limited tissue sampling options are the bottlenecks in shark research. Sharks of the family Orectolobiformes act as model species in transcriptome research with exceptionally high reproductive fecundity, catch prominence and oviparity. The present study illustrates a de novo transcriptome for an adult grey bamboo shark, Chiloscyllium griseum (Chondrichthyes; Hemiscyllidae) using paired-end RNA sequencing. Around 150 million short Illumina reads were obtained from five different tissues and assembled using the Trinity assembler. 70,647 hits on Uniprot by BLASTX was obtained after the transcriptome annotation. The data generated serve as a basis for transcriptome-based population genetic studies and open up new avenues in the field of comparative transcriptomics and conservation biology.
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Affiliation(s)
- Pooja Harshan
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
- Cochin University of Science and Technology, South Kalamassery, Ernakulam, Kerala, 682022, India.
| | - Sandhya Sukumaran
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
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6
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Eastment RV, Wong BBM, McGee MD. Convergent genomic signatures associated with vertebrate viviparity. BMC Biol 2024; 22:34. [PMID: 38331819 PMCID: PMC10854053 DOI: 10.1186/s12915-024-01837-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: 08/29/2023] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Viviparity-live birth-is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes? RESULTS We reveal convergent changes in protein family sizes, protein-coding regions, introns, and untranslated regions (UTRs) in a number of distantly related viviparous lineages. Specifically, we identify 15 protein families showing evidence of contraction or expansion associated with viviparity. We additionally identify elevated substitution rates in both coding and noncoding sequences in several viviparous lineages. However, we did not find any convergent changes-be it at the nucleotide or protein level-common to all viviparous lineages. CONCLUSIONS Our results highlight the value of macroevolutionary comparative genomics in determining the genomic basis of complex evolutionary transitions. While we identify a number of convergent genomic changes that may be associated with the evolution of viviparity in vertebrates, there does not appear to be a convergent molecular signature shared by all viviparous vertebrates. Ultimately, our findings indicate that a complex trait such as viviparity likely evolves with changes occurring in multiple different pathways.
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Affiliation(s)
- Rhiannon V Eastment
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia.
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
| | - Matthew D McGee
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
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Wagner CI, Kopp MEL, Thorburn J, Jones CS, Hoarau G, Noble LR. Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome. G3 (BETHESDA, MD.) 2023; 13:jkad146. [PMID: 37395764 PMCID: PMC10468316 DOI: 10.1093/g3journal/jkad146] [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: 02/28/2023] [Revised: 02/28/2023] [Accepted: 06/12/2023] [Indexed: 07/04/2023]
Abstract
Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish's genome, of which 31,979 are functionally annotated.
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Affiliation(s)
- C Isabel Wagner
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Martina E L Kopp
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - James Thorburn
- School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, EH11 4BN, UK
| | - Catherine S Jones
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3FX, UK
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Leslie R Noble
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
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Kuraku S, Kaiya H, Tanaka T, Hyodo S. Evolution of Vertebrate Hormones and Their Receptors: Insights from Non-Osteichthyan Genomes. Annu Rev Anim Biosci 2023; 11:163-182. [PMID: 36400012 DOI: 10.1146/annurev-animal-050922-071351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Homeostatic control and reproductive functions of humans are regulated at the molecular levels largely by peptide hormones secreted from endocrine and/or neuroendocrine cells in the central nervous system and peripheral organs. Homologs of those hormones and their receptors function similarly in many vertebrate species distantly related to humans, but the evolutionary history of the endocrine system involving those factors has been obscured by the scarcity of genome DNA sequence information of some taxa that potentially contain their orthologs. Focusing on non-osteichthyan vertebrates, namely jawless and cartilaginous fishes, this article illustrates how investigating genome sequence information assists our understanding of the diversification of vertebrate gene repertoires in four broad themes: (a) the presence or absence of genes, (b) multiplication and maintenance of paralogs, (c) differential fates of duplicated paralogs, and (d) the evolutionary timing of gene origins.
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Affiliation(s)
- Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan; .,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan.,Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Hiroyuki Kaiya
- Grandsoul Research Institute of Immunology, Inc., Uda, Japan
| | - Tomohiro Tanaka
- Department of Gastroenterology and Metabolism, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
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Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead. iScience 2022; 26:105815. [PMID: 36632067 PMCID: PMC9826928 DOI: 10.1016/j.isci.2022.105815] [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: 08/08/2022] [Revised: 11/23/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead (Sphyrna mokarran) and the Endangered shortfin mako (Isurus oxyrinchus) sharks, with genetic diversity and historical demographic comparisons to other shark species. The great hammerhead exhibited low genetic variation, with 8.7% of the 2.77 Gbp genome in runs of homozygosity (ROH) > 1 Mbp and 74.4% in ROH >100 kbp. The 4.98 Gbp shortfin mako genome had considerably greater diversity and <1% in ROH > 1 Mbp. Both these sharks experienced precipitous declines in effective population size (Ne) over the last 250 thousand years. While shortfin mako exhibited a large historical Ne that may have enabled the retention of higher genetic variation, the genomic data suggest a possibly more concerning picture for the great hammerhead, and a need for evaluation with additional individuals.
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