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Cheng WX, Wang J, Mao ML, Lu YB, Zou JX. The mitochondrial genome of Bottapotamon fukienense (Brachiura: Potamidae) is fragmented into two chromosomes. BMC Genomics 2024; 25:755. [PMID: 39095713 PMCID: PMC11295360 DOI: 10.1186/s12864-024-10657-9] [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: 03/30/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND China is the hotspot of global freshwater crab diversity, but their wild populations are facing severe pressures associated with anthropogenic factors, necessitating the need to map their taxonomic and genetic diversity and design conservation policies. RESULTS Herein, we sequenced the mitochondrial genome of a Chinese freshwater crab species Bottapotamon fukienense, and found that it is fragmented into two chromosomes. We confirmed that fragmentation was not limited to a single specimen or population. Chromosome 1 comprised 15,111 base pairs (bp) and there were 26 genes and one pseudogene (pseudo-nad1) encoded on it. Chromosome 2 comprised 8,173 bp and there were 12 genes and two pseudogenes (pseudo-trnL2 and pseudo-rrnL) encoded on it. Combined, they comprise the largest mitogenome (23,284 bp) among the Potamidae. Bottapotamon was the only genus in the Potamidae dataset exhibiting rearrangements of protein-coding genes. Bottapotamon fukienense exhibited average rates of sequence evolution in the dataset and did not differ in selection pressures from the remaining Potamidae. CONCLUSIONS This is the first experimentally confirmed fragmentation of a mitogenome in crustaceans. While the mitogenome of B. fukienense exhibited multiple signs of elevated mitogenomic architecture evolution rates, including the exceptionally large size, duplicated genes, pseudogenisation, rearrangements of protein-coding genes, and fragmentation, there is no evidence that this is matched by elevated sequence evolutionary rates or changes in selection pressures.
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Affiliation(s)
- Wang-Xinjun Cheng
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Jun Wang
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Mei-Lin Mao
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Yuan-Biao Lu
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Jie-Xin Zou
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China.
- Provincial Key Laboratory for Drug Targeting and Drug Screening, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
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Gendron EMS, Qing X, Sevigny JL, Li H, Liu Z, Blaxter M, Powers TO, Thomas WK, Porazinska DL. Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection. BMC Genomics 2024; 25:615. [PMID: 38890582 PMCID: PMC11184840 DOI: 10.1186/s12864-024-10500-1] [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: 02/22/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. RESULTS Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. CONCLUSIONS Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.
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Affiliation(s)
- Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA.
| | - Xue Qing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.
| | - Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Hongmei Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyin Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | | | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - W Kelly Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
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Zhang D, Jakovlić I, Zou H, Liu F, Xiang CY, