1
|
Prochotta D, Winter S, Fennessy J, Janke A. Population genomics reveals mito-nuclear discordance and admixed populations in southern giraffe. Mol Phylogenet Evol 2024:108198. [PMID: 39276822 DOI: 10.1016/j.ympev.2024.108198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 07/30/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
Studying wildlife taxonomic diversity and identifying distinct populations has traditionally been largely based on morphology and geographic origin. More recently, this method has been supplemented by genetic data from the mitochondrial genome. However, this is limited as only maternally inherited and may not reflect the true nature of a population's genetics. Within the giraffe (Giraffa spp.), subspecies and unique populations were successfully characterized using both mitochondrial and genomic DNA studies, which led to new insights and, in some cases, unexpected results that required further verification. Here, we sequenced the genomes of 85 southern giraffe (G. giraffa) individuals from ten populations across southern Africa for a detailed investigation into the genetic diversity and history of its two subspecies, the Angolan (G. g. angolensis) and the South African (G. g. giraffa) giraffe. While the overall genotypes show low levels of runs of homozygosity compared to other mammals, the degree of heterozygosity is limited despite the large population size of South African giraffe. The nuclear genotype is largely congruent with the mitochondrial genotype. However, we have identified that the distribution of the Angolan giraffe is not as far east as indicated in an earlier mitochondrial DNA study. Botswana's Central Kalahari Game Reserve giraffe are unique, with a clear admixture of Angolan and South African giraffe populations. However, the enigmatic desert-dwelling giraffe of northwest Namibia is locally distinct from other Angolan giraffe yet exhibits intra-subspecies signs of admixture resulting from a recent introduction of individuals from Namibia's Etosha National Park. Whole genome sequencing is an invaluable and nearly indispensable tool for wildlife management to uncover genetic diversity that is undetectable through mitogenomic, geographical, and morphological means.
Collapse
Affiliation(s)
- David Prochotta
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany; Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria.
| | - Julian Fennessy
- Giraffe Conservation Foundation, PO Box 86099, Eros, Windhoek, Namibia; School of Biology and Environmental Science, University College Dublin, Ireland.
| | - Axel Janke
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany.
| |
Collapse
|
2
|
Nguyen MTP, Nguyen TTT, Ha TT, Ho CNQ, Le CPM, Hoang HNQ, Nguyen QTN, Nguyen TT, Luu DT, Dang KD, Thai QK, Le LT. Characterization of the Complete Mitochondrial Genome of the Central Highland Grey-Shanked Douc Langur ( Pygathrix cinerea), a Critically Endangered Species Endemic to Vietnam (Mammalia: Primates). Curr Issues Mol Biol 2024; 46:9928-9947. [PMID: 39329944 PMCID: PMC11430490 DOI: 10.3390/cimb46090592] [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: 07/16/2024] [Revised: 08/22/2024] [Accepted: 09/02/2024] [Indexed: 09/28/2024] Open
Abstract
The grey-shanked douc langur (Pygathrix cinerea) is a recently described, critically endangered primate, endemic to Vietnam. In this study, we describe the Central Highland species' complete mitochondrial genome (mitogenome-mtDNA). It is a circular molecule with a length of 16,541 base pairs (bp). The genome consists of 37 genes, consistent with those found in most other vertebrates, including 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs. A comparison with the mitogenomes of more than 50 primates showed that the mitogenome of Vietnamese Central Highland Pygathrix cinerea has a conservative gene order. We identified 43 nucleotide differences when comparing this genome with a previously published mitogenome of Pygathrix cinerea. It is evident that there are distinct differences between the Pygathrix cinerea we are currently studying and other Pygathrix cinerea specimens. These differences are unlikely to be solely the result of sequencing errors, as the mitogenomes were generated using high-quality methods. The genetic divergence observed between the two Pygathrix cinerea mitogenomes implies the potential existence of at least two distinct lineages or forms of this primate species within its native range in Vietnam.
Collapse
Affiliation(s)
- Mai Thi Phuong Nguyen
- Tay Nguyen Institute for Scientific Research, Academy of Science and Technology, Dalat City 670000, Vietnam
| | - Tram Thi Thuy Nguyen
- Biotechnology Department, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam
- Department of General and Biomedical Science, Ho Chi Minh City University of Physical Education and Sports, Ho Chi Minh 700000, Vietnam
| | - Tung Thanh Ha
- Tay Nguyen Institute for Scientific Research, Academy of Science and Technology, Dalat City 670000, Vietnam
| | - Chi Nguyen Quynh Ho
- Biotechnology Department, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam
- Animal Biotechnology Department, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Ho Chi Minh 700000, Vietnam
| | - Cuong Phan Minh Le
- Animal Biotechnology Department, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Ho Chi Minh 700000, Vietnam
| | - Huy Nghia Quang Hoang
- Animal Biotechnology Department, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Ho Chi Minh 700000, Vietnam
| | - Quynh Thi Nhu Nguyen
- Department of Bioactive Compounds, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Ho Chi Minh 700000, Vietnam
| | - Tao Thien Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam
| | - Dung Tri Luu
- Department of General and Biomedical Science, Ho Chi Minh City University of Physical Education and Sports, Ho Chi Minh 700000, Vietnam
| | - Khoa Dang Dang
- Faculty of Biotechnology, Ho Chi Minh Open University, Ho Chi Minh 700000, Vietnam
| | - Quan Ke Thai
- Faculty of Natural Sciences Education, Saigon University, Ho Chi Minh 700000, Vietnam
| | - Long Thanh Le
- Biotechnology Department, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam
- Animal Biotechnology Department, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Ho Chi Minh 700000, Vietnam
| |
Collapse
|
3
|
Marnis H, Syahputra K, Iswanto B, Cartealy IC, Sularto, Darmawan J, Hayuningtyas EP, Hidayat R, Tirta Subangkit A, Arianto. The complete mitochondrial genome of the blackskin catfish ( Clarias meladerma: Clariidae) from Rokan River, Riau, Indonesia. Mitochondrial DNA B Resour 2024; 9:1093-1097. [PMID: 39165382 PMCID: PMC11334743 DOI: 10.1080/23802359.2024.2392742] [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: 02/18/2024] [Accepted: 08/10/2024] [Indexed: 08/22/2024] Open
Abstract
Clarias meladerma Bleeker, 1846, a native catfish species in Indonesia belonging to the family Clariidae. The present study the complete mitochondrial genome sequence of C. meladerma from the Rokan River was sequenced by using next-generation sequencing, and its phylogenetic relationship was analyzed. The mitochondrial genome comprises 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, with a total length of 16,808 bp. The mitogenome of C. meladerma exhibits a base composition of 32.49% adenine, 25.75% thymine, 14.51% guanine, and 27.25% cytosine. Phylogenetic analysis indicated that C. meladerma has the same clade with C. macrocephalus, C. batrachus, and C. fucus. In essence, the findings of this study lay down a genetic foundation for future investigations into C. meladerma.
Collapse
Affiliation(s)
- Huria Marnis
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Khairul Syahputra
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Bambang Iswanto
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Imam Civi Cartealy
- Research Center for Computation, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Sularto
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Jadmiko Darmawan
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | | | - Rahmat Hidayat
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Arsad Tirta Subangkit
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Arianto
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| |
Collapse
|
4
|
Chowdhury LM, Mohindra V, Kumar R, Jena J. Genome sequencing and assembly of Indian major carp, Cirrhinus mrigala (Hamilton, 1822). Sci Data 2024; 11:898. [PMID: 39154040 PMCID: PMC11330464 DOI: 10.1038/s41597-024-03747-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024] Open
Abstract
The freshwater aquaculture species, Cirrhinus mrigala, commonly known as mrigal, holds significance in the carp-dominated aquaculture system, globally. Despite constituting 1.08% of the total freshwater aquaculture production, mrigal is the third most important Indian major carp. However, its genome and associated information is not available. This study aims to address this gap by generation high quality genome assembly using PacBio long reads, Illumina short reads and Hi-C scaffolding. The characterization of assembled highly contiguous genome, 1.057 Gb in size, revealed 39,091 genes with functional annotations. The orthology analysis based on direct orthologs and single copy ortholgs places C. mrigala in a distinct position within the Otophysi clade. Additionally, the study delves into Hox gene clusters, identifying 38 Hox genes distributed in seven clusters. The present genomic information offers potential applications for sustainable aquaculture management, including selection programs for economic traits.
Collapse
Affiliation(s)
- Labrechai Mog Chowdhury
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Vindhya Mohindra
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, Dilkusha, Lucknow, 226002, India.
| | - Rajesh Kumar
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Joykrushna Jena
- Indian Council of Agricultural Research (ICAR), Krishi Anusandhan Bhawan-II, New Delhi, 110012, India
| |
Collapse
|
5
|
Nhat NH, Saito M, Onodera SI, Hamada M, Hyodo F, Nagare H. Environmental DNA Reveals the Impact of Submarine Groundwater Discharge on the Spatial Variability of Coastal Fish Diversity. BIOLOGY 2024; 13:609. [PMID: 39194547 DOI: 10.3390/biology13080609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 08/29/2024]
Abstract
Submarine groundwater discharge (SGD) has recently been recognized as an influential factor in coastal ecosystems; however, little research has been conducted on its effects on coastal fish diversity. To investigate the relationship between SGD and fish diversity, we conducted a survey at the coastal island scale using the environmental DNA (eDNA) method. Our findings indicate that fish species richness and functional richness peak at stations with high SGD. Environmental variables, such as salinity, dissolved inorganic nitrogen (DIN) concentration, and SGD, significantly influence fish diversity. Carnivore fish richness was negatively correlated with salinity, while planktivore fish richness was positively correlated. Additionally, SGD and DIN concentrations were found to be crucial in shaping omnivorous and pelagic communities, respectively. This study highlights the role of SGD in enhancing nutrient conditions favorable for diverse fish communities and demonstrates the effectiveness of eDNA metabarcoding for rapid marine biodiversity assessment. These findings provide valuable insights for coastal ecosystem monitoring and management.
Collapse
Affiliation(s)
- Nguyen Hong Nhat
- Graduate School of Environmental and Life Science, Okayama University, Okayama 7008530, Japan
- Faculty of Technology-Engineering-Environment, An Giang University, Vietnam National University-Ho Chi Minh City, Ho Chi Minh City 880000, Vietnam
| | - Mitsuyo Saito
- Graduate School of Advanced Science and Engineering, Hiroshima University, Higashi Hiroshima 7398521, Japan
| | - Shin-Ichi Onodera
- Graduate School of Advanced Science and Engineering, Hiroshima University, Higashi Hiroshima 7398521, Japan
| | - Mayuko Hamada
- Ushimado Marine Institute (UMI), Graduate School of Environment, Life, Natural Science and Technology, Okayama University, Okayama 7014303, Japan
| | - Fujio Hyodo
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 7008530, Japan
| | - Hideaki Nagare
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 7008530, Japan
| |
Collapse
|
6
|
Fuhrmann N, Brasseur MV, Bakowski CE, Podsiadlowski L, Prost S, Krehenwinkel H, Mayer C. Chromosome-Level Genome Assembly of the Viviparous Eelpout Zoarces viviparus. Genome Biol Evol 2024; 16:evae155. [PMID: 39018026 PMCID: PMC11331339 DOI: 10.1093/gbe/evae155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/24/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024] Open
Abstract
The viviparous eelpout Zoarces viviparus is a common fish across the North Atlantic and has successfully colonized habitats across environmental gradients. Due to its wide distribution and predictable phenotypic responses to pollution, Z. viviparus is used as an ideal marine bioindicator organism and has been routinely sampled over decades by several countries to monitor marine environmental health. Additionally, this species is a promising model to study adaptive processes related to environmental change, specifically global warming. Here, we report the chromosome-level genome assembly of Z. viviparus, which has a size of 663 Mb and consists of 607 scaffolds (N50 = 26 Mb). The 24 largest represent the 24 chromosomes of the haploid Z. viviparus genome, which harbors 98% of the complete Benchmarking Universal Single-Copy Orthologues defined for ray-finned fish, indicating that the assembly is highly contiguous and complete. Comparative analyses between the Z. viviparus assembly and the chromosome-level genomes of two other eelpout species revealed a high synteny, but also an accumulation of repetitive elements in the Z. viviparus genome. Our reference genome will be an important resource enabling future in-depth genomic analyses of the effects of environmental change on this important bioindicator species.
