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Fam YQ, Jamaluddin JAF, Muhammad-Rasul AH, Ilham-Norhakim ML, Rosely NFN, Lavoué S. Contrasting genetic and morphological differentiation among geographical lineages of a stenotopic miniature rasborine, Boraras maculatus, in Peninsular Malaysia. J Fish Biol 2024; 104:171-183. [PMID: 37775959 DOI: 10.1111/jfb.15572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/12/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
The variability in the stenotopic miniature rasborine Boraras maculatus (Cypriniformes: Danionidae: Rasborinae) across acidic-water habitats of Peninsular Malaysia (PM) was investigated using two molecular markers (the mitochondrial cytochrome c oxidase subunit I [COI] gene and the nuclear rhodopsin gene), as well as morphological evidence. Molecular phylogenetic analyses revealed differentiation among populations of B. maculatus in PM with the distinction of four allopatric lineages. Each of them was recognized as a putative species by automatic species delimitation methods. These lineages diverged from each other between 7.4 and 1.9 million years ago. A principal component analysis (PCA) was conducted to examine the multivariate variation in 11 morphometric measurements among three of these lineages. PCA results showed a significant overlap in morphological characteristics among these lineages. Additionally, a photograph-based machine learning approach failed to fully differentiate these lineages, suggesting limited morphological differentiation. B. maculatus represents a case of morphological stasis in a stenotopic miniature species. Strong habitat preference, coupled with long-term habitat fragmentation, may explain why each lineage of B. maculatus has a restricted distribution and did not disperse to other regions within and outside of PM, despite ample possibilities when the Sunda shelf was emerged and drained by large paleodrainages for most of the past 7 million years. The conservation status of B. maculatus and its peat swamp habitats are discussed, and it is concluded that peat swamps comprise several evolutionary units. Each of these units is considered a conservation unit and deserves appropriate protection.
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Affiliation(s)
- Yi Qing Fam
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | | | | | - Mohd Lokman Ilham-Norhakim
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Johor, Malaysia
- Kim Ichthyologist Centre, Kg Parit Samsu, Jalan Temenggong Ahmad, Johor, Malaysia
| | - Nik Fadzly N Rosely
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
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2
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Alexandre NM, Cameron AC, Tian D, Chatla K, Kolora SRR, Whiteman NK, Turner TF, Reinthal PN. Chromosome-level reference genomes of two imperiled desert fishes: spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis). G3 (Bethesda) 2023; 13:jkad157. [PMID: 37466215 PMCID: PMC10542311 DOI: 10.1093/g3journal/jkad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/20/2023]
Abstract
North American minnows (Cypriniformes: Leuciscidae) comprise a diverse taxonomic group, but many members, particularly those inhabiting deserts, face elevated extinction risks. Despite conservation concerns, leuciscids remain under sampled for reference assemblies relative to other groups of freshwater fishes. Here, we present 2 chromosome-scale reference genome assemblies spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis) using PacBio, Illumina and Omni-C technologies. The complete assembly for spikedace was 882.1 Mb in total length comprised of 83 scaffolds with N50 = 34.8 Mb, L50 = 11, N75 = 32.3 Mb, and L75 = 18. The complete assembly for loach minnow was 1.3 Gb in total length comprised of 550 scaffolds with N50 = 48.6 Mb, L50 = 13, N75 = 42.3 Mb, and L75 = 20. Completeness assessed via Benchmarking Universal Single-Copy Orthologues (BUSCO) metrics using the Actinopterygii BUSCO database showed ∼97% for spikedace and ∼98% for loach minnow of complete BUSCO proportions. Annotation revealed approximately 32.58 and 29.04% of spikedace and loach minnow total genome lengths to be comprised of protein-coding genes, respectively. Comparative genomic analyses of these endangered and co-distributed fishes revealed widespread structural variants, gene family expansions, and evidence of positive selection in both genomes.
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Affiliation(s)
- Nicolas M Alexandre
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Alexander C Cameron
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - David Tian
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Sree R R Kolora
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, Berkeley, CA 94720, USA
| | - Thomas F Turner
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Peter N Reinthal
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Li C, Xiao H, Zhang X, Lin H, Elmer KR, Zhao J. Deep genome-wide divergences among species in White Cloud Mountain minnow Tanichthys albonubes ( Cypriniformes: Tanichthyidae) complex: Conservation and species management implications. Mol Phylogenet Evol 2023; 182:107734. [PMID: 36804428 DOI: 10.1016/j.ympev.2023.107734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Identifying cryptic species is important for the assessments of biodiversity. Further, untangling mechanisms underlying the origins of cryptic species can facilitate our understanding of evolutionary processes. Advancements in genomic approaches for non-model systems have offered unprecedented opportunities to investigate these areas. The White Cloud Mountain minnow (Tanichthys albonubes) is a popular freshwater pet fish worldwide but its wild populations in China are critically endangered. Recent research based on a few molecular markers suggested that this species in fact comprised seven cryptic species, of which six were previously unknown. Here, we tested six of these cryptic species and quantified genomic interspecific divergences between species in the T. albonubes complex by analyzing genome-wide restriction site-associated DNA sequencing (RADseq) data generated from 189 individuals sampled from seven populations (including an outgroup congeneric species, T. micagemmae). We found that six cryptic species previously suggested were well supported by RADseq data. The genetic diversity of each species in the T. albonubes complex was low compared with T. micagemmae and the contemporary effective population sizes (Ne) of each cryptic species were small. Phylogenetic analysis showed seven clades with high support values confirmed with Neighbor-Net trees. The pairwise divergences between species in T. albonubes complex were deep and the highly differentiated loci were evenly distributed across the genome. We proposed that the divergence level of T. albonubes complex is at a late stage of cryptic speciation and lacking gene flow. Our findings provide new insights into cryptic speciation and have important implications for conservation and species management of T. albonubes complex.
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Affiliation(s)
- Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Han Xiao
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Xiuxia Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Hungdu Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China.
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Xuan B, Li M, Ni X, Fu C. Complete mitochondrial genome of Belligobio pengxianensis ( Cypriniformes: Gobionidae). Mitochondrial DNA B Resour 2023; 8:434-438. [PMID: 36998785 PMCID: PMC10044147 DOI: 10.1080/23802359.2023.2192310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
Belligobio pengxianensis is a small fish endemic to the upper Yangtze River of China. In this study, the complete mitochondrial genome of B. pengxianensis is determined for the first time, and it should become a reference sequence to aid in species identification, biodiversity monitoring and conservation. The mitogenome has overall length of 16,610 bp and AT content of 55.23%, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one non-coding control region. The results of phylogenetic analyses show that B. pengxianensis is nested within the genus Hemibarbus.
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Affiliation(s)
- Bo Xuan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Mingyue Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaomin Ni
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
- CONTACT Cuizhang Fu Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
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Cavallino L, Rincón L, Scaia MF. Social behaviors as welfare indicators in teleost fish. Front Vet Sci 2023; 10:1050510. [PMID: 37168096 PMCID: PMC10164990 DOI: 10.3389/fvets.2023.1050510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
Animal welfare is a key issue not only for aquaculture industry and food production, but also for daily husbandry practices in research topics related to physiology in wild and farmed animals. In this context, teleost fish constitute interesting models to assess alternative welfare indicators because of their wide diversity in reproductive and social structures. Any framework for assessing teleost fish welfare needs to account for the physiological mechanisms involved in each species as a first step. A comprehensive approach should also take into account how these physiological and behavioral parameters can be altered by environmental enrichment considering the specific requirements in each case and identifying intrinsic biological characteristics of individual species. This review will show how cortisol and sex steroids regulate social behavior in teleost fish, and how different aspects of social behavior can be employed as welfare indicators according to specific characteristics in each case. This article will consider evidence in teleost fish, including cichlids, characids and cyprinids with different reproductive strategies and social structures (e.g., territorial social hierarchies or shoaling behavior). Neotropical species will be particularly emphasized. The main laboratory-based animal welfare indicators are cortisol, a classical stress hormone, together with sex steroids. Considering that the endocrine landscape is intrinsically related to social behavior, reproductive and agonistic behavioral traits such as aggression, anxiety and courtship are key elements to assess welfare under housing and culture conditions. This review highlights the importance of assessing physiological mechanisms and identifying behavioral characteristics in teleost fish, especially in Neotropical species, as a baseline to understand which environmental enrichment can improve animal welfare in each individual species.
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Affiliation(s)
- Luciano Cavallino
- Instituto de Biodiversidad y Biología Experimental y Aplicada – CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Neuroendocrinología y Comportamiento, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Rincón
- Instituto de Biodiversidad y Biología Experimental y Aplicada – CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Neuroendocrinología y Comportamiento, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Florencia Scaia
- Instituto de Biodiversidad y Biología Experimental y Aplicada – CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Neuroendocrinología y Comportamiento, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- *Correspondence: María Florencia Scaia,
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Schedel FDB, Musilova Z, Indermaur A, Bitja‐Nyom AR, Salzburger W, Schliewen UK. Towards the phylogenetic placement of the enigmatic African genus Prolabeops Schultz, 1941. J Fish Biol 2022; 101:1333-1342. [PMID: 36053860 PMCID: PMC9826184 DOI: 10.1111/jfb.15205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
The small cyprinid genus Prolabeops Schultz, 1941 is restricted to the Nyong and Sanaga River systems in Cameroon. In the past, the genus had been suggested to be either a member of the Labeoninae, Torinae or the Smiliogastrinae mainly on the basis of morphological similarities, and it is nowadays considered as incertae sedis within the Cypriniformes. This study provides the first attempt to reveal the phylogenetic position of Prolabeops using molecular data. For this purpose, the authors sequenced a large fraction of the mitochondrial genome (c. 13,600 bp), including all mitochondrial protein coding genes, of two Prolabeops melanhypopterus specimens and an additional four Enteromius specimens. The large-scale phylogenetic analysis was based on an alignment including all mitochondrial protein coding genes of 902 specimens representing c. 899 cypriniform species. Prolabeops was clearly recovered within the African Smiliogastrinae, forming a weakly supported clade together with Enteromius jae, Enteromius hulstaerti and Barboides gracilis. The study data underline the urgent need of a thorough taxonomic revision of the small African barbs collectively placed in the genus Enteromius.
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Affiliation(s)
- Frederic D. B. Schedel
- Zoological InstituteUniversity of BaselBaselSwitzerland
- Faculty of Biology, Division of Evolutionary BiologyLMU MunichMartinsriedGermany
| | - Zuzana Musilova
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Arnold Roger Bitja‐Nyom
- Department of Biological SciencesUniversity of NgaoundéréNgaoundéréCameroon
- Department of Management of Fisheries and Aquatic EcosystemsUniversity of DoualaDoualaCameroon
| | | | - Ulrich K. Schliewen
- Department of IchthyologySNSB‐Bavarian State Collection Zoology (ZSM)MunichGermany
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Abstract
Although Mesogobio lachneri is the type species of the genus Mesogobio, its systematic position and status have remained unresolved to date. In this study, for the first time, we report the complete mitochondrial genome of M. lachneri using Sanger sequencing. It is a circular genome with a length of 16,602 bp, comprising 22 tRNAs, 13 protein-coding genes (PCGs), two rRNAs, and one non-coding control region. Our phylogenetic analysis reveals that M. lachneri is the close relative of the genus Gobio, indicating that Mesogobio may be a valid genus.
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Affiliation(s)
- Wei Tian
- School of Life Sciences, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, Fudan University, Shanghai, China
| | - Xiaomin Ni
- School of Life Sciences, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, Fudan University, Shanghai, China
| | - Cuizhang Fu
- School of Life Sciences, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, Fudan University, Shanghai, China,CONTACT Cuizhang Fu School of Life Sciences, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, Fudan University, Shanghai, China
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Stout C, Schonhuth S, Mayden R, Garrison NL, Armbruster JW. Phylogenomics and classification of Notropis and related shiners ( Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups. PeerJ 2022; 10:e14072. [PMID: 36248715 PMCID: PMC9558623 DOI: 10.7717/peerj.14072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/27/2022] [Indexed: 01/20/2023] Open
Abstract
North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).
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Affiliation(s)
- Carla Stout
- Department of Biological Sciences, California State Polytechnic University, Pomona, Pomona, CA, United States of America
| | - Susana Schonhuth
- Department of Biology, Saint Louis University, St. Louis, MO, United States of America
| | - Richard Mayden
- Department of Biology, Saint Louis University, St. Louis, MO, United States of America
| | - Nicole L. Garrison
- Department of Biology, West Liberty University, West Liberty, WV, United States of America
| | - Jonathan W. Armbruster
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
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Yang X, Ni X, Fu C. Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis ( Cypriniformes: Gobionidae) in Southern China. Life (Basel) 2022; 12:1024. [PMID: 35888112 PMCID: PMC9318155 DOI: 10.3390/life12071024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/17/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023] Open
Abstract
The freshwater gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) is a small fish endemic to southern China. In this study, we used mitochondrial cytochrome b gene (Cytb), from wide-ranging samplings of H. chenhsienensis from the Ou River (the central of southern China) to the Yangtze River Basin (the northernmost part of southern China) to explore genetic variations and the evolutionary history of H. chenhsienensis in southern China. In total, 66 haplotypes were identified from Cytb sequences of 142 H. chenhsienensis individuals, which could be divided into lineages A, B, and C with divergence times of ~4.24 Ma and ~3.03 Ma. Lineage A was distributed in the lower reaches of the Yangtze River, the Oujiang River, and the Jiao River, lineage B was distributed in the Qiantang River and the Cao'e River, whereas lineage C was restricted to the Poyang Lake drainage from the middle reaches of the Yangtze River. Lineage A could be subdivided into sub-lineages A-I, A-II, A-III, and A-IV, with divergence times of 1.30, 0.97, and 0.44 Ma. Lineage C could be subdivided into sub-lineages C-I and C-II, with a divergence time of 0.85 Ma. Our findings indicate that climate change during the Pliocene and Pleistocene eras, as well as the limited dispersal ability of H. chenhsienensis, have been major drivers for shaping the phylogeographical patterns of H. chenhsienensis.
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Cheng Y, Zhang S, Linhartová Z, Shazada NE, Linhart O. Common carp (Cyprinus carpio) sperm reduction during short-term in vitro storage at 4 °C. Anim Reprod Sci 2022; 243:107017. [PMID: 35714400 DOI: 10.1016/j.anireprosci.2022.107017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/10/2022] [Accepted: 06/05/2022] [Indexed: 11/16/2022]
Abstract
This study was designed to optimize a short-term storage protocol for common carp sperm at 4 °C under aerobic condition. Sperm from individual males were collected directly with or without extenders. The results demonstrated that in general, it was similar effect to collect sperm directly in extenders and keeping sperm for 0.5 h after collection without extenders. Sperm was diluted with eight selected extenders (sperm: extender = 2:1, 1:1 and 1:9) and undiluted sperm was used as a control. Sperm and seminal plasma parameters (sperm motility, velocity, membrane integrity, sperm concentration, osmolality and pH in seminal plasma) were evaluated in sperm stored on ice under aerobic conditions at 0, 2, 4, 6 and 8 days post stripping (DPS) using the computer- assisted sperm analysis system. Results showed that 1:1 and 2:1 dilution maintained higher sperm function and more sperm for a longer period. After 8 DPS, the best sperm quality and quantity was recorded in the common carp seminal plasma supplemented with 50 mM NaCl, Cejko extender (2 mM CaCl2, 1 mM MgSO4, 20 mM Tris, 110 mM NaCl, 40 mM KCl, pH 7.5 and 310 mOsm/kg) supplemented with/without 25 mM KCl/NaCl. The reduction of spermatozoa number with time during short-term storage but varied according to different dilution ratios and extenders. At 8 DPS, sperm count has dropped by 22.9 % in a dilution of 1:1 compared to 50.3 % in sperm without dilution. Extenders with diluted 1:1, especially Cejko solution, largely postponed sperm reduction, 21.3 % compared to 55.5 % for sperm stored without extenders.
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Affiliation(s)
- Yu Cheng
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Zatisi 728, 38925 Vodnany, Czech Republic.
| | - Songpei Zhang
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Zatisi 728, 38925 Vodnany, Czech Republic.
| | - Zuzana Linhartová
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Zatisi 728, 38925 Vodnany, Czech Republic
| | - Nururshopa Eskander Shazada
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Zatisi 728, 38925 Vodnany, Czech Republic.
| | - Otomar Linhart
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Zatisi 728, 38925 Vodnany, Czech Republic.
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11
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Jin J, Li C, Zhao J. Descriptions of six new species in White Cloud Mountain minnow Tanichthys albonubes complex ( Cypriniformes: Tanichthyidae) in southern China. J Fish Biol 2022; 100:1062-1087. [PMID: 35174507 DOI: 10.1111/jfb.15012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Tanichthys albonubes is a critically endangered freshwater fish in South China and is classified as a second-class state-protected animal in China. It is also a colourful ornamental fish and has been introduced into many countries and regions around the world. Previous studies have revealed that there are seven cryptic species in the T. albonubes complex. Here, six new species of these cryptic species were diagnosed and described based on external morphology, colour patterns and osteological characteristics: Tanichthys shenzhenensis sp. nov., Tanichthys huidongensis sp. nov., Tanichthys luheensis sp. nov., Tanichthys dongxingensis sp. nov., Tanichthys guipingensis sp. nov. and Tanichthys hainanensis sp. nov. In addition, an identification key to the genus Tanichthys was provided. The key diagnosable characteristics of six new species in T. albonubes complex include the margin colour of dorsal and anal fins, the number of branched dorsal and anal fins, the relative position of the orbitosphenoid to the parasphenoid, the states of the neural complex, the states of the neural spine of the fourth vertebra and the anterior process of the innominatum. These six new species were also well supported by the phylogenetic tree and uncorrected p-distances based on Cyt b sequences. The distribution pattern of the genus Tanichthys is characterized by point-like, discontinuous distribution and geographically isolated on a large scale with narrow distribution ranges of each species. This study provides scientific data for the taxonomy, conservation status assessment and evolution of Tanichthys.
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Affiliation(s)
- Jinjin Jin
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chao Li
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
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12
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Abstract
Mitochondrial genomes of two individuals of Tachanovsky’s gudgeon Ladislavia taczanowskii have been determined on the basis of Sanger dideoxy sequencing. The gene compositions of two genomes contain 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region with the same length 16,614 bp. The phylogenetic tree reveals that the monotypic genus Ladislavia is a sister group of the subfamily Gobioninae within the family Gobionidae.
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Affiliation(s)
- Qi An
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
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13
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Viñuela Rodríguez N, Šanda R, Zogaris S, Vukić J. Evolutionary history of the Pelasgus minnows (Teleostei: Leuciscidae), an ancient endemic genus from the Balkan Peninsula. Mol Phylogenet Evol 2021; 164:107274. [PMID: 34333114 DOI: 10.1016/j.ympev.2021.107274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022]
Abstract
The Balkans are one of the European biodiversity hotspots, hosting outstandingly rich, yet threatened, flora and fauna. This region hosts one of the richest endemic freshwater ichthyofauna in Europe, including several genera occurring exclusively here. One of these is the genus of the primary freshwater minnows Pelasgus, which was designated only in 2007. The genus is one of the most ancient genera of the family Leuciscidae and comprises seven small-bodied species, inhabiting slower, well-vegetated courses of rivers. This work is the first molecular multilocus phylogeny of the genus, based on one mitochondrial and three nuclear markers. In total, 305 individuals across almost entire distribution range of the genus were analysed. We inferred the evolutionary history of the species by comparing the results of our calibrated multilocus coalescent species-tree to palaeogeological events. The diversification of the genus started in the early Miocene and continued through to the beginning of Pleistocene. We identified the regions of the oldest colonization by Pelasgus, the drainages of the ancient lakes Ohrid and Prespa, and the southernmost part of the Peloponnese, hosting Pelasgus minutus, P. prespensis and P. laconicus, respectively. We showed that P. prespensis is not endemic to Lake Prespa, as previously thought; it occurs also in the Albanian River Devoll. This corroborates the emerging opinion that the endemic taxa of ancient lakes evolved within larger-scale historic drainages and not only within the lakes. Our results showed that the species with the most recent common ancestor of the early Pliocene origin, P. thesproticus, P. epiroticus, P. stymphalicus and P. marathonicus, have neighbouring distribution ranges. Pelasgus epiroticus is especially interesting, not only for its pronounced genetic diversity with a geographic pattern, but also for being found at three localities within the native distribution range of P. stymphalicus as a result of a translocation. At two of these localities, we identified hybrids between the two species, and at one of them, the genetically pure native species was not found at all. This points to a threat of the loss of the native ichthyofauna due to unintentional translocations.
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Affiliation(s)
- Nuria Viñuela Rodríguez
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic
| | - Radek Šanda
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic; Department of Zoology, National Museum, Václavské nám. 68, Prague 1, 11000, Czech Republic
| | - Stamatis Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Sciences and Inland Waters, Athinon-Souniou Ave., Anavissos, Attica, 19013, Greece
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic.
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Guo DM, Zhang E. Re-description of the loach species Leptobotia citrauratea (Teleostei, Botiidae), with the description of L. brachycephala from southern Zhejiang Province, China. Zookeys 2021; 1017:89-109. [PMID: 33633484 PMCID: PMC7895807 DOI: 10.3897/zookeys.1017.57503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/22/2021] [Indexed: 12/05/2022] Open
Abstract
Leptobotiacitrauratea (Nichols, 1925), a loach species, originally described from Dongting Lake, was recently rehabilitated, based on the examination of the holotype and non-topotypical specimens. Several field surveys conducted from 2016 to 2019 in Zhejiang, Jiangxi and Hunan Provinces, P.R. China, yielded many specimens of Leptobotia which were initially identified as L.citrauratea. Molecular and morphological analyses of these specimens demonstrated that two distinct species are involved. One was identified as L.citrauratea, represented by specimens from both the Poyang and Dongting Lake (type locality) systems in Jiangxi and Hunan Provinces, and the other species is described as L.brachycephala, represented by specimens from the Ou-Jiang and Qu-Jiang, two coastal rivers of Zhejiang Province, China. Leptobotiabrachycephala resembles L.citrauratea and L.micra in having a row of orange dots or an orange stripe along the dorsal mid-line of the body, extending from the nape to the caudal-fin base – a unique character in Leptobotia. Leptobotiabrachycephala differs from L.citrauratea and L.micra Bohlen & Šlechtová, 2017, in caudal-fin shape and pelvic-fin insertion and proportional measurements including caudal-fin length, head length, predorsal length and anal-fin length. Its species status was further corroborated by position in a molecular phylogenetic analysis, based on the mitochondrial cyt b gene and its minimum uncorrected p-distance (2.9%) from congeneric species.
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Affiliation(s)
- Dong-Ming Guo
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China Institute of Hydrobiology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences, Beijing, 100049, China University of Chinese Academy of Sciences Beijing China
| | - E Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China Institute of Hydrobiology, Chinese Academy of Sciences Wuhan China
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Scholz T, Waeschenbach A, Oros M, Brabec J, Littlewood DTJ. Phylogenetic reconstruction of early diverging tapeworms (Cestoda: Caryophyllidea) reveals ancient radiations in vertebrate hosts and biogeographic regions. Int J Parasitol 2020; 51:263-277. [PMID: 33275944 DOI: 10.1016/j.ijpara.2020.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022]
Abstract
Tapeworms of the order Caryophyllidea are the earliest diverging 'true' tapeworms (Eucestoda) and parasitise cypriniform and siluriform fishes almost exclusively. They are typified by a monozoic (non-proglottised) body plan, which is a characteristic shared with early diverging 'cestodarians' Gyrocotylidea and Amphilinidea. Here we present the most comprehensive multi-gene molecular phylogeny of this group, to date. Specimens of 63 species from 32 genera (~50% and ~75% of known species and genus diversity, respectively) were gathered during an intense and targeted 15-year collecting effort. Phylogenetic reconstructions provide high nodal support for three major lineages, which only partly correspond to currently recognised families. The three well-supported clades were as follows: Clade A was in an unsupported position at the base of the tree and was almost exclusively comprised of parasites of catfishes (Siluriformes) from the Afrotropical and Indomalayan regions, including the type genus of the Lytocestidae (Lytocestus). Clade B formed the sister group to the remaining taxa (Clade C) and was composed of species that parasitise cyprinids and loaches (Cypriniformes: Cyprinoidei and Cobitoidei) from the Palaearctic Region. This clade included the type genus of the Caryophyllaeidae (Caryophyllaeus). Clade C comprised Nearctic species from suckers and minnows (Cypriniformes: Catostomidae and Cyprinoidei), which were previously accommodated in two families, i.e. Capingentidae and Caryophyllaeidae. This clade included the type genus of the Capingentidae (Capingens). In addition to Clades A-C, Balanotaenia bancrofti from the monotypic Balanotaeniidae, which parasitises plotosid catfishes in Australia, and Lytocestoides tanganyikae, which parasitises African cichlids, formed a poorly supported clade at the base of the tree. Whereas morphological characteristics traditionally used to differentiate caryophyllidean families do not characterise molecular lineages, host association and biogeographical distribution play a key role in the circumscription of the three well-supported clades revealed by molecular data. Thus, the taxonomic rearrangement proposed herein was guided by the molecular clades. The names of all four extant families were preserved and family affinity was determined by topological clustering with the type genera of the families. The family diagnoses of the Lytocestidae, Caryophyllaeidae and Capingentidae are amended. Biogeographic patterns are indicative of separate Gondwanan and Laurasian radiations having taken place. Regarding the Gondwanan radiation in the Siluriformes, the topology in Clade A indicates an Asian origin with a subsequent African colonisation. Concerning Laurasia, separate radiations appear to have taken place in the Cypriniformes in the temperate zones of North America and Eurasia. Complete absence of caryophyllideans in the Neotropical Region, where numerous catfishes occur, may be due to the Gondwanan radiation having taken place after the continental separation of Africa and South America.
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Affiliation(s)
- Tomáš Scholz
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic.
| | - Andrea Waeschenbach
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Mikuláš Oros
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 040 10 Košice, Slovak Republic
| | - Jan Brabec
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - D Timothy J Littlewood
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
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16
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Abstract
Mitochondrial genomes of Squalidus mantschuricus, S. chankaensis, and S. longifilis have been determined using Sanger sequencing (GenBank Accession No. MT767745-MT767747). The three mitochondrial genomes consist of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region with the length of 16,605, 16,611, and 16,607 bp. Phylogenetic analysis of the three species showed that S. mantschuricus is nested within a fully supported terminal clade with S. argentatus, and S. chankaensis is a sister group of S. mantschuricus, S. argentatus, and S. wolterstorffi. Squalidus longifilis is positioned in a clade with S. multimaculatus and S. gracilis.
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Affiliation(s)
- Jie Chai
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, PR China
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Ksepka SP, Whelan N, Whipps CM, Bullard SA. A New Species of ThelohanellusKudo, 1933 (Myxozoa: Bivalvulida) Infecting Skeletal Muscle of Blacktail Shiner, Cyprinella venusta Girard, 1856 ( Cypriniformes: Cyprinidae) in the Chattahoochee River Basin, Georgia. J Parasitol 2020; 106:350-359. [PMID: 32227224 DOI: 10.1645/19-162] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Thelohanellus magnacysta n. sp. (Bivalvulida: Myxobolidae) infects the skeletal muscle of blacktail shiner, Cyprinella venusta Girard, 1856 (Cypriniformes: Cyprinidae) in Bull Creek, Chattahoochee River Basin, eastern Georgia. Although numerous members of ThelohanellusKudo, 1933 have overlapping myxospore dimensions with the new species, it differs from all nominal congeners by polar filament coil number and polar capsule width as well as by lacking a mucous envelope, iodinophilic vacuole, and sutural markings. With the use of novel primers for Myxozoa, a phylogenetic analysis of the small subunit ribosomal DNA (SSU rDNA) suggests that the new species shares a recent common ancestor with a clade of cyprinid-infecting species of Myxobolus Bütschli, 1882 (Bivalvulida: Myxobolidae) and Thelohanellus. Consistent with other published research concerning the systematics of Thelohanellus, this result suggested that Thelohanellus and Myxobolus are polyphyletic and need revision. Histological sections of infected blacktail shiners confirmed that myxospores were only found within a plasmodium and only infected skeletal muscle and that plasmodia were encapsulated by a granuloma comprising varying degrees of acute granulomatous inflammation. The new species is the fourth of Thelohanellus reported from North America and the first reported from Cyprinella, as well as the first myxozoan described from the blacktail shiner.
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Affiliation(s)
- Steven P Ksepka
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
| | - Nathan Whelan
- Warm Springs Fish Technology Center, U.S. Fish and Wildlife Service, Auburn, Alabama 36849.,School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
| | - Christopher M Whipps
- College of Environmental Science and Forestry, State University of New York (SUNY-ESF), 1 Forestry Drive, Syracuse, New York 13210
| | - Stephen A Bullard
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
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18
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Abstract
Two complete mitochondrial genomes of Gobio acutipinnatus and G. microcephalus are assembled, and they have the same length with slightly high A + T contents (54.88% and 56.57%) in base compositions. Results in the reconstructed phylogeny show that the genus Gobio is a monophyletic group, and it is a sister taxon of the genus Romanogibio.
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Affiliation(s)
- Tianyu Yi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
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19
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Abstract
New mitochondrial genomes of Pseudogobio guilinensis, P. giganteus, and P. anderssoni have the length of 16,605, 16,606, and 16,609 bp with A + T bias. Inferred phylogeny shows that P. guilinensis occupies basal position. P. esocinus and P. anderssoni+P. longirostris are sister groups, and they together are a sister taxa of P. giganteus.
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Affiliation(s)
- Junwei Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
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20
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Chen H, Wang D, Duan X, Liu S, Chen D. The mitochondrial genome of Culter oxycephaloides ( Cypriniformes, Cyprinidae). Mitochondrial DNA B Resour 2019; 4:2392-2393. [PMID: 33365558 PMCID: PMC7687434 DOI: 10.1080/23802359.2017.1383196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In the present study, the complete mitogenome sequence of Culter oxycephaloides was determined using PCR amplification and DNA sequencing, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with the total length of 16,619 bp. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). There are 12 regions of gene share totalling 55 bp and 11 intergenic spacer regions totalling 84 bp. The complete mitochondrial genome sequence is useful for phylogenetic analysis and studies of population genetics of C. oxycephaloides.
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Affiliation(s)
- Huijuan Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.,College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Dengqiang Wang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Xinbin Duan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Shaoping Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Daqing Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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21
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Chen Y, Fu C. Three complete mitochondrial genomes of freshwater fishes in the genus Abbottina ( Cypriniformes: Gobionidae). Mitochondrial DNA B Resour 2019; 4:2179-2180. [PMID: 33365463 PMCID: PMC7687625 DOI: 10.1080/23802359.2019.1623728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 05/17/2019] [Indexed: 10/26/2022] Open
Abstract
Abbottina binhi has been misidentified as Abbottina rivularis in China for a long time. In this study, we determined three mitochondrial genomes of A. rivularis and A. binhi such that these data should contribute to molecular identifications of the two species. The size of new mitochondrial genomes was 16,609 or 16,599 bp with A + T bias of 55.7-56.5% in the base compositions. Our reconstructed phylogeny showed that A. rivularis and A. binhi formed a sister taxon relationship, and they together were a monophyletic group.
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Affiliation(s)
- Yun Chen
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
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22
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Tong J, Fu C. Four complete mitochondrial genomes of Saurogobio fishes ( Cypriniformes: Gobionidae). Mitochondrial DNA B Resour 2019; 4:2175-2176. [PMID: 33365461 PMCID: PMC7687549 DOI: 10.1080/23802359.2019.1623126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/17/2019] [Indexed: 01/08/2023] Open
Abstract
In this study, we determined complete mitochondrial genomes of Saurogobio gracilicaudatus, S. xiangjiangensis, S. gymnocheilus, and S. lissilabris so that these data could contribute to reconstruct interspecific phylogenetic relationships within the genus Saurogobio. The four mitochondrial genomes showed A + T bias (55.2-57.0%) of base compositions with the length from 16,594 to 16,608 bp. Phylogenetic relationships among Saurogobio fishes and their close relatives showed that the genus Saurogobio was a monophyletic group and it could be divided into two major groups.
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Affiliation(s)
- Jie Tong
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
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23
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Sousa-Santos C, Jesus TF, Fernandes C, Robalo JI, Coelho MM. Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data. Mol Phylogenet Evol 2018; 133:263-285. [PMID: 30583043 DOI: 10.1016/j.ympev.2018.12.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 01/05/2023]
Abstract
The evolutionary history of western Iberian Leuciscinae, obligatory freshwater fish, is directly linked to the evolution of the hydrographic network of the Iberian Peninsula after its isolation from the rest of Europe, which involved dramatic rearrangements such as the transition from endorheic lakes to open basins draining to the Atlantic. Previous phylogenetic research on western Iberian leuciscines, using mainly mitochondrial DNA and more recently one or two nuclear genes, has found contradictory results and there remain many unresolved issues regarding species relationships, taxonomy, and evolutionary history. Moreover, there is a lack of integration between phylogenetic and divergence time estimates and information on the timing of geomorphological changes and paleobasin rearrangements in the Iberian Peninsula. This study presents the first comprehensive fossil-calibrated multilocus coalescent species tree of western Iberian Leuciscinae (including 14 species of Achondrostoma, Iberochondrostoma, Pseudochondrostoma and Squalius endemic to the Iberian Peninsula, seven of which endemic to Portugal) based on seven nuclear genes, and from which we infer their biogeographic history by comparing divergence time estimates to known dated geological events. The phylogenetic pattern suggests slow-paced evolution of leuciscines during the Early-Middle Miocene endorheic phase of the main Iberian river basins, with the shift to exorheism in the late Neogene-Quaternary allowing westward dispersals that resulted in many cladogenetic events and a high rate of endemism in western Iberia. The results of this study also: (i) confirm the paraphyly of S. pyrenaicus with respect to S. carolitertii, and thus the possible presence of a new taxon in the Portuguese Tagus currently assigned to S. pyrenaicus; (ii) support the taxonomic separation of the Guadiana and Sado populations of S. pyrenaicus; (iii) show the need for further population sampling and taxonomic research to clarify the phylogenetic status of A. arcasii from the Minho basin and of the I. lusitanicum populations in the Sado and Tagus basins; and (iv) indicate that A. occidentale, I. olisiponensis and P. duriensis are the most ancient lineages within their respective genera.
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Affiliation(s)
- C Sousa-Santos
- MARE - Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal.
| | - T F Jesus
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisbon, Portugal(2).
| | - C Fernandes
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal.
| | - J I Robalo
- MARE - Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal.
| | - M M Coelho
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal.
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Lee S. Complete mitochondrial genome of the mud loach Misgurnus mizolepis ( Cypriniformes, Cobitidae) and its phylogenetic position in the Cypriniformes. Mitochondrial DNA B Resour 2016; 1:839-840. [PMID: 33473648 PMCID: PMC7799515 DOI: 10.1080/23802359.2016.1247675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The mud loach (Misgurnus mizolepis) is a small benthic species belonging to the family Cobitidae. In this study, I report the first sequencing and assembly of the complete mitochondrial genome of M. mizolepis. The complete mitochondrial genome is 16,647 bp long, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 20 species showed that M. mizolepis is clustered with M. anguillicaudatus and M. bipartitus. This mitochondrial genome provides potentially important resources for studying molecular evolution and biogeography.
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Affiliation(s)
- Seungki Lee
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea
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25
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Abstract
The complete mitochondrial genome of Yaoshania pachychilus (Protomyzon pachychilus) was determined for the first time. This mitogenome was 16 564 bp in length, including two ribosomal RNA genes, 22 transfer RNA genes, containing 13 protein-coding genes and a control region (D-loop). The base composition of the heavy strand was 28.9% A, 25.2% T, 28.7% C and 17.2% G. As in other vertebrates, with the exception of the eight tRNA genes and NADH dehydrogenase subunit 6 (ND6), all other mitochondrial genes are encoded on the heavy strand. Only the tRNA-Ser was not folded into a typical clover-leaf secondary structure as it lacks the dihydrouridine arm.
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Affiliation(s)
- Kang Xu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Engineering Research Center of Healthy Livestock, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, People's Republic of China
| | - Fangzhou Hu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
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Wang C, Liang YQ, Li M, Zhang Y, Shen ZJ, Jiang ZW. Complete mitochondrial DNA genome of Triplophysa venusta ( Cypriniformes: Cobitida). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4617-4619. [PMID: 26681152 DOI: 10.3109/19401736.2015.1101584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial DNA sequence of Triplophysa venusta was determined using a PCR-based method in our present study. The genome is totally 16 574 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, and 1 non-coding control region. The overall base composition of T. venusta is A 27.8%, T 26.9%, C 26.9%, and G 18.4%, with an A + T bias of 54.7%. This complete mitogenome of T. venusta provides a basic data for studies on species identification, molecular systematics, and conservation genetics. The phylogenetic trees consistently showed that the Family Cobitidae was divided into three major clades: the subfamily Botiidae, the subfamily Nemaeheilidae, and the subfamily Cobitinae. Cobitinae and Nomaeheilidae formed a main Loach clade, with Botiidae clustered at the basal.
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Affiliation(s)
- Chong Wang
- a Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences , Wuhan , China
| | - Yin-Quan Liang
- a Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences , Wuhan , China
| | - Ming Li
- b Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University , Wuhan , China , and
| | - Yu Zhang
- c Jin Sha River Ludila Hydropower Company , Kunming , China
| | - Zai-Jun Shen
- c Jin Sha River Ludila Hydropower Company , Kunming , China
| | - Zhi-Wu Jiang
- c Jin Sha River Ludila Hydropower Company , Kunming , China
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27
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Bock SL, Malley MM, Lema SC. Complete mitochondrial genome of the speckled dace Rhinichthys osculus, a widely distributed cyprinid minnow of western North America. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4416-4418. [PMID: 26488409 DOI: 10.3109/19401736.2015.1089551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The speckled dace Rhinichthys osculus (order Cypriniformes), also known as the carpita pinta, is a small cyprinid minnow native to western North America. Here, we report the sequencing of the full mitochondrial genome (mitogenome) of R. osculus from a male fish collected from the Amargosa River Canyon in eastern California, USA. The assembled mitogenome is 16 658 base pair (bp) nucleotides, and encodes 13 protein-coding genes, and includes both a 12S and a 16S rRNA, 22 tRNAs, and a 985 bp D-loop control region. Mitogenome synteny reflects that of other Ostariophysian fishes with the majority of genes and RNAs encoded on the heavy strand (H-strand) except nd6, tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Glu, and tRNA-Pro. The availability of this R. osculus mitochondrial genome - the first complete mitogenome within the lineage of Rhinichthys riffle daces - provides a foundation for resolving evolutionary relationships among morphologically differentiated populations of R. osculus.
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Affiliation(s)
- Samantha L Bock
- a Department of Biological Sciences , Center for Coastal Marine Sciences, California Polytechnic State University , San Luis Obispo , CA , USA
| | - Morgan M Malley
- a Department of Biological Sciences , Center for Coastal Marine Sciences, California Polytechnic State University , San Luis Obispo , CA , USA
| | - Sean C Lema
- a Department of Biological Sciences , Center for Coastal Marine Sciences, California Polytechnic State University , San Luis Obispo , CA , USA
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Yan SL, Sun ZY, Guo YS. A new species of Triplophysa Rendahl ( Cypriniformes, Nemacheilidae) from Sichuan Province, China. Dongwuxue Yanjiu 2015; 36:299-304. [PMID: 26452694 DOI: 10.13918/j.issn.2095-8137.2015.5.299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Triplophysa yajiangensis sp. nov. is described from the upper and middle reaches of the Yalong River, Yangtze Basin, Ganzi Prefecture, Sichuan Province, China. This new species can be distinguished from other congeneric species by the following characters: body surface smooth and scaleless; lateral line complete; caudal peduncle compressed and tapered slightly; lower jaw shovel-shaped; head shorter than caudal peduncle; dorsal-fin origin anterior to pelvic-fin origin and closer to tip of snout than to caudal-fin base, last unbranched ray hard; pelvic-fin reaches or exceeds anus; posterior chamber of gas bladder absent; intestine spiral type with 3-5 winding coils.
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Affiliation(s)
- Si-Li Yan
- College of Life Sciences, China West Normal University, Nanchong Sichuan 637009, China
| | - Zhi-Yu Sun
- Sichuan Academy of Forestry, Chengdu Sichuan 610081, China
| | - Yan-Shu Guo
- College of Life Sciences, China West Normal University, Nanchong Sichuan 637009, China.
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Yu JN, Jun J, Lim CE, Kim S. Sequence and organization of the complete mitogenome of a Siberian stone loach, Barbatula toni (Dybowsky, 1869) ( Cypriniformes: Balitoridae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:1798-9. [PMID: 26305807 DOI: 10.3109/19401736.2014.963818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we determined the complete mitogenome sequence of Siberian stone loach, Barbatula toni (Dybowsky, 1869). The total length of mitogenome is 16 623 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loop). The genome organization and gene order were identical to that of the typical vertebrates. The control region harbors conserved sequence blocks (CSB-D, E, F, CSB-1, CBS-2 and CBS-3) and TA-nucleotide microsatellite repeats in its 3' end. The complete mitogenome may provide important molecular data for further phylogenetic analyses for higher taxa of teleost fishes, especially for the fishes in order Cypriniformes.
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Affiliation(s)
- Jeong-Nam Yu
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Jumin Jun
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Chae Eun Lim
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Soonok Kim
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
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Gidmark NJ, Taylor C, LoPresti E, Brainerd E. Functional morphology of durophagy in black carp, Mylopharyngodon piceus. J Morphol 2015; 276:1422-32. [PMID: 26289832 DOI: 10.1002/jmor.20430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 07/01/2015] [Accepted: 07/11/2015] [Indexed: 11/08/2022]
Abstract
The black carp, Mylopharyngodon piceus (Osteichthyes: Cyprinidae), crushes its snail and other molluscan prey with robust pharyngeal jaws and strong bite forces. Using gross morphology, histological sectioning, and X-ray reconstruction of moving morphology (XROMM), we investigated structural, behavioral, and mechanical aspects of pharyngeal jaw function in black carp. Strut-like trabeculae in their pharyngeal jaws support large, molariform teeth. The teeth occlude with a hypertrophied basioccipital process that is also reinforced with stout trabeculae. A keratinous chewing pad is firmly connected to the basioccipital process by a series of small bony projections from the base of the pedestal. The pharyngeal jaws have no bony articulations with the skull, and their position is controlled by five paired muscles and one unpaired median muscle. Black carp can crush large molluscs, so we used XROMM to compare pharyngeal jaw postures as fish crushed ceramic tubes of increasing sizes. We found that black carp increase pharyngeal jaw gape primarily by ventral translation of the jaws, with ventral rotation and lateral flaring of the jaws also increasing the space available to accommodate large prey items. A stout, robust ligament connects left and right jaws together firmly, but allows some rotation of the jaws relative to each other. Contrasting with the pharyngeal jaw mechanism of durophagous perciforms with fused left and right lower pharyngeal jaws, we hypothesize that this ligamentous connection may serve to decouple tensile and compressive forces, with the tensile forces borne by the ligament and the compressive forces transferred to the prey.
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Affiliation(s)
- Nicholas J Gidmark
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island
| | - Chantel Taylor
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island
| | - Eric LoPresti
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island
| | - Elizabeth Brainerd
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island
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Zhu M, Liu F. Mitochondrial genome sequence of Paramisgurnus dabryanus from the Yellow River estuary: implication for Cobitidae phylogeny. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3039-40. [PMID: 26162049 DOI: 10.3109/19401736.2015.1063124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Paramisgurnus dabryanus Sauvage (Cobitidae, Cypriniformes) is a native large-scale loach widely distributed in main inland freshwater systems of China. The complete mitochondrial genome sequence of P. dabryanus from the Yellow River (YR) estuary was characterized in the present study. The circular mitogenome is 16 570 bp in size and contains two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes. The overall A + T content is 56.64% in the range of other Cobitidae studied. The mitogenome of P. dabryanus YR has an overall nucleotide sequence identity of 96.9% with that from Zhejiang, and 89.2% with that from Hubei. All the Misgurnus and Paramisgurnus species were clustered into two Misgurnus/Paramisgurnus complex clades with high bootstrap values based on the whole mitogenome sequences. The mitochondrial phylogenomic analysis indicates that the relationships in Cobitidae are inconsistent with the current classification system and taxonomic revision is required on the basis of molecular phylogeny and morphology.
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Affiliation(s)
- Ming Zhu
- a College of Marine Science and Key Laboratory of Marine Biotechnology of Jiangsu Province, Huaihai Institute of Technology , Lianyungang , PR China .,b Lianyungang Long-Yangtze Biotech Company , Lianyungang , PR China , and
| | - Feng Liu
- c Key Laboratory of Experimental Marine Biology , Institute of Oceanology, Chinese Academy of Sciences , Qingdao , PR China
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Gao T, Tian H, Wang D, Duan X, Liu S, Chen D. The mitochondrial genome of Gnathopogon imberbis ( Cypriniformes, Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2543-4. [PMID: 26017045 DOI: 10.3109/19401736.2015.1038796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, the complete mitogenome sequence of Gnathopogon imberbis is determined using PCR amplification and DNA sequencing, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,598 bp. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the H-strand. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). The overall nucleotide composition was 30.0% A, 27.0% T, 25.8% C and 17.2% G, with an A + T bias of 57.0%. The complete mitochondrial genome sequence will be useful for phylogenetic analysis and studies of population genetics of G. imberbis.
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Affiliation(s)
- Tianheng Gao
- a Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education , School of Life Science, Southwest University , Chongqing , China and.,b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , China
| | - Huiwu Tian
- b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , China
| | - Dengqiang Wang
- b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , China
| | - Xinbin Duan
- b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , China
| | - Shaoping Liu
- b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , China
| | - Daqing Chen
- b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , China
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Chen H, Wang D, Duan X, Liu S, Chen D. The mitochondrial genome of Pseudolaubuca sinensis ( Cypriniformes, Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3356-7. [PMID: 25714142 DOI: 10.3109/19401736.2015.1018219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, the complete mitogenome sequence of Pseudolaubuca sinensis was determined using PCR amplificationand DNA sequencing, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with the total length of 16,617 bp. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). There are 6 regions of gene share totaling 22 bp and 14 intergenic spacer regions totaling 66 bp. The complete mitochondrial genome sequence is useful for phylogenetic analysis and studies of population genetics of Pseudolaubuca sinensis.
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Affiliation(s)
- Huijuan Chen
- a College of Animal Science and Technology, Southwest University , Chongqing , P.R. China and.,b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , P.R. China
| | - Dengqiang Wang
- b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , P.R. China
| | - Xinbin Duan
- b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , P.R. China
| | - Shaoping Liu
- b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , P.R. China
| | - Daqing Chen
- b Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , P.R. China
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Li C, Chen Y, Liu C, Juan T, He D. The complete mitochondrial genome sequence of Herzensteinia microcephalus ( Cypriniformes: Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2255-6. [PMID: 25431822 DOI: 10.3109/19401736.2014.984168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Herzensteinia microcephalus (Herzenstein, 1891) is the highest naturally occurring cyprinid in the world, and inhabits rivers in the Tibetan Plateau at elevations of 4500-5200 m. Few studies on this species have been contributed. In this study, we got the mitochondrial genome sequences of H. microcephalus. The mitogenome of H. microcephalus is16,726 in length, which includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes and two non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The overall nucleotide base composition is 28.41% for A, 27.16% for T, 26.04% for C and 18.38% for G. This study can provide important molecular theory basis for carrying out the study on the genetics, phylogeny and adaptive evolution of Herzensteinia.
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Affiliation(s)
- Chunhua Li
- a The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China and.,b University of Chinese Academy of Sciences , Beijing , China
| | - Yifeng Chen
- a The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China and
| | - Chunlong Liu
- a The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China and.,b University of Chinese Academy of Sciences , Beijing , China
| | - Tao Juan
- a The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China and.,b University of Chinese Academy of Sciences , Beijing , China
| | - Dekui He
- a The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China and
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Abstract
Chuanchia labiosa Herzenstein, 1891 (Cyprinidae: Schizothoracinae) is the sole species of genus Chuanchia and is endemic to China. This species plays an important role in the upper reaches of the Yellow River and has been listed in both the China Red Data Book of Endangered Animal and the China Species Red List. In this study, the complete mitochondrial DNA genome sequence of C. labiosa was determined. The mitogenome is 16,705 bp in length, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. Overall basic composition of mitochondrial genome of C. labiosa is 28.39% for A, 27.16% for T, 26.09% for C, and 18.36% for G with a slightly high A + T content (55.55%). The complete mitogenome sequence of C. labiosa would be useful for stock evaluation and further conservation genetic studies for this endangered species.
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Affiliation(s)
- Dekui He
- a Laboratory of Biological Invasion and Adaptive Evolution , Institute of Hydrobiology, Chinese Academy of Sciences , Wuchang District , Wuhan , Hubei Province , P.R. China , and
| | - Chunhua Li
- a Laboratory of Biological Invasion and Adaptive Evolution , Institute of Hydrobiology, Chinese Academy of Sciences , Wuchang District , Wuhan , Hubei Province , P.R. China , and.,b University of Chinese Academy of Sciences , Beijing , P.R. China
| | - Juan Tao
- a Laboratory of Biological Invasion and Adaptive Evolution , Institute of Hydrobiology, Chinese Academy of Sciences , Wuchang District , Wuhan , Hubei Province , P.R. China , and.,b University of Chinese Academy of Sciences , Beijing , P.R. China
| | - Yifeng Chen
- a Laboratory of Biological Invasion and Adaptive Evolution , Institute of Hydrobiology, Chinese Academy of Sciences , Wuchang District , Wuhan , Hubei Province , P.R. China , and
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Xue Y, Chen HJ, Li Y, Tang M, Chen HJ, Ye Q, Li Y. Mitochondrial genome of the sucking disc gudgeon, Discogobio yunnanensis (Teleostei, Cypriniformes). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1451-2. [PMID: 25162381 DOI: 10.3109/19401736.2014.953088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Discogobio yunnanensis was determined using the polymerase chain reaction and directly sequenced with the primer walking method. The whole mitogenome was 16,602 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region. It had the typical circular molecule structure of vertebrate's mitogenome. The whole base composition was estimated to be 32.10% A, 26.79% T, 25.95% C, 15.16% G with AT bias of 58.89%. The complete mitogenome of D. yunnanensis provides the fundamental data for conservation genetics study on this freshwater fish species.
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Affiliation(s)
- Yang Xue
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Beibei , Chongqing , P. R. China and
| | - Hui-Juan Chen
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Beibei , Chongqing , P. R. China and
| | - Yang Li
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Beibei , Chongqing , P. R. China and
| | - Min Tang
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Beibei , Chongqing , P. R. China and
| | - Hong-Jun Chen
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Beibei , Chongqing , P. R. China and
| | - Qin Ye
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Beibei , Chongqing , P. R. China and.,b School of Chemistry and Chemical Engineering, Southwest University , Beibei , Chongqing , P. R. China
| | - Yun Li
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Beibei , Chongqing , P. R. China and
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Chen JH, Wang CH, Li YL, Wang HM, Zhang XJ, Yan BL. cDNA cloning and expression characterization of serum transferrin gene from oriental weatherfish Misgurnus anguillicaudatus. J Fish Biol 2014; 84:885-896. [PMID: 24673686 DOI: 10.1111/jfb.12307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 11/16/2013] [Indexed: 06/03/2023]
Abstract
In this study, the cDNA coding serum transferrin (stf) of Misgurnus anguillicaudatus (mastf) was cloned. mastf cDNA is composed of 2326 bp with a 2007 bp open reading frame encoding 668 amino acids. The deduced Mastf protein consists of a signal peptide, two lobes (N and C-lobes) and signature motifs of transferrin (Tf) family. The results of tissue distribution indicated that mastf mRNA was predominantly expressed in the liver. The results indicate that the mastf expression increased significantly in liver, blood, spleen and head kidney after the challenge with Aeromonas sobria, acting as a positive acute protein, suggesting that mastf is related to the immune response. The cloning and expression analysis of mastf further demonstrates the evolutionary conservation of Stf and immune function in vertebrates.
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Affiliation(s)
- J H Chen
- Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang 222005, China; Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai 200090, China; Jiangsu Province R & D Institute of Marine Resources, Huaihai Institute of Technology, Lianyungang 222005, China
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Pasco-Viel E, Yang L, Veran M, Balter V, Mayden RL, Laudet V, Viriot L. Stability versus diversity of the dentition during evolutionary radiation in cyprinine fish. Proc Biol Sci 2014; 281:20132688. [PMID: 24523268 DOI: 10.1098/rspb.2013.2688] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evolutionary radiations, especially adaptive radiations, have been widely studied but mainly for recent events such as in cichlid fish or Anolis lizards. Here, we investigate the radiation of the subfamily Cyprininae, which includes more than 1300 species and is estimated to have originated from Southeast Asia around 55 Ma. In order to decipher a potential adaptive radiation, within a solid phylogenetic framework, we investigated the trophic apparatus, and especially the pharyngeal dentition, as teeth have proved to be important markers of ecological specialization. We compared two tribes within Cyprininae, Poropuntiini and Labeonini, displaying divergent dental patterns, as well as other characters related to their trophic apparatus. Our results suggest that the anatomy of the trophic apparatus and diet are clearly correlated and this explains the difference in dental patterns observed between these two tribes. Our results illustrate the diversity of mechanisms that account for species diversity in this very diverse clade: diversification of dental characters from an ancestral pattern on the one hand, conservation of a basal synapomorphy leading to ecological specialization on the other hand. By integrating morphological, ecological and phylogenetic analyses, it becomes possible to investigate ancient radiation events that have shaped the present diversity of species.
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Affiliation(s)
- Emmanuel Pasco-Viel
- Evo-devo of Vertebrate Dentition, Institut de Génomique Fonctionnelle de Lyon (IGFL), UMR CNRS 5242, Université de Lyon, Université Claude Bernard Lyon 1, , Ecole Normale Supérieure de Lyon, Lyon, France, Molecular Zoology, Institut de Génomique Fonctionnelle de Lyon (IGFL), UMR CNRS 5242, Université de Lyon, Université Claude Bernard Lyon 1, , Ecole Normale Supérieure de Lyon, Lyon, France, Department of Biology, Saint Louis University, , St Louis, MO 63103, USA, Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements (CRP2), Département Histoire de la Terre, UMR CNRS 7207, Muséum National d'Histoire Naturelle, , Paris, France, Laboratoire de Géologie de Lyon (LGLTPE), UMR CNRS 5276, Université de Lyon, Université Claude Bernard Lyon 1, , Ecole Normale Supérieure de Lyon, Lyon, France
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Ma Q, Luo W. The complete mitochondrial genome of a cyprinid fish; Metzia longinasus (Teleostei, Cypriniformes). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:185-6. [PMID: 24491097 DOI: 10.3109/19401736.2013.879652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The long polymerase chain reaction and primer walking method were applied for the sequencing of the complete mitochondrial genome sequence of a cyprinid species (Metzia longinasus) collected from the Hongshuihe River of the Pearl River drainage, Guangxi Province in China. It is 16,614 bp in length, containing 2 rRNA, 22 tRNA, 13 protein-coding genes and 1 control region generally found in most vertebrates. Most of the mitochondrial genes are encoded on the heavy strand except for eight tRNA and ND6 genes. The base composition of this genome was 31.9% A, 26.2%C, 26.2%T and 15.7%G, showing a lower level of G (15.7%) and a slighter AT bias (58.1%). This is the 2nd completely sequenced mitogenome from genus Metzia. The mtDNA sequence of M. longinasus shared 93% sequence similarity with that of M. formosae and it could contribute to a better solution of its phylogenetic position within cyprinid fishes based on the complete mitogenomic data.
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Affiliation(s)
- Qinqin Ma
- a College of Life Sciences, Sichuan Normal University , Chengdu , China and
| | - Wen Luo
- a College of Life Sciences, Sichuan Normal University , Chengdu , China and.,b School of Life Sciences, Southwest University , Beibei , Chongqing , China
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Xu H, Xue Y, Ye Q, Luo X, Lü HJ, Chen DQ, Li Y. Mitochondrial genome of the flat-lip gudgeon, Platysmacheilus exiguus (Teleostei, Cypriniformes). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:153-4. [PMID: 24450708 DOI: 10.3109/19401736.2013.878920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitogenome of an endemic fish in China flat-lip gudgeon, Platysmacheilus exiguous, was determined using the polymerase chain reaction and directly sequenced with the primer walking method. The whole mitogenome was 16,604 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region. It had the typical circular molecule structure of vertebrate's mitogenome. The whole base composition was estimated to be 30.77%A, 26.06%T, 26.64%C and 16.53%G with AT bias of 56.83%. The complete mitogenome of P. exiguus provides the fundamental data for conservation genetics study on this species.
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Affiliation(s)
- Hao Xu
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Chongqing , P.R. China
| | - Yang Xue
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Chongqing , P.R. China
| | - Qin Ye
- b School of Chemistry and Chemical Engineering, Southwest University , Chongqing , P.R. China , and
| | - Xi Luo
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Chongqing , P.R. China
| | - Hong-Jian Lü
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Chongqing , P.R. China
| | - Da-Qing Chen
- c Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Wuhan , P.R. China
| | - Yun Li
- a Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) , College of Animal Science and Technology, Southwest University , Chongqing , P.R. China
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Xu R, Zhao ZX, Zhang Y, Xu P, Sun XW. Complete mitochondrial genome of rosy barb, Puntius conchonius. Mitochondrial DNA 2014; 26:955-6. [PMID: 24409910 DOI: 10.3109/19401736.2013.865173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we sequenced and determined the complete mitochondrial genome of rosy barb (Puntius conchonius). The circular mitochondrial genome (17,082 bp) consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. This is the first report on the complete mitogenome sequence of rosy barb (P. conchonius).
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Affiliation(s)
- Ru Xu
- a Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences , Beijing , People's Republic of China and.,b College of Fisheries and Life Science, Dalian Ocean University , Dalian , People's Republic of China
| | - Zi-Xia Zhao
- a Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences , Beijing , People's Republic of China and
| | - Yan Zhang
- a Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences , Beijing , People's Republic of China and
| | - Peng Xu
- a Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences , Beijing , People's Republic of China and
| | - Xiao-Wen Sun
- a Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences , Beijing , People's Republic of China and
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Liu M, Huang F, Liu S. The mitochondrial genome of Hampala macrolepidota ( Cypriniformes, Cyprinidae). Mitochondrial DNA 2014; 26:807-8. [PMID: 24409854 DOI: 10.3109/19401736.2013.855903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitogenome sequence of Hampala macrolepidota was determined using PCR reactions. The genome is 16,766 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). There are seven regions of gene overlap totaling 25 bp and 13 intergenic spacer regions totaling 70 bp. The control region harbor 88 bp tandem repeats.
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Affiliation(s)
- Mingdian Liu
- a Yangtze River Fisheries Research Institute of Chinese Academy of Fishery Science, Key Field Scientific Observing and Experimental Station of Fishery Resources and Environment of the Middle and Upper Reaches of the Yangtze River of the Ministry of Agriculture , Wuhan , Hubei , China
| | - Fujiang Huang
- a Yangtze River Fisheries Research Institute of Chinese Academy of Fishery Science, Key Field Scientific Observing and Experimental Station of Fishery Resources and Environment of the Middle and Upper Reaches of the Yangtze River of the Ministry of Agriculture , Wuhan , Hubei , China
| | - Shaoping Liu
- a Yangtze River Fisheries Research Institute of Chinese Academy of Fishery Science, Key Field Scientific Observing and Experimental Station of Fishery Resources and Environment of the Middle and Upper Reaches of the Yangtze River of the Ministry of Agriculture , Wuhan , Hubei , China
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Abstract
The complete mitogenome sequence of Tor sinensis was determined using long PCR reactions. The genome is 16,579 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The gene order and composition of T. sinensis was similar to that of most other vertebrates. The descending order of the base composition on heavy strand was 31.9% A, 27.4% C, 24.9% T, 15.7% G, with a relatively lower level of G and a slight AT bias of 56.8%. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). There are 9 regions of gene overlap totaling 29 bp and 14 inter-genic spacer regions totaling 71 bp.
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Affiliation(s)
- Fujiang Huang
- a Yangtze River Fisheries Research Institute of Chinese Academy of Fishery Science, Scientific Observing and Experimental Station of Fishery and Environment in the Upper and Middle Reaches of the Yangtze River, Ministry of Agriculture , Wuhan , China and
| | - Mingdian Liu
- a Yangtze River Fisheries Research Institute of Chinese Academy of Fishery Science, Scientific Observing and Experimental Station of Fishery and Environment in the Upper and Middle Reaches of the Yangtze River, Ministry of Agriculture , Wuhan , China and
| | - Chao Ye
- a Yangtze River Fisheries Research Institute of Chinese Academy of Fishery Science, Scientific Observing and Experimental Station of Fishery and Environment in the Upper and Middle Reaches of the Yangtze River, Ministry of Agriculture , Wuhan , China and.,b Key Laboratory of Freshwater Fish Reproduction and Development , Ministry of Education, School of Life Science, Southwest University , Chongqing , China
| | - Shaoping Liu
- a Yangtze River Fisheries Research Institute of Chinese Academy of Fishery Science, Scientific Observing and Experimental Station of Fishery and Environment in the Upper and Middle Reaches of the Yangtze River, Ministry of Agriculture , Wuhan , China and
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Liu SW, Chen XY. [Two new Cypriniformes fish records from Yunnan Province-Carassioides acuminatus and Hemimyzon pumilicorpora]. Dongwuxue Yanjiu 2013; 34:504-506. [PMID: 24115664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Two new Cypriniformes fish records from Yunnan Province, Carassioides acuminatus (collected from mainstream of Red River in Hekou County) and Hemimyzon pumilicorpora (collected from Gula River, Gula Town, Funing County, upper stream of the Pearl River drainage), were identified during fish specimen sorting at Kunming Institute of Zoology, Chinese Academy of Sciences. These two new records not only clarify the distribution patterns of the two species, but also enrich the knowledge of native fishes of Yunnan Province.
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Affiliation(s)
- Shu-Wei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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Hu YX, Zhou Q, Song Y, Chen DQ, Li Y. Complete mitochondrial genome of the smallscale yellowfin, Plagiognathops microlepis (Teleostei: Cypriniformes: Cyprinidae). Mitochondrial DNA 2013; 26:463-4. [PMID: 24059855 DOI: 10.3109/19401736.2013.830298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The smallscale yellowfin, Plagiognathops microlepis is the only one species in the genus Plagiognathops. In this study, we sequenced the complete mitochondrial genome of the P. microlepis. The complete mitogenome was 16,623 bp in size, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 control region. It has the typical circular molecule structure of vertebrate's mitochondrial genome. The whole base composition was estimated to be 30.60% A, 25.19% T, 27.32% C and 16.89% G with AT bias of 55.79%. The complete mitogenome of P. microlepis provides the basis for preservation of genetic resources and genetic breeding studies on this species.
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Affiliation(s)
- Ying-Xiong Hu
- The Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Animal Science and Technology, Southwest University , Beibei, Chongqing 400716 , P.R. China and
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Abstract
Phylogenetic placement of Pseudorasbora elongate remains unresolved. We determined the first complete mitochondrial genome of P. elongate that its mitogenome data should contribute to clarify the systematics of Pseudorasbora fishes. The mitogenome was 16,607 bp in length, including 13 typical protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The overall base composition of the heavy strain was 31.1% for A, 24.8% for C, 28.2% for T and 15.9% for G, with the A + T bias of 59.3%.
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Affiliation(s)
- Anhui Chen
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University , Shanghai , China and
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Abstract
Rhynchocypris lagowskii sensu lato (Cypriniformes: Cyprinidae) has been revealed as a species complex including two species, i.e. R. lagowskii sensu stricto and a cryptic species R. cf. lagowskii. We determined the first complete mitochondrial genome (mitogenome) of R. cf. lagowskii by comparing with a published mitogenome of R. lagowskii sensu stricto. The two species displayed similar pattern of mitochondrial gene arrangements and similar base compositions of the heavy strain with a bias in the A+T content. There were the nucleotide sequence similarity of 91.8% for mitogenomes and pairwise p-distance of 6.9% for COI genes between R. cf. lagowskii and R. lagowskii sensu stricto and these results supported the two species as different species.
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Affiliation(s)
- Wang Xu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Biodiversity Science, Fudan University , Shanghai 200433 , China
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Ma X, Huang F, Wang Z. The complete mitochondrial genome sequence of Acrossocheilus monticolus (Teleostei, Cypriniformes, Cyprinidae). Mitochondrial DNA 2013; 25:245-6. [PMID: 23795852 DOI: 10.3109/19401736.2013.796517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitogenome sequence of Acrossocheilus monticolus, which is endemic to China, was determined using long PCR reactions. The genome is 16,599 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The gene order and composition of A. monticolus was similar to that of most other vertebrates. The descending order of the base composition on heavy strand was 31.4% A, 28.2% C, 24.5% T, 15.8% G, with a relatively lower level of G and a slight AT bias of 55.9%. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). There are 7 regions of gene overlap totaling 23 bp and 13 intergenic spacer regions totaling 69 bp.
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Affiliation(s)
- Xiuhui Ma
- The Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) and
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Kaur H, Singh R. Two new species of Myxobolus (Myxozoa: Myxosporea: Bivalvulida) infecting an Indian major carp and a cat fish in wetlands of Punjab, India. J Parasit Dis 2011; 35:169-76. [PMID: 23024499 DOI: 10.1007/s12639-011-0061-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 07/19/2011] [Indexed: 10/17/2022] Open
Abstract
A survey of parasites of freshwater fishes in Kanjali and Harike wetlands of Punjab (India) revealed the presence of two new myxosporean species belonging to the genus Myxobolus Bütschli (Winter (ed): Protozoa, 1882). Spores of the first species, M. saugati sp. nov. parasitizing scales of Labeo rohita (Cypriniformis: Cyprinidae) vern. rohu are characterized in having 'spores measuring 8.3 × 6.6 μm in size, oval to spherical in valvular view having rounded anterior and posterior ends; polar capsules are two, equal, measuring 4.0 × 2.4 μm, pyriform with distinct neck at the anterior end; an intercapsular process is absent'. Spores of the second species, Myxobolus szekeli sp. nov. parasitizing internal wall of stomach of Wallago attu (Cypriniformis: Siluridae) vern. mulle are '8.7 × 4.1 μm in size, elongately ovoidal in valvular view having tapering, bluntly pointed anterior end and rounded posterior end; polar capsules are two, equal, measuring 4.4 × 1.5 μm, tubular with blunt anterior and rounded posterior ends; polar capsules converge anteriorly but are placed at a distance posteriorly and occupies nearly half of the spore body cavity; an intercapsular process is absent'.
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Bogutskaya NG, Zupančič P, Bogut I, Naseka AM. Two new freshwater fish species of the genus Telestes (Actinopterygii, Cyprinidae) from karst poljes in Eastern Herzegovina and Dubrovnik littoral (Bosnia and Herzegovina and Croatia). Zookeys 2012:53-80. [PMID: 22539906 PMCID: PMC3332009 DOI: 10.3897/zookeys.180.2127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 03/19/2012] [Indexed: 11/12/2022] Open
Abstract
Two new species, Telestes dabar and Telestes miloradi, are described on the basis of morphological comparisons of isolated geographical populations of fishes identified earlier as Telestes metohiensis. A lectotype is designated for Telestes metohiensis, whose range is shown to include waters of Gatačko, Cerničko, and Nevesinjsko poljes in Eastern Herzegovina. Telestes dabar from Dabarsko Polje (Eastern Herzegovina) and Telestes miloradi from Konavosko Polje (south Croatia) share with Telestes metohiensis the following combination of characters that distinguish them from the rest of the genus Telestes: pharyngeal teeth in one row, usually 5–4; preoperculo-mandibular canal not communicating with the infraorbital canal; mouth subterminal, the tip of the mouth cleft on or below the level of the ventral margin of the eye; postcleithrum minute or absent; ventral portion of the trunk with a dark stripe on a pale background; and dorsal portion of trunk uniformly dark and bordered ventrally by a dark midlateral stripe. Telestes dabar and Telestes miloradi are distinguishable from Telestes metohiensis in usually having 8½ branched dorsal-fin rays (vs. usually 7½), 9 or 10 gill rakers (vs. 7–10, usually 8), and the dark stripe on the ventral portion of the trunk below the main pigmented area of the back narrow and usually not reaching posteriorly to the caudal peduncle (vs. dark stripe wide and extending posteriorly to the caudal peduncle). Telestes dabar is distinguished from Telestes miloradi by having scales on most of the body situated close to one another and overlapping in a region behind the pectoral girdle and usually on the caudal peduncle (vs. overlapping scales on most of the body); the lateral line usually incomplete and interrupted, with 24–69, usually 54–65, total scales (vs. lateral line usually complete, with 55–67 total scales); scales above and below the lateral line slightly smaller than lateral-line scales (vs. of about equal size); head width 43–52% HL (vs. 48–58% HL); and lower jaw length 10–12% SL or 36–41% HL (vs. 8–10% SL or 33–38% HL). Telestes miloradi, a very local endemic species,is known only by historical samples. Telestes dabar is an abundant fish in Dabarsko Polje, but its range is critically restricted during the dry season by a few permanent sources. Nothing is known about its occurrence in underground karst waters.
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Affiliation(s)
- Nina G Bogutskaya
- Zoological Institute, Russian Academy of Sciences, 1 Universitetskaya Emb., St Petersburg 199034, Russia
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