1
|
Wang C, Lai T, Ye P, Yan Y, Feutry P, He B, Huang Z, Zhu T, Wang J, Chen X. Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae. Gene 2022; 820:146232. [PMID: 35114282 DOI: 10.1016/j.gene.2022.146232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/22/2021] [Accepted: 01/18/2022] [Indexed: 01/08/2023]
Abstract
In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region and specially a 594 bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.
Collapse
Affiliation(s)
- Chen Wang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China
| | - Tinghe Lai
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Peiyuan Ye
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Yunrong Yan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524000, China
| | - Pierre Feutry
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, Tasmania 7000, Australia
| | - Binyuan He
- Guangxi Academy of Oceanography, Nanning 530000, China
| | | | - Ting Zhu
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiao Chen
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; Guangxi Mangrove Research Center, Beihai 536000, China.
| |
Collapse
|
2
|
Pears JB, Johanson Z, Trinajstic K, Dean MN, Boisvert CA. Mineralization of the Callorhinchus Vertebral Column (Holocephali; Chondrichthyes). Front Genet 2020; 11:571694. [PMID: 33329708 PMCID: PMC7732695 DOI: 10.3389/fgene.2020.571694] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/30/2020] [Indexed: 12/12/2022] Open
Abstract
Members of the Chondrichthyes (Elasmobranchii and Holocephali) are distinguished by their largely cartilaginous endoskeletons, which comprise an uncalcified core overlain by a mineralized layer; in the Elasmobranchii (sharks, skates, rays) most of this mineralization takes the form of calcified polygonal tiles known as tesserae. In recent years, these skeletal tissues have been described in ever increasing detail in sharks and rays, but those of Holocephali (chimaeroids) have been less well-studied, with conflicting accounts as to whether or not tesserae are present. During embryonic ontogeny in holocephalans, cervical vertebrae fuse to form a structure called the synarcual. The synarcual mineralizes early and progressively, anteroposteriorly and dorsoventrally, and therefore presents a good skeletal structure in which to observe mineralized tissues in this group. Here, we describe the development and mineralization of the synarcual in an adult and stage 36 elephant shark embryo (Callorhinchus milii). Small, discrete, but irregular blocks of cortical mineralization are present in stage 36, similar to what has been described recently in embryos of other chimaeroid taxa such as Hydrolagus, while in Callorhinchus adults, the blocks of mineralization are more irregular, but remain small. This differs from fossil members of the holocephalan crown group (Edaphodon), as well as from stem group holocephalans (e.g., Symmorida, Helodus, Iniopterygiformes), where tesserae are notably larger than in Callorhinchus and show similarities to elasmobranch tesserae, for example with respect to polygonal shape.
Collapse
Affiliation(s)
- Jacob B Pears
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Zerina Johanson
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Kate Trinajstic
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Mason N Dean
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | | |
Collapse
|
3
|
López‐Romero FA, Klimpfinger C, Tanaka S, Kriwet J. Growth trajectories of prenatal embryos of the deep-sea shark Chlamydoselachus anguineus (Chondrichthyes). JOURNAL OF FISH BIOLOGY 2020; 97:212-224. [PMID: 32307702 PMCID: PMC7497067 DOI: 10.1111/jfb.14352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/03/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
Chlamydoselachus anguineus, Garman 1884, commonly called the frilled shark, is a deep-sea shark species occurring up to depths of 1300 m. It is assumed to represent an ancient morphotype of sharks (e.g., terminal mouth opening, more than five gill slits) and thus is often considered to represent plesiomorphic traits for sharks. Therefore, its early ontogenetic developmental traits are important for understanding the evolution of its particular phenotype. Here, we established six stages for prenatal embryos and used linear measurements and geometric morphometrics to analyse changes in shape and size as well as their timing during different embryonic stages. Our results show a change in head shape and a relocation of the mouth opening at a late stage of development. We also detected a negative allometric growth of the head and especially the eye compared to the rest of the body and a sexual dimorphism in total body length, which differs from the known data for adults. A multivariate analysis of covariance shows a significant interaction of shape related to the logarithm of centroid size and developmental stage. Geometric morphometrics results indicate that the head shape changes as a covariate of body size while not accounting for differences between sexes. The growth pattern of stages 32 and 33 indicates a shift in head shape, thus highlighting the moment in development when the jaws start to elongate anteriorly to finally achieve the adult condition of terminal mouth opening rather than retaining the early embryonic subterminal position as is typical for sharks. Thus, the antero-terminal mouth opening of the frilled shark has to be considered a derived feature.