Collapse
Affiliation(s)
- Nico Fuhrmann
- Department of Biogeography, Trier University, Trier 54296, Germany
| | - Marie V Brasseur
- Department of Biogeography, Trier University, Trier 54296, Germany
| | - Christina E Bakowski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn 53113, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn 53113, Germany
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Oulu 90014, Finland
- South African National Biodiversity Institute, National Zoological Garden, Pretoria 0002, South Africa
- Central Research Laboratories, Natural History Museum Vienna, Vienna 1010, Austria
| | | | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn 53113, Germany
| |
Collapse
|
7
|
Baraf LM, Hung JY, Pratchett MS, Cowman PF. Comparative mitogenomics of marine angelfishes (F: Pomacanthidae). Ecol Evol 2024; 14:e70127. [PMID: 39119180 PMCID: PMC11307104 DOI: 10.1002/ece3.70127] [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: 03/27/2024] [Revised: 06/16/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
The targeted capture of ultraconserved elements (UCEs) has substantially increased the amount of genetic data available for phylogenomic reconstructions. These capture datasets frequently contain mitochondrial DNA as a by-product, often in the form of complete mitogenomes. These can be efficiently harvested to expand existing datasets without additional costs. Here, we present new mitochondrial genomes for six marine angelfish species (F: Pomacanthidae), assembled and annotated from off-target UCE reads. We provide the first comparative analysis of all mitochondrial genomes available for the Pomacanthidae. Results showed that the average length of pomacanthid mitogenomes is 16.8 kbp. Total GC and AT content varied between 44.5% and 46.3%, and 53.7% and 55.5%, respectively. The architecture of angelfish mitogenomes was comparable to that seen in other fish species with 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and the control region. All 13 PCGs evolved under purifying selection, highlighting a high level of selection pressure and gene expression to preserve genetic integrity. The ND6 and ATP8 genes had the highest ratio of non-synonymous (dN) to synonymous (dS) substitutions, indicating a relaxation of purifying selection constraints. Finally, these newly assembled mitogenomes will allow further investigations of the population genetics, systematics and evolutionary biology of one of the most prominent reef fish family in the aquarium trade.
Collapse
Affiliation(s)
- Lauriane M. Baraf
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Julia Y. Hung
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Morgan S. Pratchett
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Peter F. Cowman
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Biodiversity and Geosciences ProgramQueensland Museum TropicsTownsvilleQueenslandAustralia
| |
Collapse
|
8
|
Chen W, Hubert N, Li Y, Zhu S, Wang J, Xiang D, Gao S, Kou C, Wang J, Wang T, Liang Z, Wu J, Li X, Li J. Mitogenomic phylogeny, biogeography, and cryptic divergence of the genus Silurus (Siluriformes: Siluridae). Zool Res 2024; 45:711-723. [PMID: 38766761 PMCID: PMC11298680 DOI: 10.24272/j.issn.2095-8137.2023.311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/25/2023] [Indexed: 05/22/2024] Open
Abstract
The genus Silurus, an important group of catfish, exhibits heterogeneous distribution in Eurasian freshwater systems. This group includes economically important and endangered species, thereby attracting considerable scientific interest. Despite this interest, the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus. Herein, we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes (mitogenomes) from 13 morphological species to reconstruct the phylogenetic relationships, biogeographic history, and species diversity of Silurus. Our phylogenetic reconstructions identified eight clades, supported by both maximum-likelihood and Bayesian inference. Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units (MOTUs) in several taxa, including the Silurus asotus complex (four MOTUs) and Silurus microdorsalis (two MOTUs), suggesting that species diversity is underestimated in the genus. A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago (Ma), with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma, and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma. Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula, with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma. Key factors such as the Eocene-Oligocene extinction event, onset and intensification of the monsoon system, and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus.
Collapse
Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
- China Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, Guangdong 510380, China
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong 510380, China
- Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong 510380, China
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, Montpellier, UMR 226 ISEM (UM-CNRS-IRD), France. E-mail:
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
- China Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, Guangdong 510380, China
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong 510380, China
- Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong 510380, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
- China Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, Guangdong 510380, China
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong 510380, China
- Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong 510380, China
| | - Jun Wang
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, China
| | - Denggao Xiang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Shang Gao
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Chunni Kou
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Jilong Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang 150076, China
| | - Tai Wang
- Gansu Fisheries Research Institute, Lanzhou, Gansu 730030, China
| | - Zhiqiang Liang
- Hunan Fisheries Science Institute, Changsha, Hunan 410153, China
| | - Junjie Wu
- Yunnan Institute of Fishery Sciences Research, Kunming, Yunnan 650111, China
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
- China Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, Guangdong 510380, China
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong 510380, China
- Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong 510380, China. E-mail:
| |
Collapse
|
9
|
Morales P, Gajardo F, Valdivieso C, Valladares MA, Di Genova A, Orellana A, Gutiérrez RA, González M, Montecino M, Maass A, Méndez MA, Allende ML. Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes. BMC Genomics 2024; 25:614. [PMID: 38890559 PMCID: PMC11184842 DOI: 10.1186/s12864-024-10416-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. RESULTS We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. CONCLUSIONS The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
Collapse
Affiliation(s)
- Pamela Morales
- Millennium Institute Center for Genome Regulation, Santiago, Chile.
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Felipe Gajardo
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Moisés A Valladares
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Grupo de Biodiversidad y Cambio Global (GBCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Alex Di Genova
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- DiGenoma-Lab, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
- Centro de Modelamiento Matemático UMI-CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Ariel Orellana
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- ANID Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Mauricio González
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Martin Montecino
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, 837001, Chile
| | - Alejandro Maass
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Modelamiento Matemático IRL 2807 CNRS, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Matemática, Universidad de Chile, Santiago, Chile
| | - Marco A Méndez
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Ecología Aplicada y Sustentabilidad (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Cape Horn International Center (CHIC), Parque Etnobotánico Omora, Universidad de Magallanes, Puerto Williams, Chile
| | - Miguel L Allende
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| |
Collapse
|
10
|
Xu CH, Song L, Wang Q, Chen XJ. Complete mitochondrial genome of Devario shanensis (Cypriniformes: Danionidae: Danioninae): genome characterization and phylogenetic consideration. Mitochondrial DNA B Resour 2024; 9:797-801. [PMID: 38895506 PMCID: PMC11185080 DOI: 10.1080/23802359.2024.2363367] [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: 04/14/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
In this study, a comprehensive analysis is presented on the complete mitochondrial genome and phylogenetic relationships of Devario shanensis, an endemic species to the Irrawaddy drainage in southwestern China. The complete mitogenome sequence of D. shanensis was sequenced to be 16,860 bp long and encompassed 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a non-coding control region. The overall AT content (61.1%) was much higher than GC content (38.9%). Phylogenetic analyses employing maximum-likelihood and Bayesian inference methods on the complete mitogenomes, including D. shanensis and 13 other species, unveiled a close genomic relationship between D. shanensis and Devario interruptus. This work will contribute to the genetic resource enrichment and phylogenetic researches on genus Devario.
Collapse
Affiliation(s)
- Chun Hui Xu
- College of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College. Taizhou, Jiangsu Province, P.R. China
| | - Lin Song
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu Province, P.R. China)
| | - Quan Wang
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu Province, P.R. China)
| | - Xiao Jiang Chen
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu Province, P.R. China)
| |
Collapse
|
11
|
Mwamburi SM, Kawato S, Furukawa M, Konishi K, Nozaki R, Hirono I, Kondo H. De Novo Assembly and Annotation of the Siganus fuscescens (Houttuyn, 1782) Genome: Marking a Pioneering Advance for the Siganidae Family. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10325-9. [PMID: 38850360 DOI: 10.1007/s10126-024-10325-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024]
Abstract
This study presents the first draft genome of Siganus fuscescens, and thereby establishes the first whole-genome sequence for a species in the Siganidae family. Leveraging both long and short read sequencing technologies, i.e., Oxford Nanopore and Illumina sequencing, we successfully assembled a mitogenome spanning 16.494 Kb and a first haploid genome encompassing 498 Mb. The assembled genome accounted for a 99.6% of the estimated genome size and was organized into 164 contigs with an N50 of 7.2 Mb. This genome assembly showed a GC content of 42.9% and a high Benchmarking Universal Single-Copy Orthologue (BUSCO) completeness score of 99.5% using actinopterygii_odb10 lineage, thereby meeting stringent quality standards. In addition to its structural aspects, our study also examined the functional genomics of this species, including the intricate capacity to biosynthesize long-chain polyunsaturated fatty acids (LC-PUFAs) and secrete venom. Notably, our analyses revealed various repeats elements, which collectively constituted 17.43% of the genome. Moreover, annotation of 28,351 genes uncovered both shared genetic signatures and those that are unique to S. fuscescens. Our assembled genome also displayed a moderate prevalence of gene duplication compared to other fish species, which suggests that this species has a distinctive evolutionary trajectory and potentially unique functional constraints. Taken altogether, this genomic resource establishes a robust foundation for future research on the biology, evolution, and the aquaculture potential of S. fuscescens.
Collapse
Affiliation(s)
- Samuel Mwakisha Mwamburi
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
- Department of Fisheries, Kenya Marine and Fisheries Research Institute, P.O BOX 81651-80100, Mombasa, Kenya
| | - Satoshi Kawato
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Miho Furukawa
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Kayo Konishi
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Reiko Nozaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Ikuo Hirono
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Hidehiro Kondo
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan.
| |
Collapse
|
12
|
Winn JC, Bester-van der Merwe AE, Maduna SN. Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae). Data Brief 2024; 54:110280. [PMID: 38962188 PMCID: PMC11220847 DOI: 10.1016/j.dib.2024.110280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 07/05/2024] Open
Abstract
Here, we present, for the first time, the Ion TorrentⓇ next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include Galeorhinus galeus (number of bases pairs (bp) 17,487; GenBank accession number ON652874), Mustelus asterias (16,708; ON652873), Mustelus mosis (16,755; ON075077), Mustelus palumbes (16,708; ON075076), and Triakis megalopterus (16,746; ON075075). All assembled mitogenomes encode 13 protein-coding genes (PCGs), two ribosomal (r)RNA genes, and 22 transfer (t)RNA genes (tRNALeu and tRNASer are duplicated), except for G. galeus which contains 23 tRNA genes where tRNAThr is duplicated. The data presented in this paper can assist other researchers in further elucidating the diversification of triakid species and the phylogenetic relationships within Carcharhiniformes (groundsharks) as mitogenomes accumulate in public repositories.
Collapse
Affiliation(s)
- Jessica C. Winn
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, 7602, South Africa
| | - Aletta E. Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, 7602, South Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway
| |
Collapse
|
13
|
Iguchi A, Nishijima M, Ikeuchi E, Yokooka H, Sugishima H, Ikeda K, Miwa R, Sekido Y, Iwasaki N, Suzumura M, Tsukasaki A, Tanaka Y, Kato S, Minatoya J, Okamoto N, Kunishima T, Ise Y, Suzuki A. Utilizing environmental DNA and imaging to study the deep-sea fish community of Takuyo-Daigo Seamount. NPJ BIODIVERSITY 2024; 3:14. [PMID: 39242887 PMCID: PMC11331990 DOI: 10.1038/s44185-024-00042-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/29/2024] [Indexed: 09/09/2024]
Abstract
The increase in interest of mining at seamounts means there is a critical need to establish baseline inventories through environmental survey, with the aim of promoting the conservation and stewardship of these remote habitats. To efficiently evaluate fish biodiversity around a seamount, we compared environmental DNA (eDNA) methods using seawater and sponge samples against methods using imagery obtained with a remotely operated vehicle (ROV) and a free-fall deep-sea camera lander called the Edokko Mark I on the Takuyo-Daigo Seamount (153.0°E, 23.5°N) in the northwestern Pacific Ocean. We detected a total of 18 fish families by these methods. The fish fauna detected on the seamount included many families commonly found in deep-sea areas and were similar to the fish fauna of other seamounts located at similar latitudes in the northwestern Pacific. Significant differences in the patterns of detection of fish families between the eDNA and imaging methods is attributed to the differing powers of detection of some fish groups between methods (related to primer compatibility and fish size). For deep-sea fish, the difference in fish composition at the family level between seawater and sponge eDNA methods was not significant, but the difference between Edokko Mark I and ROV methods was significant; the latter difference is likely due to whether or not bait is used to attract fish. Although the eDNA workflow implemented here requires improvements, the use of eDNA and imaging methods in combination provided better insight into the biodiversity of deep-sea fishes in the deep-sea around a seamount, where our knowledge of the fish fauna has been extremely limited. Our recovery of eDNA from seawater and sponge samples around the seamount demonstrates the potential of these methods for facilitating environmental baseline surveys and impact assessments of mining activities to obtain results not previously possible with the use of visual methods only.
Collapse
Affiliation(s)
- Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
- Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan.
| | - Miyuki Nishijima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Eri Ikeuchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Hiroyuki Yokooka
- IDEA Consultants, Inc., 1334-5 Riemon, Yaizu, Shizuoka, 421-0212, Japan
| | - Hideki Sugishima
- IDEA Consultants, Inc., 1334-5 Riemon, Yaizu, Shizuoka, 421-0212, Japan
| | - Kazumasa Ikeda
- Okamoto Glass Co., Ltd., 380 Toyofuta, Kashiwa, Chiba, 277-0872, Japan
| | - Ryuichi Miwa
- Kaiyo Engineering Co., Ltd., 4-28-11 Taito, Taito, Tokyo, 110-0016, Japan
| | - Yoshiro Sekido
- Marine Biological Research Institute of Japan Co., Ltd., 4-28-11 Taito, Taito, Tokyo, 110-0016, Japan
| | - Nozomu Iwasaki
- Faculty of Geo-Environmental Science, Rissho University, 1700 Magechi, Kumagaya, Saitama, 360-0194, Japan
| | - Masahiro Suzumura
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Ayumi Tsukasaki
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Yuichiro Tanaka
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Shogo Kato
- IDEA Consultants, Inc., 1334-5 Riemon, Yaizu, Shizuoka, 421-0212, Japan
| | - Jumpei Minatoya
- Marine Biological Research Institute of Japan Co., Ltd., 4-28-11 Taito, Taito, Tokyo, 110-0016, Japan
| | - Nobuyuki Okamoto
- Deep Ocean Resources Development CO., Ltd., 2-3-5, Nihonbashi Horidome-cho, Chuoh-ku, Tokyo, 103-0012, Japan
| | - Taiga Kunishima
- Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Yuji Ise
- Kuroshio Biological Research Foundation, 560 Nishidomari, Otsuki, Kochi, 788-0333, Japan
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
- Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan.
| |
Collapse
|
14
|
Parikh A, Pansu J, Stow A, Warne MSJ, Chivas C, Greenfield P, Boyer F, Simpson S, Smith R, Gruythuysen J, Carlin G, Caulfield N, Viard F, Chariton AA. Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123954. [PMID: 38604307 DOI: 10.1016/j.envpol.2024.123954] [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: 10/03/2023] [Revised: 03/14/2024] [Accepted: 04/09/2024] [Indexed: 04/13/2024]
Abstract
Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly elevated during the sampled wet season with the influx of freshwater and agricultural run-off. Fish taxa richness significantly decreased in all three estuaries (F = 164.73, P = <0.001), along with pronounced changes in community composition (F = 46.68, P = 0.001) associated with environmental variables (largely salinity: 27.48% contribution to total variance). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Among the four sampled locations, variation in fish community composition was more pronounced within the wet season (F = 2.5, P = 0.001). Notably, variation in the wet season was significantly correlated with agricultural contaminants (phosphorus: 6.25%, pesticides: 5.22%) alongside environmental variables (salinity: 5.61%, DOC: 5.57%). Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects play a key role in shaping the community structure of fish in this region, agricultural contaminants are also important contributors in estuarine systems.
Collapse
Affiliation(s)
- Aashi Parikh
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Johan Pansu
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia; CSIRO Environment, Lucas Heights, NSW, 2234, Australia; ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34095, France; Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France.
| | - Adam Stow
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Michael St J Warne
- Reef Catchments Science Partnership, Mackay, QLD, 4740, Australia; School of Earth and Environmental Sciences, University of Queensland, QLD, 4067, Australia; Centre for Agroecology, Water and Resilience, Coventry University, West Midlands, United Kingdom; Queensland Department of Environment and Science, Brisbane, QLD, 4179, Australia.
| | - Christine Chivas
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Paul Greenfield
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia; CSIRO Energy, Lindfield, NSW, 2070, Australia.
| | - Frédéric Boyer
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, 38000, France.
| | | | - Rachael Smith
- Office of the Great Barrier Reef, Queensland Department of Environment and Science, Brisbane, QLD, 4179, Australia.
| | - Jacob Gruythuysen
- Science Division, Queensland Department of Environment and Science, Brisbane, QLD, 4179, Australia.
| | - Geoffrey Carlin
- CSIRO Environment, Dutton Park, Queensland, 4102, Australia.
| | - Natalie Caulfield
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| | - Frédérique Viard
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34095, France.
| | - Anthony A Chariton
- School of Natural Sciences, Wallumattagal (North Ryde) Campus, Macquarie University, NSW, 2113, Australia.
| |
Collapse
|
15
|
Munian K, Ramli FF, Othman N, Mahyudin NAA, Sariyati NH, Abdullah-Fauzi NAF, Haris H, Ilham-Norhakim ML, Abdul-Latiff MAB. Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool. Mol Ecol Resour 2024; 24:e13936. [PMID: 38419264 DOI: 10.1111/1755-0998.13936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia. Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost-effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning.
Collapse
Affiliation(s)
- Kaviarasu Munian
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
- Zoology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Farah Farhana Ramli
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nursyuhada Othman
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nur Aina Amira Mahyudin
- Zoology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Nur Hartini Sariyati
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Nurfatiha Akmal Fawwazah Abdullah-Fauzi
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| | - Hidayah Haris
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, 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), Muar, Johor, Malaysia
- Kim Ichthyologist Centre, Kg Parit Samsu, Jalan Temenggong Ahmad, Parit Jawa, Muar, Johor, Malaysia
- Akim Fishes Enterprise, Muar, Johor, Malaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Johor, Malaysia
| |
Collapse
|
16
|
Denton JSS, Kneebone J, Yang L, Lynghammar A, McElroy D, Corrigan S, Jakobsdóttir K, Miri C, Simpson M, Naylor GJP. Mitogenomic evidence of population differentiation of thorny skate, Amblyraja radiata, in the North Atlantic. JOURNAL OF FISH BIOLOGY 2024; 104:1513-1524. [PMID: 38403290 DOI: 10.1111/jfb.15689] [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: 07/05/2023] [Revised: 01/16/2024] [Accepted: 02/01/2024] [Indexed: 02/27/2024]
Abstract
Management of thorny skate (Amblyraja radiata) in the Northwest Atlantic has posed a conservation dilemma for several decades due to the species' lack of response to strong conservation efforts in the US Gulf of Maine and the Canadian Scotian Shelf, confusion over the relationship between two reproductive size morphs of differing life histories that are sympatric in the Northwest Atlantic, and conflicting data on regional population connectivity throughout the species' broader range. To better assess potential A. radiata regional population differentiation and genetic links to life-history variation, we analysed complete mitochondrial genome sequences from 527 specimens collected across the species' North Atlantic geographic range, with particular emphasis on the Northwest Atlantic region. A high level of genetic diversity was evident across the North Atlantic, but significant genetic differentiation was identified between specimens inhabiting the Northwest (Gulf of Maine and Newfoundland) and Northeast (Greenland, Iceland, North Sea, and Arctic Circle) Atlantic. In the Northwest Atlantic, significant differentiation between the Gulf of Maine and Newfoundland regions was revealed; however, the overall level of differentiation was very low. No genetic difference was identified between the large and small reproductive morphs. The results of this study advance our understanding of A. radiata population structure in the North Atlantic but do not resolve all the questions confounding our understanding of the species' biology and evolutionary history.
Collapse
Affiliation(s)
- John S S Denton
- Florida Museum of Natural History, Dickinson Hall, Gainesville, Florida, USA
| | - Jeff Kneebone
- Anderson Cabot Center for Ocean Life, New England Aquarium, Boston, Massachusetts, USA
| | - Lei Yang
- Florida Museum of Natural History, Dickinson Hall, Gainesville, Florida, USA
| | - Arve Lynghammar
- Faculty of Biosciences, Fisheries and Economics, The Norwegian College of Fishery Science UiT The Arctic University of Norway, Tromsø, Norway
| | - David McElroy
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, Woods Hole, Massachusetts, USA
| | - Shannon Corrigan
- Florida Museum of Natural History, Dickinson Hall, Gainesville, Florida, USA
| | - Klara Jakobsdóttir
- Marine and Freshwater Research Institute, Demersal Division, Hafnarfjörður, Iceland
| | - Carolyn Miri
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Center, St John's, Newfoundland, Canada
| | - Mark Simpson
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Center, St John's, Newfoundland, Canada
| | - Gavin J P Naylor
- Florida Museum of Natural History, Dickinson Hall, Gainesville, Florida, USA
| |
Collapse
|
17
|
Liao X, Shih Y, Jia C, Gao T. Complete Mitochondrial Genome of Four Peristediidae Fish Species: Genome Characterization and Phylogenetic Analysis. Genes (Basel) 2024; 15:557. [PMID: 38790187 PMCID: PMC11121196 DOI: 10.3390/genes15050557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, this study aims to investigate the mitochondrial genomic characteristics and intra-family phylogenetic relationships of Peristediidae by utilizing mitochondrial genome analysis. Therefore, this study aims to investigate the phylogenetic relationship of Peristediidae by utilizing mitochondrial genome analysis. The mitochondrial genome of four species of Peristediidae (Peristedion liorhynchus, Satyrichthys welchi, Satyrichthys rieffeli, and Scalicus amiscus) collected in the East China Sea was studied. The mitochondrial gene sequence lengths of four fish species were 16,533 bp, 16,526 bp, 16,527 bp, and 16,526 bp, respectively. They had the same mitochondrial structure and were all composed of 37 genes and one control region. Most PCGs used ATG as the start codon, and a few used GTG as the start codon. An incomplete stop codon (TA/T) occurred. The AT-skew and GC-skew values of 13 PCGs from four species were negative, and the GC-skew amplitude was greater than that of AT-skew. All cases of D-arm were found in tRNA-Ser (GCT). The Ka/Ks ratio analysis indicated that 13 PCGs were suffering purifying selection. Based on 12 PCGs (excluding ND6) sequences, a phylogenetic tree was constructed using Bayesian inference (BI) and maximum likelihood (ML) methods, providing a further supplement to the scientific classification of Peristediidae fish. According to the results of divergence time, the four species of fish had apparent divergence in the Early Cenozoic, which indicates that the geological events at that time caused the climax of species divergence and evolution.
Collapse
Affiliation(s)
- Xianhui Liao
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Yijia Shih
- Fisheries College, Jimei University, Xiamen 361021, China;
| | - Chenghao Jia
- School of Ecology and Environment, Hainan University, Haikou 570228, China;
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China;
| |
Collapse
|
18
|
Girard MG, Santos MD, Bemis KE. New species of redbait from the Philippines (Teleostei, Emmelichthyidae, Emmelichthys). Zookeys 2024; 1196:95-109. [PMID: 38602272 PMCID: PMC10999954 DOI: 10.3897/zookeys.1196.111161] [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: 08/14/2023] [Accepted: 02/15/2024] [Indexed: 04/12/2024] Open
Abstract
We describe a new species of redbait in the genus Emmelichthys collected from fish markets on Panay and Cebu islands in the Visayas region of the Philippines. The species is externally similar to E.struhsakeri but is diagnosable by two prominent fleshy papillae associated with the cleithrum and fewer pectoral-fin rays (18-19 vs. 19-21) and gill rakers (30-33 vs. 34-41). Additionally, mitochondrial DNA differentiates this taxon from other species of Emmelichthys. We generate mitochondrial genomes for two of the three type specimens and several other emmelichthyids to place the new taxon in a phylogenetic context. Analysis of the protein-coding mitochondrial loci calls into question the monophyly of two emmelichthyid genera (Emmelichthys and Erythrocles) and highlights the need for subsequent analyses targeting the intrarelationships of the Emmelichthyidae.
Collapse
Affiliation(s)
- Matthew G. Girard
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USAUniversity of KansasLawrenceUnited States of America
| | - Mudjekeewis D. Santos
- Genetic Fingerprinting Laboratory, National Fisheries Research and Development Institute, Quezon City, 1103, PhilippinesGenetic Fingerprinting Laboratory, National Fisheries Research and Development InstituteQuezon CityPhilippines
| | - Katherine E. Bemis
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
- National Systematics Laboratory, Office of Science and Technology, NOAA Fisheries, Washington, DC, 20560, USANational Systematics Laboratory, Office of Science and TechnologyWashingtonUnited States of America
| |
Collapse
|
19
|
Zhang G, Xu T, Chen Y, Xu W, Wang Y, Li Y, Zhu F, Liu H, Ruan H. Complete Mitochondrial Genomes of Nedyopus patrioticus: New Insights into the Color Polymorphism of Millipedes. Curr Issues Mol Biol 2024; 46:2514-2527. [PMID: 38534775 DOI: 10.3390/cimb46030159] [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: 02/19/2024] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
There has been debate about whether individuals with different color phenotypes should have different taxonomic status. In order to determine whether the different color phenotypes of Nedyopus patrioticus require separate taxonomic status or are simply synonyms, here, the complete mitochondrial genomes (mitogenomes) of two different colored N. patrioticus, i.e., red N. patrioticus and white N. patrioticus, are presented. The two mitogenomes were 15,781 bp and 15,798 bp in length, respectively. Each mitogenome contained 13 PCGs, 19 tRNAs, 2 rRNAs, and 1 CR, with a lack of trnI, trnL2, and trnV compared to other Polydesmida species. All genes were located on a single strand in two mitogenomes. Mitochondrial DNA analyses revealed that red N. patrioticus and white N. patrioticus did not show clear evolutionary differences. Furthermore, no significant divergence was discovered by means of base composition analysis. As a result, we suggest that white N. patrioticus might be regarded as a synonym for red N. patrioticus. The current findings confirmed the existence of color polymorphism in N. patrioticus, which provides exciting possibilities for future research. It is necessary to apply a combination of molecular and morphological methods in the taxonomy of millipedes.
Collapse
Affiliation(s)
- Gaoji Zhang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Tangjun Xu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yukun Chen
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Xu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yinuo Wang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yuanyuan Li
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Fuyuan Zhu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyi Liu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Honghua Ruan
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| |
Collapse
|
20
|
Fast KM, Larrimore JD, Alley ZD, Sandel MW. Complete mitochondrial genome of the Starhead Topminnow Fundulus dispar (Cyprinodontiformes: Fundulidae). Mitochondrial DNA B Resour 2024; 9:342-346. [PMID: 38476840 PMCID: PMC10930100 DOI: 10.1080/23802359.2024.2327564] [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: 11/14/2023] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Topminnows of the Teleost genus Fundulus serve as model organisms in ecotoxicology because of their broad physiological tolerance and propensity to breed in captivity. This research has been primarily limited to intraspecific comparisons, due to incomplete understanding of the evolutionary history of the genus, which is necessary for use of phylogenetic comparative methods. Interspecific relationships of topminnows remain unresolved, despite recent advances in mitochondrial and nuclear genome sequencing. Specifically, interrelationships of a group containing the starhead topminnows (Fundulus blairae, F. dispar, F. escambiae, F. lineolatus, and F. nottii) typically yield low node support values. Here, we present the first annotated mitochondrial genome of the Starhead Topminnow (F. dispar) and provide a phylogenetic hypothesis for starhead topminnows within the genus Fundulus. DNA was isolated from a specimen of F. dispar collected in Kentucky, USA. The circular genome is 16,564 bp long and contains 13 protein-coding genes, two ribosomal RNAs (rRNA), 22 transfer RNAs (tRNA), and one control region (D-loop). Our phylogenetic analysis supports a sister relationship between F. dispar and a group containing F. notatus and F. olivaceus. This data helps to resolve the phylogenetic placement of starhead topminnows.
Collapse
Affiliation(s)
- Kayla M. Fast
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Mississippi State, MS, USA
| | | | - Zachariah D. Alley
- Edge Engineering and Science, LLC, Houston, TX, USA
- Department of Biological and Environmental Sciences, The University of West Alabama, Livingston, AL, USA
| | - Michael W. Sandel
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Mississippi State, MS, USA
- Forest and Wildlife Research Center, Mississippi State University, Mississippi State, MS, USA
| |
Collapse
|
21
|
Alvarenga M, D'Elia AKP, Rocha G, Arantes CA, Henning F, de Vasconcelos ATR, Solé-Cava AM. Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic. BMC Genomics 2024; 25:215. [PMID: 38413941 PMCID: PMC10898094 DOI: 10.1186/s12864-024-10035-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/21/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Phylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related references. We applied target-enrichment to obtain complete mitochondrial genomes of marine ichthyofauna from the Brazilian coast selected based on economic significance, conservation status and lack of phylogenetically-close references. These included sardines (Dorosomatidae, Alosidae), mackerels (Scombridae) croakers (Sciaenidae), groupers (Epinephelidae) and snappers (Lutjanidae). RESULTS Custom baits were designed to enrich mitochondrial DNA across a broad phylogenetic range of fishes. Sequencing generated approximately 100k reads per sample, which were assembled in a total of 70 complete mitochondrial genomes and include fifty-two new additions to GenBank, including five species with no previous mitochondrial data. Departures from the typical gene content and order occurred in only three taxa and mostly involved tRNA gene duplications. Start-codons for all genes, except Cytochrome C Oxidase subunit I (COI), were consistently ATG, whilst a wide range of stop-codons deviated from the prevailing TAA. Phylogenetic analysis confirmed assembly accuracy and revealed signs of cryptic diversification within the Mullus genus. Lineage delimitation methods using Sardinella aurita and S. brasiliensis mitochondrial genomes support a single Operational Taxonomic Unit. CONCLUSIONS Target enrichment was highly efficient, providing complete novel mitochondrial genomes with little sequencing effort. These sequences are deposited in public databases to enable subsequent studies in population genetics and adaptation of Latin American fish species and serve as a vital resource for conservation and management programs that rely on molecular data for species and genus-level identification.
Collapse
Affiliation(s)
- Marcela Alvarenga
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, 4485-661, Portugal
| | - Ananda Krishna Pereira D'Elia
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
| | - Graciane Rocha
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
| | - Clara Alvarez Arantes
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
| | - Frederico Henning
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil.
| | | | - Antonio Mateo Solé-Cava
- CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brasil
| |
Collapse
|
22
|
Wang YC, Liu SH, Ho HC, Su HY, Chang CH. DNA mini-barcoding reveals the mislabeling rate of canned cat food in Taiwan. PeerJ 2024; 12:e16833. [PMID: 38406290 PMCID: PMC10893872 DOI: 10.7717/peerj.16833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/04/2024] [Indexed: 02/27/2024] Open
Abstract
Background Domestic cats are important companion animals in modern society that live closely with their owners. Mislabeling of pet food can not only harm pets but also cause issues in areas such as religious beliefs and natural resource management. Currently, the cat food market is booming. However, despite the risk that mislabeling poses to cats and humans, few studies have focused on species misrepresentation in cat food products. Methods To address this issue, we used DNA barcoding, a highly effective identification methodology that can be applied to even highly processed products. We targeted a short segment (~85 basepairs) of the mitochondrial 16S rRNA (16S) gene as a barcode and employed Sanger or next generation sequencing (NGS) to inspect 138 canned cat food products in the Taiwanese market. Results We discovered that the majority of mislabeling incidents were related to replacement of tuna with other species. Moreover, our metabarcoding revealed that numerous undeclared ingredients were present in all examined canned products. One product contained CITES Appendix II-listed shortfin mako shark (Isurus oxyrinchus). Overall, we uncovered a mislabeling rate of at least 28.99%. To verify cases of mislabeling, an official standardized list of vernacular names, along with the corresponding scientific species names, as well as a dependable barcoding reference sequence database are necessary.
Collapse
Affiliation(s)
- Yu-Chun Wang
- Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan
- Technical Service Division, Fisheries Research Institute, Keelung, Taiwan
| | - Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Hsuan Ching Ho
- Department and Graduate Institute of Aquaculture, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Hsiao-Yin Su
- Department of Science Education, National Taipei University of Education, Taipei, Taiwan
| | - Chia-Hao Chang
- Department of Science Education, National Taipei University of Education, Taipei, Taiwan
| |
Collapse
|
23
|
Chen W, Xiang D, Gao S, Zhu S, Wu Z, Li Y, Li J. Whole-genome resequencing confirms the genetic effects of dams on an endangered fish Hemibagrus guttatus (Siluriformes: Bagridae): A case study in a tributary of the Pearl River. Gene 2024; 895:148000. [PMID: 37979951 DOI: 10.1016/j.gene.2023.148000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/31/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023]
Abstract
Dam construction in riverine ecosystems has fragmented natural aquatic habitats and has altered environmental conditions. As a result, damming has been demonstrated to threaten aquatic biodiversity by reducing species distribution ranges and hindering gene exchange, leading to the inability to adapt to environmental changes. Knowledge of the contemporary genetic diversity and genetic structure of fish populations that are separated by dams is vital to developing effective conservation strategies, particularly for endangered fish species. We chose the Lianjiang River, a tributary of the Pearl River, as a case study to assess the effects of dams on the genetic diversity and genetic structure of an endangered fish species, Hemibagrus guttatus, using whole-genome resequencing data from 63 fish samples. The results indicated low levels of genetic diversity, high levels of inbreeding and decreasing trend of effective population size in fragmented H. guttatus populations. In addition, there were significant genetic structure and genetic differentiation among populations, suggesting that the dams might have affected H. guttatus populations. Our findings may benefit management and conservation practices for this endangered species that is currently suffering from the effects of dam construction.
Collapse
Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Denggao Xiang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Shang Gao
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Zhi Wu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China.
| |
Collapse
|
24
|
Kundu S, Kang HE, Kim AR, Lee SR, Kim EB, Amin MHF, Andriyono S, Kim HW, Kang K. Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae). Int J Mol Sci 2024; 25:1822. [PMID: 38339100 PMCID: PMC10855530 DOI: 10.3390/ijms25031822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost's, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.
Collapse
Affiliation(s)
- Shantanu Kundu
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Eun-Bi Kim
- Ocean Georesources Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea;
| | - Muhammad Hilman Fu’adil Amin
- Advance Tropical Biodiversity, Genomics, and Conservation Research Group, Department of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia;
| | - Sapto Andriyono
- Department of Marine, Faculty of Fisheries and Marine, Airlangga University, Surabaya 60115, Indonesia
| | - Hyun-Woo Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Kyoungmi Kang
- International Graduate Program of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
| |
Collapse
|
25
|
Li A, Fan J, Guo F, Carpenter-Bundhoo L, Huang G, Shi Y, Ao Y, Wang J. Assessing the impact of river connectivity on fish biodiversity in the Yangtze River Basin using a multi-index evaluation framework. ENVIRONMENTAL RESEARCH 2024; 242:117729. [PMID: 38036204 DOI: 10.1016/j.envres.2023.117729] [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: 10/18/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023]
Abstract
The Yangtze River Basin, the world's third-largest river basin and a hot spot for global biodiversity conservation, is facing biodiversity crisis caused by reduced river connectivity. The deterioration arises from four dimensions: longitudinal, lateral, vertical and temporal. However, limited research has quantified the spatiotemporal connectivity of the Yangtze River Basin and further evaluated the consequent impact on fish biodiversity. In our study, a multi-index evaluation framework was developed to assess the variations in the four-dimensional connectivity of the Yangtze River Basin from 1980 to 2020, and fish biodiversity affected by reduced connectivity was detected by environmental DNA metabarcoding. Our results showed that the Yangtze River Basin suffers from a pronounced connectivity reduction, with 67% of assessed rivers experiencing deteriorated connectivity in recent years. The lost fish biodiversity along the river reaches with the worst connectivity was likely attributed to the construction of hydropower plants. The headwaters and the downstreams of most hydropower plants had a higher fish biodiversity compared with reservoirs. The free-flowing reaches in the downstream of the lowest hydropower station, had higher lotic fish abundance compared with that in the upstream. As for the entire Yangtze River Basin, 67% of threatened fish species, with 70% endemic species, were threatened by reduced river connectivity. Our result indicates that the massive loss of river connectivity changes the spatiotemporal patterns of fish community and threatens protected fish. More effective measures to restore the populations of affected fish in rivers with reduced river connectivity are required.
Collapse
Affiliation(s)
- Aopu Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Juntao Fan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Fen Guo
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | | | - Guoxian Huang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yue Shi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yuyin Ao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Jingfu Wang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| |
Collapse
|
26
|
Chen F, Lu P, Liang D, Wu Y, Jiang Z, Huang W, Gao L. Phylogenetic analysis based on the complete mitochondrial genome of Discogobio brachyphysallidos (Cypriniformes: Cyprinidae) suggests the need for taxonomic revision at the genus level. Mitochondrial DNA B Resour 2024; 9:200-203. [PMID: 38288248 PMCID: PMC10823891 DOI: 10.1080/23802359.2024.2306882] [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: 10/13/2023] [Accepted: 01/13/2024] [Indexed: 01/31/2024] Open
Abstract
Discogobio brachyphysallidos Huang 1989 is a Cyprinidae fish species that is endemic to the upper Pearl River. In the present study, the complete mitochondrial genome of D. brachyphysallidos collected from the Nanpanjiang River was sequenced and annotated. The mitochondrial genome encompassed 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and the control region (D-loop). The total length of the mitochondrial genome was determined to be 16,594 base pairs (bp), with a GC content of 41.7%. Phylogenetic analyses revealed that D. brachyphysallidos may be a sister to D. longibarbatus and D. macrophysallidos. These findings provide insight into the genetic information and phylogenetic relationships of D. brachyphysallidos.
Collapse
Affiliation(s)
- Fangcan Chen
- Guangdong Hanyu Ecological Technology Co., Ltd., Guangzhou, China
| | - Pingke Lu
- Guangdong Hanyu Ecological Technology Co., Ltd., Guangzhou, China
| | - Dejin Liang
- Guangdong Tilapia Breeding Farms, Guangzhou, China
| | - Yuli Wu
- Agro-Tech Extension Center of Guangdong Province, Guangzhou, China
| | - Zhiyong Jiang
- Agro-Tech Extension Center of Guangdong Province, Guangzhou, China
| | - Wei Huang
- Guangdong Tilapia Breeding Farms, Guangzhou, China
| | - Liuling Gao
- Guangdong Hanyu Ecological Technology Co., Ltd., Guangzhou, China
| |
Collapse
|
27
|
Winn JC, Maduna SN, Bester-van der Merwe AE. A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae. Genomics 2024; 116:110771. [PMID: 38147941 DOI: 10.1016/j.ygeno.2023.110771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2023]
Abstract
The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.
Collapse
Affiliation(s)
- Jessica C Winn
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa
| | - Simo N Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway
| | - Aletta E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa.
| |
Collapse
|
28
|
Wang J, Tai J, Zhang W, He K, Lan H, Liu H. Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae. Zookeys 2023; 1184:115-132. [PMID: 38314327 PMCID: PMC10838552 DOI: 10.3897/zookeys.1184.107091] [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: 05/27/2023] [Accepted: 10/27/2023] [Indexed: 02/06/2024] Open
Abstract
In this study, mitochondrial genomes (mitogenomes) of seven cichlid species (Lamprologuskungweensis, L.meleagris, L.ornatipinnis, Neolamprologusbrevis, N.caudopunctatus, N.leleupi, and N.similis) are characterized for the first time. The newly sequenced mitogenomes contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. The mitogenomes were 16,562 ~ 16,587 bp in length with an A + T composition of 52.1~58.8%. The cichlid mitogenomes had a comparable nucleotide composition, A + T content was higher than the G + C content. The AT-skews of most mitogenomes were inconspicuously positive and the GC-skews were negative, indicating higher occurrences of C than G. Most PCGs started with the conventional start codon, ATN. There was no essential difference in the codon usage patterns of these seven species. Using Ka/Ks, we found the fastest-evolving gene were atp8. But the results of p-distance indicated that the fastest-evolving gene was nad6. Phylogenetic analysis revealed that L.meleagris did not cluster with Lamprologus species, but with species from the genus Neolamprologus. The novel information obtained about these mitogenomes will contribute to elucidating the complex relationships among cichlid species.
Collapse
Affiliation(s)
- Jiachen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Jingzhe Tai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Wenwen Zhang
- Institute of Environmental Sciences, Ministry of Ecology and Environment of China State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains Research Center for Biodiversity Conservation and Biosafety, Nanjing 210042, China Institute of Environmental Sciences, Ministry of Ecology and Environment of China State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains Research Center for Biodiversity Conservation and Biosafety Nanjing China
| | - Ke He
- Zhejiang Agriculture and Forestry University, Hangzhou 311300, China Zhejiang Agriculture and Forestry University Hangzhou China
| | - Hong Lan
- Zhejiang Open University, Hangzhou 310012, China Zhejiang Open University Hangzhou China
| | - Hongyi Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| |
Collapse
|
29
|
Kundu S, Palimirmo FS, Kang HE, Kim AR, Lee SR, Gietbong FZ, Song SH, Kim HW. Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean. BIOLOGY 2023; 12:1317. [PMID: 37887027 PMCID: PMC10604034 DOI: 10.3390/biology12101317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.
Collapse
Affiliation(s)
- Shantanu Kundu
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Flandrianto Sih Palimirmo
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Cibinong 16911, Indonesia
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Se Hyun Song
- Fisheries Resources Management Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hyun-Woo Kim
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| |
Collapse
|
30
|
Duong TY, Pham LTK, Le XTK, Nguyen NTT, Nor AM, Le TH. Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei. Zool Stud 2023; 62:e48. [PMID: 37965298 PMCID: PMC10641430 DOI: 10.6620/zs.2023.62-48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/24/2023] [Indexed: 11/16/2023]
Abstract
Pangasiidae (catfish order: Siluriformes) comprises 30 valid catfish species in four genera: Pangasius, Pangasianodon, Helicophagus, and Pseudolais. Their systematics are frequently revised due to the addition of newly described species. Although Pangasiidae is known to be a monophyletic family, the generic and phylogenetic relationships among the taxa are poorly resolved. This study characterized three newly obtained complete mitogenomes of Mekong River catfishes from Vietnam (Pangasius mekongensis, Pangasius krempfi, and Pangasianodon hypophthalmus), as well as the inter-and intrafamilial relationships of the Pangasiidae and catfish families in Siluroidei. The genomic features of their mitogenomes were similar to those of previously reported pangasiids, including all regulatory elements, extended terminal associated sequences (ETAS), and conserved sequence blocks (CSBs) (CSB-1, CSB-2, CSB-3, and CSBs, A to F) in the control region. A comprehensive phylogeny constructed from datasets of multiple 13 PCG sequences from 117 complete mitogenomes of 32 recognized siluriform families established Pangasiidae as monophyletic and a sister group of Austroglanididae. The [Pangasiidae + Austroglanididae] + (Ictaluridae + Cranoglanididae) + Ariidae] clade is a sister to the "Big Africa" major clade of Siluriformes. Furthermore, both phylogenies constructed from the single barcodes (83 partial cox1 and 80 partial cytB, respectively) clearly indicate genus relationships within Pangasiidae. Pangasianodon was monophyletic and a sister to the (Pangasius + Helicophagus + Pseudolais) group. Within the genus Pangasius, P. mekongensis was placed as a sister taxon to P. pangasius. Pangasius sanitwongsei was found to be related to and grouped with Pangasianodon, but in single-gene phylogenies, it was assigned to the Pangasius + Helicophagus + Pseudolais group. The datasets in this study are useful for studying pangasiid systematics, taxonomy and evolution.
Collapse
Affiliation(s)
- Thuy Yen Duong
- College of Aquaculture and Fisheries, Can Tho University, 3/2 street, Can Tho City, Vietnam. E-mail: (Duong)
| | - Linh Thi Khanh Pham
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam. E-mail: (Le); (Pham); (Kim Le)
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Xuyen Thi Kim Le
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam. E-mail: (Le); (Pham); (Kim Le)
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Ngoc Tran Thi Nguyen
- College of Aquaculture and Fisheries, Can Tho University, 3/2 street, Can Tho City, Vietnam. E-mail: (Duong)
| | - Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia. E-mail: (Nor)
| | - Thanh Hoa Le
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam. E-mail: (Le); (Pham); (Kim Le)
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| |
Collapse
|
31
|
Tang Q, Liu Y, Li CH, Zhao JF, Wang T. Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes). BIOLOGY 2023; 12:1273. [PMID: 37886983 PMCID: PMC10604132 DOI: 10.3390/biology12101273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
To understand the molecular mechanisms and adaptive strategies of holocentrid fish, we sequenced the mitogenome of eight species within the family Holocentridae and compared them with six other holocentrid species. The mitogenomes were found to be 16,507-16,639 bp in length and to encode 37 typical mitochondrial genes, including 13 PCGs, two ribosomal RNAs, and 22 transfer RNA genes. Structurally, the gene arrangement, base composition, codon usage, tRNA size, and putative secondary structures were comparable between species. Of the 13 PCGs, nad6 was the most specific gene that exhibited negative AT-skews and positive GC-skews. Most of the genes begin with the standard codon ATG, except cox1, which begins with the codon GTG. By examining their phylogeny, Sargocentron and Neoniphon were verified to be closely related and to belong to the same subfamily Holocentrinae, while Myripristis and Ostichthys belong to the other subfamily Myripristinae. The subfamilies were clearly distinguished by high-confidence-supported clades, which provide evidence to explain the differences in morphology and feeding habits between the two subfamilies. Selection pressure analysis indicated that all PCGs were subject to purifying selection. Overall, our study provides valuable insight into the habiting behavior, evolution, and ecological roles of these important marine fish.
Collapse
Affiliation(s)
- Qin Tang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China;
| | - Yong Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (C.-H.L.); (J.-F.Z.)
- Scientific Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province, Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China
- Observation and Research Station of Pearl River Estuary Ecosystem, Guangzhou 510300, China
| | - Chun-Hou Li
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (C.-H.L.); (J.-F.Z.)
- Scientific Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province, Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China
- Observation and Research Station of Pearl River Estuary Ecosystem, Guangzhou 510300, China
| | - Jin-Fa Zhao
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (C.-H.L.); (J.-F.Z.)
- Scientific Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province, Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China
- Observation and Research Station of Pearl River Estuary Ecosystem, Guangzhou 510300, China
| | - Teng Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.L.); (C.-H.L.); (J.-F.Z.)
- Scientific Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province, Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China
- Observation and Research Station of Pearl River Estuary Ecosystem, Guangzhou 510300, China
| |
Collapse
|
32
|
Zhang H, Song X, Liu Z, Ling J. Complete mitochondrial genome sequence and phylogenetic analysis of the Taiwan tai Argyrops bleekeri (Spariformes: Sparidae). Mitochondrial DNA B Resour 2023; 8:912-915. [PMID: 37645473 PMCID: PMC10461519 DOI: 10.1080/23802359.2023.2248681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
In this study, the complete mitochondrial genome of the Taiwan tai Argyrops bleekeri was determined for the first time by next-generation sequencing. The circular mtDNA molecule was 16,646 bp in size and the overall base composition was A (27.77%), C (28.95%), G (16.60%), and T (26.68%), with a slight bias toward A + T. The complete mitogenome encoded 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis based on the 13 PCGs of the Sparidae family revealed that Argyrops appears to be most closely related to Pagrus and Parargyrops, but further research is needed.
Collapse
Affiliation(s)
- Hanye Zhang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xiaojing Song
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Zunlei Liu
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Jianzhong Ling
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| |
Collapse
|
33
|
Kang J, Ramirez-Calero S, Paula JR, Chen Y, Schunter C. Gene losses, parallel evolution and heightened expression confer adaptations to dedicated cleaning behaviour. BMC Biol 2023; 21:180. [PMID: 37612643 PMCID: PMC10463495 DOI: 10.1186/s12915-023-01682-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Cleaning symbioses are captivating interspecific interactions in which a cleaner fish removes ectoparasites from its client, contributing to the health and diversity of natural fish communities and aquaculture systems. However, the genetic signatures underlying this specialized behaviour remain poorly explored. To shed light on this, we generated a high-quality chromosome-scale genome of the bluestreak cleaner wrasse Labroides dimidiatus, a dedicated cleaner with cleaning as primary feeding mechanism throughout its life. RESULTS Compared with facultative and non-cleaner wrasses, L. dimidiatus was found with notable contractions in olfactory receptors implying their limited importance in dedicated cleaning. Instead, given its distinct tactile pre-conflict strategies, L. dimidiatus may rely more heavily on touch sensory perception, with heightened gene expression in the brain in anticipation of cleaning. Additionally, a reduction in NLR family CARD domain-containing protein 3 might enhance innate immunity of L. dimidiatus, probably assisting to reduce the impacts from parasite infections. In addition, convergent substitutions for a taste receptor and bone development genes across cleaners (L. dimidiatus and facultative cleaners) may provide them with evolved food discrimination abilities and jaw morphology that differentiate them from non-cleaners. Moreover, L. dimidiatus may exhibit specialized neural signal transductions for cleaning, as evidenced by positive selection in genes related to the glutamatergic synapse pathway. Interestingly, numerous glutamate receptors also demonstrated significantly higher expression in L. dimidiatus not engaged in cleaning, as compared to those involved in cleaning. Besides, apparent contractions in L. dimidiatus for protocadherins, which are responsible for neuronal development, may further promote specialized neural signal transductions in this species. CONCLUSIONS This study reveals that L. dimidiatus harbours substantial losses in specific gene families, convergent evolutions across cleaners and a large-scale high gene expression in preparation for cleaning, allowing for adaptation to the dedicated cleaning behaviour.
Collapse
Affiliation(s)
- Jingliang Kang
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Sandra Ramirez-Calero
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - José Ricardo Paula
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- MARE - Marine and Environmental Sciences Centre & ARNET - Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora Do Cabo, 939, Cascais, 2750-374, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Yifang Chen
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong, SAR, China
| | - Celia Schunter
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong, SAR, China.
| |
Collapse
|
34
|
Fiedler L, Middendorf M, Bernt M. Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs. Front Genet 2023; 14:1250907. [PMID: 37636259 PMCID: PMC10448254 DOI: 10.3389/fgene.2023.1250907] [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: 06/30/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
A wide range of scientific fields, such as forensics, anthropology, medicine, and molecular evolution, benefits from the analysis of mitogenomic data. With the development of new sequencing technologies, the amount of mitochondrial sequence data to be analyzed has increased exponentially over the last few years. The accurate annotation of mitochondrial DNA is a prerequisite for any mitogenomic comparative analysis. To sustain with the growth of the available mitochondrial sequence data, highly efficient automatic computational methods are, hence, needed. Automatic annotation methods are typically based on databases that contain information about already annotated (and often pre-curated) mitogenomes of different species. However, the existing approaches have several shortcomings: 1) they do not scale well with the size of the database; 2) they do not allow for a fast (and easy) update of the database; and 3) they can only be applied to a relatively small taxonomic subset of all species. Here, we present a novel approach that does not have any of these aforementioned shortcomings, (1), (2), and (3). The reference database of mitogenomes is represented as a richly annotated de Bruijn graph. To generate gene predictions for a new user-supplied mitogenome, the method utilizes a clustering routine that uses the mapping information of the provided sequence to this graph. The method is implemented in a software package called DeGeCI (De Bruijn graph Gene Cluster Identification). For a large set of mitogenomes, for which expert-curated annotations are available, DeGeCI generates gene predictions of high conformity. In a comparative evaluation with MITOS2, a state-of-the-art annotation tool for mitochondrial genomes, DeGeCI shows better database scalability while still matching MITOS2 in terms of result quality and providing a fully automated means to update the underlying database. Moreover, unlike MITOS2, DeGeCI can be run in parallel on several processors to make use of modern multi-processor systems.
Collapse
Affiliation(s)
- Lisa Fiedler
- Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Martin Middendorf
- Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Matthias Bernt
- Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| |
Collapse
|
35
|
Kundu S, De Alwis PS, Kim AR, Lee SR, Kang HE, Go Y, Gietbong FZ, Wibowo A, Kim HW. Mitogenomic Characterization of Cameroonian Endemic Coptodon camerunensis (Cichliformes: Cichlidae) and Matrilineal Phylogeny of Old-World Cichlids. Genes (Basel) 2023; 14:1591. [PMID: 37628642 PMCID: PMC10454717 DOI: 10.3390/genes14081591] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
The mitogenomic evolution of old-world cichlids is still largely incomplete in Western Africa. In this present study, the complete mitogenome of the Cameroon endemic cichlid, Coptodon camerunensis, was determined by next-generation sequencing. The mitogenome was 16,557 bp long and encoded with 37 genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region). The C. camerunensis mitogenome is AT-biased (52.63%), as exhibited in its congener, Coptodon zillii (52.76% and 53.04%). The majority of PCGs start with an ATG initiation codon, except COI, which starts with a GTG codon and five PCGs and ends with the TAA termination codon and except seven PCGs with an incomplete termination codon. In C. camerunensis mitogenome, most tRNAs showed classical cloverleaf secondary structures, except tRNA-serine with a lack of DHU stem. Comparative analyses of the conserved blocks of two Coptodonini species control regions revealed that the CSB-II block was longer than other blocks and contained highly variable sites. Using 13 concatenated PCGs, the mitogenome-based Bayesian phylogeny easily distinguished all the examined old-world cichlids. Except for Oreochromini and Coptodinini tribe members, the majority of the taxa exhibited monophyletic clustering within their respective lineages. C. camerunensis clustered closely with Heterotilapia buttikoferi (tribe Heterotilapiini) and had paraphyletic clustering with its congener, C. zillii. The Oreochromini species also displayed paraphyletic grouping, and the genus Oreochromis showed a close relationship with Coptodinini and Heterotilapiini species. In addition, illustrating the known distribution patterns of old-world cichlids, the present study is congruent with the previous hypothesis and proclaims that prehistoric geological evolution plays a key role in the hydroclimate of the African continent during Mesozoic, which simultaneously disperses and/or colonizes cichlids in different ichthyological provinces and Rift Lake systems in Africa. The present study suggests that further mitogenomes of cichlid species are required, especially from western Africa, to understand their unique evolution and adaptation.
Collapse
Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea; (S.K.); (P.S.D.A.)
| | - Piyumi S. De Alwis
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea; (S.K.); (P.S.D.A.)
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Yunji Go
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea;
| | | | - Arif Wibowo
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia;
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea; (S.K.); (P.S.D.A.)
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| |
Collapse
|
36
|
Osborne MJ, Barela Hudgell MA, Caeiro-Dias G, Turner TF. The complete mitochondrial genomes of two imperiled species endemic to the Southwestern United States: Peppered Chub ( Macrhybopsis tetranema) and Gila Trout ( Oncorhynchus gilae). Mitochondrial DNA B Resour 2023; 8:809-814. [PMID: 37539012 PMCID: PMC10395200 DOI: 10.1080/23802359.2023.2241658] [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: 03/07/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023] Open
Abstract
Macrhybopsis tetranema and Oncorhynchus gilae are fish species endemic to the Southwestern United States. We present the complete mitochondrial genomes for these species. Each genome consisted of 13 protein-coding genes, two ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and the control region (D-loop). Mitogenome lengths were 16,916 base pairs (bp) for M. tetranema, and 16,976 bp for O. gilae. The GC content was 41% for M. tetranema and 46% for O. gilae. The relationships of M. tetranema and O. gilae were consistent with previous phylogenetic analyses.
Collapse
Affiliation(s)
- Megan J. Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico
| | - Megan A. Barela Hudgell
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico
| | - Guilherme Caeiro-Dias
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico
| | - Thomas F. Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico
| |
Collapse
|
37
|
Zhou L, Wang M, Li D, Tang S, Liu Y, Chen X, Zhong L. Complete mitochondrial genome and phylogenetic analysis of Sineleotris saccharae (Perciformes, Odontobutiae). Mitochondrial DNA B Resour 2023; 8:715-718. [PMID: 37469853 PMCID: PMC10353331 DOI: 10.1080/23802359.2023.2227744] [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: 02/09/2023] [Accepted: 06/15/2023] [Indexed: 07/21/2023] Open
Abstract
The freshwater sleeper, Sineleotris saccharae Herre, 1940 is a member of the Odontobutiae family, widely distributed in southern China. In the present study, we determined the complete mitochondrial genome of S. saccharae for the first time and analyzed its evolutionary relationship. The complete mitochondrial genome of S. saccharae was 16,487 bp long, and had 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNA (rRNAs) and a control region (CR). The mitogenome of S. saccharae shared the same gene organization and orientation as other teleosts. According to phylogenetic research, S. saccharae was sister to S. chalmersi with high support value, providing the monophyly of the genus Sineleotris. These results will be helpful for understanding the systematics of the odontobutids.
Collapse
Affiliation(s)
- Liying Zhou
- Key Laboratory of Fisheries Resources in Inland Water of Jiangsu Province, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Minghua Wang
- Key Laboratory of Fisheries Resources in Inland Water of Jiangsu Province, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Daming Li
- Key Laboratory of Fisheries Resources in Inland Water of Jiangsu Province, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Shengkai Tang
- Key Laboratory of Fisheries Resources in Inland Water of Jiangsu Province, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Yanshan Liu
- Key Laboratory of Fisheries Resources in Inland Water of Jiangsu Province, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Xiaohui Chen
- Key Laboratory of Fisheries Resources in Inland Water of Jiangsu Province, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Liqiang Zhong
- Key Laboratory of Fisheries Resources in Inland Water of Jiangsu Province, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| |
Collapse
|
38
|
Toy JA, Bernardi G. A high-quality reference genome of the kelp surfperch, Brachyistius frenatus (Embiotocidae), a wide-ranging Eastern Pacific reef fish with no pelagic larval stage. J Hered 2023; 114:404-409. [PMID: 36790952 PMCID: PMC10287144 DOI: 10.1093/jhered/esad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/13/2023] [Indexed: 02/16/2023] Open
Abstract
The surfperches (family Embiotocidae) are a unique group of mostly marine fishes whose phylogenetic position within the Ovalentaria clade (Percomorpha) is still unresolved. As a result of their viviparity and lack of a dispersive larval stage, surfperches are an excellent model for the study of speciation, gene flow, and local adaptation in the ocean. They are also the target of an immensely popular recreational fishery. Very few high-quality molecular resources, however, are available for this group and only for a single species. Here, we describe a highly complete reference genome for the kelp surfperch, Brachyistius frenatus, assembled using a combination of short-read (Illumina, ~47× coverage) and long-read (Oxford Nanopore Technologies, ~27× coverage) sequencing. The 596 Mb assembly has a completeness level of 98.1% (BUSCO), a contig N50 of 2.6 Mb (n = 56), and a contig N90 of 406.6 kb (n = 293). Comparative analysis revealed a high level of synteny between B. frenatus and its close relative, Embiotoca jacksoni. This assembly will serve as a valuable molecular resource upon which future evolutionary dynamics research will build, such as the investigation of local adaptation and the genomic potential for climate adaptation in wild populations.
Collapse
Affiliation(s)
- Jason A Toy
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| |
Collapse
|
39
|
Heinicke MP, Nielsen SV, Bauer AM, Kelly R, Geneva AJ, Daza JD, Keating SE, Gamble T. Reappraising the evolutionary history of the largest known gecko, the presumably extinct Hoplodactylus delcourti, via high-throughput sequencing of archival DNA. Sci Rep 2023; 13:9141. [PMID: 37336900 DOI: 10.1038/s41598-023-35210-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/15/2023] [Indexed: 06/21/2023] Open
Abstract
Hoplodactylus delcourti is a presumably extinct species of diplodactylid gecko known only from a single specimen of unknown provenance. It is by far the largest known gekkotan, approximately 50% longer than the next largest-known species. It has been considered a member of the New Zealand endemic genus Hoplodactylus based on external morphological features including shared toe pad structure. We obtained DNA from a bone sample of the only known specimen to generate high-throughput sequence data suitable for phylogenetic analysis of its evolutionary history. Complementary sequence data were obtained from a broad sample of diplodactylid geckos. Our results indicate that the species is not most closely related to extant Hoplodactylus or any other New Zealand gecko. Instead, it is a member of a clade whose living species are endemic to New Caledonia. Phylogenetic comparative analyses indicate that the New Caledonian diplodactylid clade has evolved significantly more disparate body sizes than either the Australian or New Zealand clades. Toe pad structure has changed repeatedly across diplodactylids, including multiple times in the New Caledonia clade, partially explaining the convergence in form between H. delcourti and New Zealand Hoplodactylus. Based on the phylogenetic results, we place H. delcourti in a new genus.
Collapse
Affiliation(s)
| | - Stuart V Nielsen
- Louisiana State University Shreveport, Shreveport, LA, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | | | - Ryan Kelly
- University of Michigan-Dearborn, Dearborn, MI, USA
| | | | - Juan D Daza
- Sam Houston State University, Huntsville, TX, USA
| | | | - Tony Gamble
- Marquette University, Milwaukee, WI, USA
- The Bell Museum of Natural History, University of Minnesota, Saint Paul, MN, USA
- Milwaukee Public Museum, Milwaukee, WI, USA
| |
Collapse
|
40
|
Zhang R, Zhu T, Luo Q. The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis. Genes (Basel) 2023; 14:1227. [PMID: 37372406 DOI: 10.3390/genes14061227] [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: 05/11/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of Onychostoma ovale. The mitogenome of O. ovale was 16,602 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide composition of the O. ovale mitogenome was 31.47% A, 24.07% T, 15.92% G, and 28.54% C, with a higher A + T content (55.54%) than G + C content (44.46%). All PCGs began with the standard ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene and the NADH dehydrogenase 3 (ND3) gene with GTG, while six PCGs ended with incomplete termination codons (TA or T). The Ka/Ks ratios of 13 PCGs were all less than one, indicating that they were under purifying selection. All tRNA genes were folded into the typical cloverleaf secondary structures with the exception of tRNASer(AGY), whose dihydrouridine (DHU) arm was absent. The phylogenetic trees showed that Onychostoma and Acrossocheilus were classified into three clades. There was a mosaic relationship between Onychostoma and Acrossocheilus. Moreover, the phylogenetic tree analysis showed that O. rarum was the closest species to O. ovale. This study can provide a useful resource for further phylogeny and population genetic analyses of Onychostoma and Acrossocheilus.
Collapse
Affiliation(s)
- Renyi Zhang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Tingting Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Qi Luo
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| |
Collapse
|
41
|
Mthethwa S, Bester‐van der Merwe AE, Roodt‐Wilding R. Addressing the complex phylogenetic relationship of the Gempylidae fishes using mitogenome data. Ecol Evol 2023; 13:e10217. [PMID: 37351481 PMCID: PMC10283032 DOI: 10.1002/ece3.10217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate seas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remained puzzling for decades prompting the need for further investigation into the underlying evolutionary history among the gempylids using molecular tools. In this study, we assembled eight complete novel mitochondrial genomes for five Gempylidae species (Neoepinnula minetomai, Neoepinnula orientalis, Rexea antefurcata, Rexea prometheoides, and Thyrsites atun) using Ion Torrent sequencing to supplement publicly available mitogenome data for gempylids. Using Bayesian inference and maximum-likelihood tree search methods, we investigated the evolutionary relationships of 17 Gempylidae species using mitogenome data. In addition, we estimated divergence times for extant gempylids. We identified two major clades that formed approximately 48.05 (35.89-52.04) million years ago: Gempylidae 1 (Thyrsites atun, Promethichthys prometheus, Nealotus tripes, Diplospinus multistriatus, Paradiplospinus antarcticus, Rexea antefurcata, Rexea nakamurai, Rexea prometheoides, Rexea solandri, Thyrsitoides marleyi, Gempylus serpens, and Nesiarchus nasutus) and Gempylidae 2 (Lepidocybium flavobrunneum, Ruvettus pretiosus, Neoepinnula minetomai, Neoepinnula orientalis, and Epinnula magistralis). The present study demonstrated the superior performance of complete mitogenome data compared with individual genes in phylogenetic reconstruction. By including T. atun individuals from different regions, we demonstrated the potential for the application of mitogenomes in species phylogeography.
Collapse
Affiliation(s)
- Siphesihle Mthethwa
- Molecular Breeding and Biodiversity Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | | | - Rouvay Roodt‐Wilding
- Molecular Breeding and Biodiversity Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| |
Collapse
|
42
|
Jeunen GJ, Dowle E, Edgecombe J, von Ammon U, Gemmell NJ, Cross H. crabs-A software program to generate curated reference databases for metabarcoding sequencing data. Mol Ecol Resour 2023; 23:725-738. [PMID: 36437603 DOI: 10.1111/1755-0998.13741] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022]
Abstract
The measurement of biodiversity is an integral aspect of life science research. With the establishment of second- and third-generation sequencing technologies, an increasing amount of metabarcoding data is being generated as we seek to describe the extent and patterns of biodiversity in multiple contexts. The reliability and accuracy of taxonomically assigning metabarcoding sequencing data have been shown to be critically influenced by the quality and completeness of reference databases. Custom, curated, eukaryotic reference databases, however, are scarce, as are the software programs for generating them. Here, we present crabs (Creating Reference databases for Amplicon-Based Sequencing), a software package to create custom reference databases for metabarcoding studies. crabs includes tools to download sequences from multiple online repositories (i.e., NCBI, BOLD, EMBL, MitoFish), retrieve amplicon regions through in silico PCR analysis and pairwise global alignments, curate the database through multiple filtering parameters (e.g., dereplication, sequence length, sequence quality, unresolved taxonomy, inclusion/exclusion filter), export the reference database in multiple formats for immediate use in taxonomy assignment software, and investigate the reference database through implemented visualizations for diversity, primer efficiency, reference sequence length, database completeness and taxonomic resolution. crabs is a versatile tool for generating curated reference databases of user-specified genetic markers to aid taxonomy assignment from metabarcoding sequencing data. crabs can be installed via docker and is available for download as a conda package and via GitHub (https://github.com/gjeunen/reference_database_creator).
Collapse
Affiliation(s)
- Gert-Jan Jeunen
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Eddy Dowle
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jonika Edgecombe
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ulla von Ammon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Hugh Cross
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,National Ecological Observatory Network, Boulder, Colorado, USA
| |
Collapse
|
43
|
Liu K, Xie N, Wang Y, Liu X. Extensive mitogenomic heteroplasmy and its implications in the phylogeny of the fish genus Megalobrama. 3 Biotech 2023; 13:115. [PMID: 36915286 PMCID: PMC10006376 DOI: 10.1007/s13205-023-03523-0] [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: 11/13/2022] [Accepted: 02/13/2023] [Indexed: 03/12/2023] Open
Abstract
Megalobrama is China's most economically valuable fish genera. Four species make up this genus: M. amblycephala (MA), M. terminalis (MT), M. pellegrini (MP), and M. hoffmanni (MH). Many researchers have investigated the genetic relationship of Megalobrama based on mitochondrial DNA (mtDNA) and discovered that the branches of the phylogenetic tree for MT and MP are intertwined. We hypothesized that this occurs because mitogenomic heteroplasmy is overlooked when working with mtDNA, which causes MP and MT positions to intersect in phylogenetic trees. To eliminate the influence of nuclear mitochondrial DNA fragments (NUMTs) before analyzing mitogenomic heteroplasmy, we used PLastZ to identify NUMTs, which were then removed from the samples for the subsequent heteroplasmy analysis. Using the heteroplasmy caller icHET, we discovered 126, 339, 135, and 203 heteroplasmic variants in six MA, MT, MP, and MH samples. We reconstructed the Megalobrama fish genus's phylogenetic tree using the RY coding method and rejecting the third position on codons, which improved the performance of the phylogenetic tree by increasing the ratio of treeness to relative component variability from 100.02 ± 1.76 to 688.59 ± 190.56. Despite this, the RY coding method cannot alter the intersection of MP and MT positions in phylogenetic trees. We hypothesize that gene flow between MT and MP leads to intertwining mtDNA-based phylogenetic trees. In conclusion, our findings on the mitogenomic heteroplasmy of Megalobrama provide new insights into mtDNA-based phylogenetic studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03523-0.
Collapse
Affiliation(s)
- Kai Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yuxi Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
44
|
Rodrigues-Oliveira IH, Pasa R, Menegidio FB, Kavalco KF. Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family. Genomics Inform 2023; 21:e10. [PMID: 37037468 PMCID: PMC10085734 DOI: 10.5808/gi.22041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/14/2023] [Indexed: 04/03/2023] Open
Abstract
The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and Amarsipidae. However, the phylogenetic position of this clade related to other Pelagiaria groups remains uncertain even when phylogenomic studies are employed. Since the low number of published mitogenomes, our study aimed to assemble six new mitochondrial genomes of Chiasmodontidae from database libraries to expand the discussion regarding the phylogeny of this group within Scombriformes. As expected, the composition and organization of mitogenomes were stable among the analyzed species, although we detected repetitive sequences in the D-loop of species of the genus Kali not seen in Chiasmodon, Dysalotus, and Pseudoscopelus. Our phylogeny incorporating 51 mitogenomes from several families of Scombriformes, including nine chiasmodontids, recovered interfamilial relationships well established in previous studies, including a clade containing Chiasmodontidae, Amarsipidae, and Tetragonuridae. However, phylogenetic relationships between larger clades remain unclear, with disagreements between different phylogenomic studies. We argue that such inconsistencies are not only due to biases and limitations in the data but mainly to complex biological events in the adaptive irradiation of Scombriformes after the Cretaceous-Paleogene extinction event.
Collapse
Affiliation(s)
- Igor Henrique Rodrigues-Oliveira
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
- Corresponding author: E-mail:
| | - Rubens Pasa
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
| | - Fabiano Bezerra Menegidio
- Technological Research Center, University of Mogi das Cruzes, Mogi das Cruzes 08780-911, Brazil
- Integrated Biotechnology Center, University of Mogi das Cruzes, Mogi das Cruzes 08780-911, Brazil
| | - Karine Frehner Kavalco
- Laboratory of Ecological and Evolutionary Genetics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
- Laboratory of Bioinformatics and Genomics, Federal University of Viçosa, Rio Paranaíba 38810-000, Brazil
| |
Collapse
|
45
|
Yoshitake K, Yanagisawa K, Sugimoto Y, Nakamura H, Mizusawa N, Miya M, Hamasaki K, Kobayashi T, Watabe S, Nishikiori K, Asakawa S. Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers. Funct Integr Genomics 2023; 23:96. [PMID: 36947319 PMCID: PMC10033627 DOI: 10.1007/s10142-023-01013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches.
Collapse
Affiliation(s)
- Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Tokyo, Japan
| | - Kyohei Yanagisawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Tokyo, Japan
| | - Yuma Sugimoto
- Tokyo Sea Life Park, 6-2-3 Rinkai-cho, Edogawa-ku, 134-8587, Tokyo, Japan
| | - Hiroshi Nakamura
- Tokyo Sea Life Park, 6-2-3 Rinkai-cho, Edogawa-ku, 134-8587, Tokyo, Japan
| | - Nanami Mizusawa
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Kanagawa, 252-0373, Sagamihara, Japan
| | - Masaki Miya
- Department of Collection Management, Natural History Museum and Institute, Chiba, 260-8682, Japan
| | - Koji Hamasaki
- Department of Marine Ecosystem Science, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takanori Kobayashi
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Kanagawa, 252-0373, Sagamihara, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Kanagawa, 252-0373, Sagamihara, Japan
| | - Kazuomi Nishikiori
- Tokyo Sea Life Park, 6-2-3 Rinkai-cho, Edogawa-ku, 134-8587, Tokyo, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Tokyo, Japan.
| |
Collapse
|
46
|
Wang J, Xu W, Liu Y, Bai Y, Liu H. Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae). Gene X 2023; 857:147186. [PMID: 36627090 DOI: 10.1016/j.gene.2023.147186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/25/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
The family Channidae, members of which are commonly known as snakehead fish, includes 53 Channa species and three Parachanna species. In this study, we characterized mitochondrial genomes (mitogenomes) of five Channa species (C. andrao, C. bleheri, C. ornatipinnis, C. pulchra, and C. stewartii) for the first time. We compared the mitogenomes with the mitogenomes of 11 other Channidae fish. The newly sequenced mitogenomes were 16,714 - 16,895 bp in length and contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. Positive AT-skews and negative GC-skews were found in the mitogenomes of Channidae. Most PCGs started with the conventional start codon, ATN; however, the sequence of the stop codon was variable. There was no essential difference in relative synonymous codon usage (RSCU) among the Channidae mitogenomes. The fastest-evolving gene atp8 and slowest-evolving gene cox1 were identified using Ka/Ks and pairwise relative genetic distance (p-distance). The displacement loop (D-loop) regions showed great variability, which affected the size of Channa mitogenomes. One origin of replication on the light strand (OL) region was found between trnN and trnC in the mitogenomes of Channidae. Phylogenetic analysis revealed three new sister pairs (C. andrao + C. bleheri, C. ornatipinnis + C. pulchra, and C. stewartii + C. gachua). Phylogenetic relationships established between the five Channa species based on mitogenomes were also supported by their morphological characteristics and geographical distribution. The novel information we obtained about these mitogenomes will contribute to elucidating the complex relationships among Channa species.
Collapse
Affiliation(s)
- Jiachen Wang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yuyao Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yawen Bai
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| |
Collapse
|
47
|
Kasmi Y, Eschbach E, Hanel R. Mare-MAGE curated reference database of fish mitochondrial genes. BMC Genom Data 2023; 24:18. [PMID: 36932341 PMCID: PMC10024356 DOI: 10.1186/s12863-023-01119-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/09/2023] [Indexed: 03/19/2023] Open
Abstract
Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website ( http://mare-mage.weebly.com/ ). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families.
Collapse
Affiliation(s)
- Yassine Kasmi
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany.
| | - Erik Eschbach
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Reinhold Hanel
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572, Bremerhaven, Germany
| |
Collapse
|
48
|
McLaughlin JF, Aguilar C, Bernstein JM, Navia-Gine WG, Cueto-Aparicio LE, Alarcon AC, Alarcon BD, Collier R, Takyar A, Vong SJ, López-Chong OG, Driver R, Loaiza JR, De León LF, Saltonstall K, Lipshutz SE, Arcila D, Brock KM, Miller MJ. Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023. [PMID: 36993716 DOI: 10.1101/2023.01.26.525769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
UNLABELLED Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated. LAY SUMMARY - What factors are common among bird species with cryptic diversity in Panama? What role do geography, ecology, phylogeographic history, and other factors play in generating bird diversity?- 19% of widely-sampled bird species form two or more distinct DNA barcode clades, suggesting widespread unrecognized diversity.- Traits associated with reduced dispersal ability, such as use of forest understory, high territoriality, low hand-wing index, and insectivory, were more common in taxa with cryptic diversity. Filogeografía comparada revela amplia diversidad críptica causada por la ecología en las aves de Panamá. RESUMEN Especies extendidas frecuentemente tiene diversidad genética no reconocida, y investigando los factores asociados con esta variación críptica puede ayudarnos a entender las fuerzas que impulsan la diversificación. Aquí, identificamos especies crípticas potenciales basadas en un conjunto de datos de códigos de barras de ADN mitocondrial de 2,333 individuos de aves de Panama en 429 especies, representando 391 (59%) de las 659 especies de aves terrestres residentes del país, además de algunas aves acuáticas muestreada de manera oportunista. Adicionalmente, complementamos estos datos con secuencias mitocondriales disponibles públicamente de otros loci, tal como ND2 o citocroma b, obtenidos de los genomas mitocondriales completos de 20 taxones. Utilizando los números de identificación de código de barras (en ingles: BINs), un sistema taxonómico numérico que proporcina una estimación imparcial de la diversidad potencial a nivel de especie, encontramos especies crípticas putativas en 19% de las especies de aves terrestres, lo que destaca la diversidad oculta en la avifauna bien descrita de Panamá. Aunque algunos de estos eventos de divergencia conciden con características geográficas que probablemente aislaron las poblaciones, la mayoría (74%) de la divergencia en las tierras bajas se encuentra entre las poblaciones orientales y occidentales. El tiempo de esta divergencia no coincidió entre los taxones, sugiriendo que eventos históricos tales como la formación del Istmo de Panamá y los ciclos climáticos del pleistoceno, no fueron los principales impulsores de la especiación. En cambio, observamos asociaciones fuertes entre las características ecológicas y la divergencia mitocondriale: las especies del bosque, sotobosque, con una dieta insectívora, y con territorialidad fuerte mostraton múltiple BINs probables. Adicionalmente, el índice mano-ala, que está asociado a la capacidad de dispersión, fue significativamente menor en las especies con BINs multiples, sugiriendo que la capacidad de dispersión tiene un rol importamente en la generación de la diversidad de las aves neotropicales. Estos resultos demonstran la necesidad de que estudios evolutivos de las comunidades de aves tropicales consideren los factores ecológicos en conjunto con las explicaciones geográficos. Palabras clave: biodiversidad tropical, biogeografía, códigos de barras, dispersión, especies crípticas.
Collapse
|
49
|
McLaughlin JF, Aguilar C, Bernstein JM, Navia-Gine WG, Cueto-Aparicio LE, Alarcon AC, Alarcon BD, Collier R, Takyar A, Vong SJ, López-Chong OG, Driver R, Loaiza JR, De León LF, Saltonstall K, Lipshutz SE, Arcila D, Brock KM, Miller MJ. Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.530646. [PMID: 36993716 PMCID: PMC10055050 DOI: 10.1101/2023.03.15.530646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.
Collapse
Affiliation(s)
- J. F. McLaughlin
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Celestino Aguilar
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - Justin M. Bernstein
- Department of Biology, Villanova University, Villanova, PA, USA
- Center for Genomics, University of Kansas, Lawrence, KS, USA
| | - Wayra G. Navia-Gine
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Pacific Biosciences, 1305 O’Brien Dr, Menlo Park, CA, USA
| | | | | | | | - Rugger Collier
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Anshule Takyar
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Sidney J. Vong
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | | | - Robert Driver
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Jose R. Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - Luis F. De León
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | | | | | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
| | - Kinsey M. Brock
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
| | - Matthew J. Miller
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Reneco International Wildlife Consultants, Abu Dhabi, UAE
| |
Collapse
|
50
|
Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Parrotfishes (Perciformes: Scaridae). BIOLOGY 2023; 12:biology12030410. [PMID: 36979102 PMCID: PMC10044791 DOI: 10.3390/biology12030410] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
In order to investigate the molecular evolution of mitogenomes among the family Scaridae, the complete mitogenome sequences of twelve parrotfish species were determined and compared with those of seven other parrotfish species. The comparative analysis revealed that the general features and organization of the mitogenome were similar among the 19 parrotfish species. The base composition was similar among the parrotfishes, with the exception of the genus Calotomus, which exhibited an unusual negative AT skew in the whole mitogenome. The PCGs showed similar codon usage, and all of them underwent a strong purifying selection. The gene rearrangement typical of the parrotfishes was detected, with the tRNAMet inserted between the tRNAIle and tRNAGln, and the tRNAGln was followed by a putative tRNAMet pseudogene. The parrotfish mitogenomes displayed conserved gene overlaps and secondary structure in most tRNA genes, while the non-coding intergenic spacers varied among species. Phylogenetic analysis based on the thirteen PCGs and two rRNAs strongly supported the hypothesis that the parrotfishes could be subdivided into two clades with distinct ecological adaptations. The early divergence of the sea grass and coral reef clades occurred in the late Oligocene, probably related to the expansion of sea grass habitat. Later diversification within the coral reef clade could be dated back to the Miocene, likely associated with the geomorphology alternation since the closing of the Tethys Ocean. This work provided fundamental molecular data that will be useful for species identification, conservation, and further studies on the evolution of parrotfishes.
Collapse
|