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Emami-Khoyi A. The complete mitogenome dataset of the Critically Endangered estuarine pipefish, Syngnathus watermeyeri. Data Brief 2024; 52:109864. [PMID: 38146291 PMCID: PMC10749243 DOI: 10.1016/j.dib.2023.109864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/27/2023] Open
Abstract
The Critically Endangered South African estuarine pipefish, Syngnathus watermeyeri, is one of the rarest teleost fish on the planet. In this analysed dataset, the complete mitochondrial genome of this species was assembled, annotated, and described. In addition, its evolutionary history was reconstructed in a Maximum Likelihood and a Bayesian framework. A circular mitochondrial contig 16 449 bp in length was assembled. A total of 13 protein-coding genes, 22 tRNAs and two rRNAs were annotated. The mitochondrial phylogenetic analysis showed that S. watermeyeri diverged from its widely distributed southern African sister species S. temminckii approximately 1.5 million years ago, and the ancestor of these two southern Afican pipefish species diverged from a clade of northern hemisphere pipefishes comprising S. acus, S. rostellatus, and S. typhle approximately 5.3 million years ago. The dataset presented here serves as the first step in understanding the evolutionary history of Africa's rarest pipefish.
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Affiliation(s)
- Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation1, University of Johannesburg, Auckland Park 2006, South Africa
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2
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Wang JF, Yu HY, Ma SB, Lin Q, Wang DZ, Wang X. Phylogenetic and Evolutionary Comparison of Mitogenomes Reveal Adaptive Radiation of Lampriform Fishes. Int J Mol Sci 2023; 24:ijms24108756. [PMID: 37240101 DOI: 10.3390/ijms24108756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Lampriform fishes (Lampriformes), which primarily inhabit deep-sea environments, are large marine fishes varying from the whole-body endothermic opah to the world's longest bony fish-giant oarfish, with species morphologies varying from long and thin to deep and compressed, making them an ideal model for studying the adaptive radiation of teleost fishes. Moreover, this group is important from a phylogenetic perspective owing to their ancient origins among teleosts. However, knowledge about the group is limited, which is, at least partially, due to the dearth of recorded molecular data. This study is the first to analyze the mitochondrial genomes of three lampriform species (Lampris incognitus, Trachipterus ishikawae, and Regalecus russelii) and infer a time-calibrated phylogeny, including 68 species among 29 orders. Our phylomitogenomic analyses support the classification of Lampriformes as monophyletic and sister to Acanthopterygii; hence, addressing the longstanding controversy regarding the phylogenetic status of Lampriformes among teleosts. Comparative mitogenomic analyses indicate that tRNA losses existed in at least five Lampriformes species, which may reveal the mitogenomic structure variation associated with adaptive radiation. However, codon usage in Lampriformes did not change significantly, and it is hypothesized that the nucleus transported the corresponding tRNA, which led to function substitutions. The positive selection analysis revealed that atp8 and cox3 were positively selected in opah, which might have co-evolved with the endothermic trait. This study provides important insights into the systematic taxonomy and adaptive evolution studies of Lampriformes species.
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Affiliation(s)
- Jin-Fang Wang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Hai-Yan Yu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Shao-Bo Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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Shalu K, Thomas L, Ramvilas G, Shabeena KS, Philip S, Sureshkumar S, Raghavan R, Ranjeet K. DNA barcodes for the pipefish genus Corythoichthys (Actinopterygii: Syngnathiformes) from the Indian Ocean provide insights into cryptic diversity. JOURNAL OF FISH BIOLOGY 2023; 102:680-688. [PMID: 36602224 DOI: 10.1111/jfb.15300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
The syngnathiform genus Corythoichthys comprises a group of taxonomically complex, tail-brooding (Syngnathinae) pipefishes widely distributed in the Indo-Pacific region. Due to the presence of overlapping interspecific morphological characters, reliable taxonomic information on Corythoichthys is still lacking. Using 52 CO1 sequences, including seven newly generated, a phylogenetic analysis was carried out to understand the genetic diversity, distribution and 'species groups' within the genus Corythoichthys. Species delimitation using Automatic Barcode Gap Discovery (ABGD) analysis confirmed the presence of 13 species which include 'species-complexes' previously considered as a single taxon. Our results revealed the presence of three species groups, 'C. amplexus', 'C. conspicillatus' and 'C. haematopterus' and four unidentified/undescribed species in the wider Indo-Pacific realm. Interestingly, 60 sequences and a mitogenome identified as Corythoichthys in GenBank are misidentified at the genus level. Based on our findings, we suggest that the taxonomy and systematics of Corythoichthys need to be re-examined and validated using integrative methods, and care should be taken while selecting specimens for genetic studies.
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Affiliation(s)
- Kannan Shalu
- Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Liju Thomas
- Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Ghosh Ramvilas
- Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | | | - Siby Philip
- Department of Zoology, Nirmalagiri College, Kannur, India
| | - Sivanpillai Sureshkumar
- Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Kutty Ranjeet
- Department of Aquatic Environment Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
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4
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Luis Molina-Quirós J, Hernández-Muñoz S, Antonio Baeza J. The complete mitochondrial genome of the roosterfish Nematistius pectoralis Gill 1862: purifying selection in protein coding genes, organization of the control region, and insights into family-level phylogenomic relationships in the recently erected order Carangiformes. Gene 2022; 845:146847. [PMID: 36058495 DOI: 10.1016/j.gene.2022.146847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/26/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022]
Abstract
The roosterfish Nematistius pectoralis is considered as one of the most magnificent sportfishes worldwide. This study developed the first genomic resource for this trophy-fish that is heavily targeted by the fly-fishing industry. The complete mitochondrial genome of N. pectoralis was assembled using short read sequences and analyzed in detail. The mitochondrial genome of N. pectoralis is 16,537 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (12S and 16S), and 22 transfer RNA genes. A long intergenic space 770 bp in length was assumed to be the D-loop or Control Region (CR). Most of the PCGs and tRNA genes are encoded in the L-strand. All PCGs are under purifying selection and atp8 and nad6 experienced the least selective pressure. All tRNAs exhibit a cloverleaf secondary structure except tRNA-Serine 1 that lacked the D-arm loop. The D-loop of N. pectoralis exhibits three domains commonly described in other fishes; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the newly recognized order Carangiformes based on all 13 mitochondrial PCGs did not support the monophyly of this clade but recognized several families as monophyletic, including Bothidae, Carangidae, Istiophoridae, Latidae, Paralichthyidae, Polynemidae, and Rhombosoleidae. Nematistius pectoralis was sister to a clade composed of Toxotes chatareus (fam. Toxotidae) + Lactarius lactarius (fam. Lactariidae). This genomic resource developed for N. pectoralis will aid in improving our understanding of the population genomics of and strengthen conservation and management strategies in this remarkable trophy-fish.
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Affiliation(s)
- José Luis Molina-Quirós
- Biomolecular Laboratory, Center for International Programs, Universidad Veritas, San José, Costa Rica.
| | - Sebastián Hernández-Muñoz
- Biomolecular Laboratory, Center for International Programs, Universidad Veritas, San José, Costa Rica; Sala de Colecciones, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA; Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, IV Región, Chile; Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA
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An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants? Funct Integr Genomics 2021; 22:35-53. [PMID: 34751851 DOI: 10.1007/s10142-021-00815-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 10/19/2022]
Abstract
Microsatellites (SSRs) are tandem repeat sequences in eukaryote genomes, including plant cytoplasmic genomes. The mitochondrial genome (mtDNA) has been shown to vary in size, number, and distribution of SSRs among different plant groups. Thus, SSRs contribute with genomic diversity in mtDNAs. However, the abundance, distribution, and evolutionary significance of SSRs in mtDNA from a wide range of algae and plants have not been explored. In this study, the mtDNAs of 204 plant and algal species were investigated related to the presence of SSRs. The number of SSRs was positively correlated with genome size. Its distribution is dependent on plant and algal groups analyzed, although the cluster analysis indicates the conservation of some common motifs in algal and terrestrial plants that reflect common ancestry of groups. Many SSRs in coding and non-coding regions can be useful for molecular markers. Moreover, mitochondrial SSRs are highly abundant, representing an important source for natural or induced genetic variation, i.e., for biotechnological approaches that can modulate mtDNA gene regulation. Thus, this comparative study increases the understanding of the plant and algal SSR evolution and brings perspectives for further studies.