Collapse
Affiliation(s)
| | | | - Sho Tanaka
- School of Marine Science and Technology, Faculty of Marine Science and TechnologyTokai UniversityShizuoka Shimizu‐kuJapan
| | - Jürgen Kriwet
- Department of PaleontologyUniversity of ViennaViennaAustria
| |
Collapse
|
4
|
Vella A, Vella N, Schembri S. A molecular approach towards taxonomic identification of elasmobranch species from Maltese fisheries landings. Mar Genomics 2017; 36:17-23. [PMID: 28923557 DOI: 10.1016/j.margen.2017.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 08/25/2017] [Accepted: 08/26/2017] [Indexed: 11/27/2022]
Abstract
The mitochondrial genome, through the application of DNA barcoding, provides a powerful tool for identifying species even when specimens are either incomplete or belong to species that exhibit cryptic diversity. In fisheries management accurate identification of whole or part of the specimens landed is a fundamental requirement for the conservation of species affected directly or indirectly by the fisheries activities. In this study cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) sequences were used to genetically distinguish 36 elasmobranch species collected from Maltese (Central Mediterranean) commercial fisheries landings. Each species was analysed using these two mtDNA loci where COI (610bp) and ND2 (990bp) efficiently distinguished between the various species studied, leading to the identification of 101 haplotypes, with the intraspecific p-distance ranging between 0 and 0.75% (mean 0.10%, SD ±0.13%). This study enhances the molecular data available on elasmobranchs by providing new ND2 sequences for various species, while providing both COI and ND2 data for poorly studied Mediterranean species including: the large pelagic sharks Alopias vulpinus, A. superciliosus, Carcharhinus altimus, C. plumbeus, Carcharadon carcharias, Isurus oxyrinchus, Prionace glauca and Odontaspis ferox; the smaller demersal sharks Somniosus rostratus, Squatina aculeata, S. oculata and Squalus sp.; and the endemic stingray Dasyatis tortonesei. It also confirmed the landings of species whose identification relies strongly on molecular tools, namely Squalus sp. and D. tortonesei, which are both first confirmed records amongst Maltese fisheries landings. Morphologically, the latter two species, can be easily misidentified with S. blainville and D. pastinaca respectively. Additionally, this study evaluated the genetic differences between different polychromatic forms of Raja clavata, R. radula and Dipturus oxyrinchus. Based on the currently analysed specimens, no significant genetic differences were found between the various forms and thus no further speciation within the species was identified.
Collapse
Affiliation(s)
- Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida MSD2080, Malta.
| | - Noel Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida MSD2080, Malta.
| | - Sarah Schembri
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida MSD2080, Malta
| |
Collapse
|
5
|
Amaral CRL, Pereira F, Silva DA, Amorim A, de Carvalho EF. The mitogenomic phylogeny of the Elasmobranchii (Chondrichthyes). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:867-878. [DOI: 10.1080/24701394.2017.1376052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Cesar R. L. Amaral
- Departamento de Ecologia, Laboratório de Diagnósticos por DNA, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Filipe Pereira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Dayse A. Silva
- Departamento de Ecologia, Laboratório de Diagnósticos por DNA, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - António Amorim
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Elizeu F. de Carvalho
- Departamento de Ecologia, Laboratório de Diagnósticos por DNA, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
6
|
Kryukova NV. Functional analysis of the musculo-skeletal system of the gill apparatus in Heptranchias perlo (Chondrichthyes: Hexanchidae). J Morphol 2017; 278:1075-1090. [PMID: 28470783 DOI: 10.1002/jmor.20695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 03/15/2017] [Accepted: 04/13/2017] [Indexed: 11/09/2022]
Abstract
Musculo-skeletal morphology is an indispensable source for understanding functional adaptations. Analysis of morphology of the branchial apparatus of Hexanchiform sharks can provide insight into aspects of their respiration that are difficult to observe directly. In this study, I compare the structure of the musculo-skeletal system of the gill apparatus of Heptranchias perlo and Squalus acanthias in respect to their adaptation for one of two respiratory mechanisms known in sharks, namely, the active two-pump (oropharyngeal and parabranchial) ventilation and the ram-jet ventilation. In both species, the oropharyngeal pump possesses two sets of muscles, one for compression and the other for expansion. The parabranchial pump only has constrictors. Expansion of this pump occurs only due to passive elastic recoil of the extrabranchial cartilages. In Squalus acanthias the parabranchial chambers are large and equipped by powerful superficial constrictors. These muscles and the outer walls of the parabranchial chambers are much reduced in Heptranchias perlo, and thus it likely cannot use this pump. However, this reduction allows for vertical elongation of outer gill slits which, along with greater number of gill pouches, likely decreases branchial resistance and, at the same time, increases the gill surface area, and can be regarded as an adaptation for ram ventilation at lower speeds.
Collapse
Affiliation(s)
- Nadezhda V Kryukova
- Laboratory of morphological adaptations of vertebrates, Severtsov Institute of Ecology and Evolution, RAS, Moscow, 119071, Russia
| |
Collapse
|
7
|
Bustamante C, Bennett MB, Ovenden JR. Genetype and phylogenomic position of the frilled shark Chlamydoselachus anguineus inferred from the mitochondrial genome. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:18-20. [PMID: 33473392 PMCID: PMC7799599 DOI: 10.1080/23802359.2015.1137801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The genetype of Chlamydoselachus anguineus from Australian waters is described using the whole mitochondrial genome obtained from Illumina NGS technology. Total length of the mitogenome is 17 313 bp, consisting of 2 rRNAs, 13 protein-coding genes, 22 tRNA genes and 2 non-coding regions thus updating the previously available mitogenome for this species. The phylogenomic reconstruction comprising all available species of Superorder Squalomorphi supports the inclusion of C. anguineus in a divergent clade inside Order Hexanchiformes. Phyletic relationships inferred from the whole mitochondrial genomes are in agreement with traditional taxonomy. The low divergence between C. anguineus genomes (>99.9% genetic identity) is consistent with a widespread population in the west Pacific Ocean.
Collapse
Affiliation(s)
- Carlos Bustamante
- Shark and Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia.,Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Michael B Bennett
- Shark and Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Jennifer R Ovenden
- Shark and Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| |
Collapse
|
8
|
The complete mitochondrial genome sequence of the world's largest fish, the whale shark (Rhincodon typus), and its comparison with those of related shark species. Gene 2014; 539:44-9. [DOI: 10.1016/j.gene.2014.01.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/16/2014] [Accepted: 01/26/2014] [Indexed: 11/22/2022]
|