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Zhang L, Sun K, Csorba G, Hughes AC, Jin L, Xiao Y, Feng J. Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats. BMC Ecol Evol 2021; 21:199. [PMID: 34732135 PMCID: PMC8565063 DOI: 10.1186/s12862-021-01926-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In genus Rhinolophus, species in the Rhinolophus philippinensis and R. macrotis groups are unique because the horseshoe bats in these group have relatively low echolocation frequencies and flight speeds compared with other horseshoe bats with similar body size. The different characteristics among bat species suggest particular evolutionary processes may have occurred in this genus. To study the adaptive evidence in the mitochondrial genomes (mitogenomes) of rhinolophids, especially the mitogenomes of the species with low echolocation frequencies, we sequenced eight mitogenomes and used them for comparative studies of molecular phylogeny and adaptive evolution. RESULTS Phylogenetic analysis using whole mitogenome sequences produced robust results and provided phylogenetic signals that were better than those obtained using single genes. The results supported the recent establishment of the separate macrotis group. The signals of adaptive evolution discovered in the Rhinolophus species were tested for some of the codons in two genes (ND2 and ND6) that encode NADH dehydrogenases in oxidative phosphorylation system complex I. These genes have a background of widespread purifying selection. Signals of relaxed purifying selection and positive selection were found in ND2 and ND6, respectively, based on codon models and physicochemical profiles of amino acid replacements. However, no pronounced overlap was found for non-synonymous sites in the mitogenomes of all the species with low echolocation frequencies. A signal of positive selection for ND5 was found in the branch-site model when R. philippinensis was set as the foreground branch. CONCLUSIONS The mitogenomes provided robust phylogenetic signals that were much more informative than the signals obtained using single mitochondrial genes. Two mitochondrial genes that encoding proteins in the oxidative phosphorylation system showed some evidence of adaptive evolution in genus Rhinolophus and the positive selection signals were tested for ND5 in R. philippinensis. These results indicate that mitochondrial protein-coding genes were targets of adaptive evolution during the evolution of Rhinolophus species, which might have contributed to a diverse range of acoustic adaptations in this genus.
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Affiliation(s)
- Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China.
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China.
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Alice Catherine Hughes
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla County, 666303, Yunnan, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China.
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China.
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7
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He L, Long X, Qi J, Wang Z, Huang Z, Wu S, Zhang X, Luo H, Chen X, Lin J, Yang Q, Huang S, Zhou Q, Zheng L. Genome and gene evolution of seahorse species revealed by the chromosome-level genome of Hippocampus abdominalis. Mol Ecol Resour 2021; 22:1465-1477. [PMID: 34698429 PMCID: PMC9298228 DOI: 10.1111/1755-0998.13541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Seahorses belong to the teleost family Syngnathidae that evolved a distinct body plan and unique male pregnancy compared to other teleosts. As a classic model for studying evolution of viviparity and sexual selection of teleosts, seahorse species still lack a publicly available high‐quality reference genome. Here, we generated the genome assembly of the big‐belly seahorse, Hippocampus abdominalis with long‐read and Hi‐C technologies. We managed to place over 99% of the total length of 444.7 Mb of assembled genome into 21 linkage groups with almost no gaps. We reconstructed a phylogenomic tree with the big‐belly seahorse genome and other representative Syngnathidae and teleost species. We also reconstructed the historical population dynamics of four representative Syngnathidae species. We found the gene families that underwent expansion or contraction in the Syngnathidae ancestor were enriched for immune‐related or ion transporter gene ontology terms. Many of these genes were also reported to show a dynamic expression pattern during the pregnancy stages of H. abdominalis. We also identified putative positively selected genes in the Syngnathidae ancestor or in H. abdominalis, whose mouse mutants are enriched for abnormal craniofacial and limb morphological phenotypes. Overall, our study provides an important genome resource for evolutionary and developmental studies of seahorse species, and candidate genes for future experimental works.
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Affiliation(s)
- Libin He
- Fisheries Research Institute of Fujian, Xiamen, China
| | - Xin Long
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jianfei Qi
- Fisheries Research Institute of Fujian, Xiamen, China
| | - Zongji Wang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Institute of Animal Sex and Development, Zhejiang Wanli University, Ningbo, China
| | - Zhen Huang
- Fujian Key Laboratory of Sustainable Utilization of Featured Marine Bioresources, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Shuiqing Wu
- Fisheries Research Institute of Fujian, Xiamen, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huiyu Luo
- Fisheries Research Institute of Fujian, Xiamen, China
| | - Xinxin Chen
- Xiamen Xiaodeng Aquatic Science and Technology Company Limited, Xiamen, China
| | - Jinbo Lin
- Xiamen Xiaodeng Aquatic Science and Technology Company Limited, Xiamen, China
| | - Qiuhua Yang
- Fisheries Research Institute of Fujian, Xiamen, China
| | - Shiyu Huang
- Fisheries College of Jimei University, Xiamen, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.,Center for Reproductive Medicine, the Second Affiliated Hospital School of Medicine School of Medicine, Zhejiang University, Zhejiang University, Hangzhou, China
| | - Leyun Zheng
- Fisheries Research Institute of Fujian, Xiamen, China
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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9
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Teske PR. Mitochondrial genome announcements need to consider existing short sequences from closely related species to prevent taxonomic errors. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01214-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractThe reconstruction of complete mitochondrial genomes (mitogenomes) has considerable potential to clarify species relationships in cases where morphological analysis and DNA sequencing of individual genes are inconclusive. However, the trend to use only mitogenomes for the phylogenies presented in mitogenome announcements carries the inherent risk that the study species’ taxonomy is incorrect because no mitogenomes have yet been reconstructed for its sister species. Here, I illustrate this problem using the mitogenomes of two seahorses, Hippocampus capensis and H. queenslandicus. Both specimens used for mitogenome reconstruction originated from traditional Chinese medicine markets rather than native habitats. Although mitogenome phylogenies placed these specimens correctly among the seahorses from which mitogenomes were available at the time, incorporating single-marker sequence from closely related species into the phylogenies revealed that both mitogenomes are problematic. The mitogenome of the endemic South African H. capensis did not cluster among single-marker DNA sequences of seahorses from the species’ native habitat, but among sequences submitted under the names H. casscsio, H. fuscus and H. kuda that originated from all over the Indo-Pacific, including China. Phylogenetic placement of the mitogenome of H. queenslandicus within a cluster of seahorses that also included H. spinosissimus confirms an earlier finding that H. queenslandicus is a synonym of H. spinosissimus, a widespread Indo-Pacific species that also occurs in China. It is recommended that mitogenome announcements incorporate available single-marker sequences of closely related species, not only mitogenomes. The reconstruction of mitogenomes can exacerbate taxonomic confusion if existing information is ignored.
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Diversity of Seahorse Species (Hippocampus spp.) in the International Aquarium Trade. DIVERSITY 2021. [DOI: 10.3390/d13050187] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Seahorses (Hippocampus spp.) are threatened as a result of habitat degradation and overfishing. They have commercial value as traditional medicine, curio objects, and pets in the aquarium industry. There are 48 valid species, 27 of which are represented in the international aquarium trade. Most species in the aquarium industry are relatively large and were described early in the history of seahorse taxonomy. In 2002, seahorses became the first marine fishes for which the international trade became regulated by CITES (Convention for the International Trade in Endangered Species of Wild Fauna and Flora), with implementation in 2004. Since then, aquaculture has been developed to improve the sustainability of the seahorse trade. This review provides analyses of the roles of wild-caught and cultured individuals in the international aquarium trade of various Hippocampus species for the period 1997–2018. For all species, trade numbers declined after 2011. The proportion of cultured seahorses in the aquarium trade increased rapidly after their listing in CITES, although the industry is still struggling to produce large numbers of young in a cost-effective way, and its economic viability is technically challenging in terms of diet and disease. Whether seahorse aquaculture can benefit wild populations will largely depend on its capacity to provide an alternative livelihood for subsistence fishers in the source countries. For most species, CITES trade records of live animals in the aquarium industry started a few years earlier than those of dead bodies in the traditional medicine trade, despite the latter being 15 times higher in number. The use of DNA analysis in the species identification of seahorses has predominantly been applied to animals in the traditional medicine market, but not to the aquarium trade. Genetic tools have already been used in the description of new species and will also help to discover new species and in various other kinds of applications.
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11
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Sahoo L, Barat A, Das P, Sahoo B, Das G, Sundaray JK, Sahoo SK, Swain SK, Murmu K, Sarma D. Complete mitochondrial genome of nearly threatened freshwater ornamental fish, Microphis deocata and its phylogenetic relationship within Syngnathidae. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1207-1208. [PMID: 33829086 PMCID: PMC8008872 DOI: 10.1080/23802359.2020.1835572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Microphis deocata (deocata pipefish), belonging to family Syngnathidae, is one of the important indigenous ornamental fish species listed as near threatened in the IUCN red list. Here, we first report the complete mitochondrial genome of deocata pipefish using Illumina next-generation sequencing platform. The total length of the mitogenome is 16,526 bp. It encompasses 13 protein coding genes, 2 ribosomal rRNAs, and 22 tRNAs. The WANCY region (a cluster of five tRNA genes) contains the 50 bp OL light strand origin of replication. Phylogenetic analysis of Syngnathidae revealed M. deocata to cluster with Oostethus manadensis, forming a sister group with Doryrhamphus japonicas and Dunckerocampus dactyliophorus. The mitochondrial genome sequence data generated in the present study will play an important role in population genetic analysis and developing conservation strategies for this species.
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Affiliation(s)
- Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Ashoktaru Barat
- Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Bismay Sahoo
- Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Gargee Das
- Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Jitendra K Sundaray
- Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Sangram K Sahoo
- Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Saroj K Swain
- Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Khuntia Murmu
- Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, India
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12
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Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc 2020; 95:1252-1272. [PMID: 32372478 DOI: 10.1111/brv.12607] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 12/24/2022]
Abstract
The seahorses, pipefishes and seadragons (Syngnathidae) are among the few vertebrates in which pregnant males incubate developing embryos. Syngnathids are popular in studies of sexual selection, sex-role reversal, and reproductive trade-offs, and are now emerging as valuable comparative models for the study of the biology and evolution of reproductive complexity. These fish offer the opportunity to examine the physiology, behavioural implications, and evolutionary origins of embryo incubation, independent of the female reproductive tract and female hormonal milieu. Such studies allow us to examine flexibility in regulatory systems, by determining whether the pathways underpinning female pregnancy are also co-opted in incubating males, or whether novel pathways have evolved in response to the common challenges imposed by incubating developing embryos and releasing live young. The Syngnathidae are also ideal for studies of the evolution of reproductive complexity, because they exhibit multiple parallel origins of complex reproductive phenotypes. Here we assay the taxonomic distribution of syngnathid parity mode, examine the selective pressures that may have led to the emergence of male pregnancy, describe the biology of syngnathid reproduction, and highlight pressing areas for future research. Experimental tests of a range of hypotheses, including many generated with genomic tools, are required to inform overarching theories about the fitness implications of pregnancy and the evolution of male pregnancy. Such information will be widely applicable to our understanding of fundamental reproductive and evolutionary processes in animals.
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Affiliation(s)
- Camilla M Whittington
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, 2006, Australia.,The University of Sydney, Sydney School of Veterinary Science, Sydney, New South Wales, 2006, Australia
| | - Christopher R Friesen
- The University of Wollongong, School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, Wollongong, New South Wales, 2522, Australia.,Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, New South Wales, 2522, Australia
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Chen J, Lai M, Sun S, Zhang G, Ge Y, Cheng R. Complete mitochondrial genome and phylogenetic analysis of the Gray's pipefish Halicampus grayi Kaup 1856. Mitochondrial DNA B Resour 2019; 4:3754-3755. [PMID: 33366175 PMCID: PMC7707414 DOI: 10.1080/23802359.2019.1681915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 10/13/2019] [Indexed: 11/09/2022] Open
Abstract
In the present study, the complete mitochondrial genome of H. grayi was determined and annotated. The circular mitogenome is 16,959 bp in length and contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and a control region. Most of the PCGs start with ATG, but CO1 begins with a GTG start codon. Phylogenetic analysis revealed that H. grayi was strictly related to network pipefish Corythoichthys flavofasciatus with 100% bootstrap support value. This work provides basic molecular information that would be useful for further investigation on conservation genetics and evolutionary relationships of H. grayi.
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Affiliation(s)
- Jianzhen Chen
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, P. R. China
| | - Mengru Lai
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, P. R. China
| | - Siya Sun
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, P. R. China
| | - Guangji Zhang
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, P. R. China
| | - Yuqing Ge
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, P. R. China
| | - Rubin Cheng
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, P. R. China
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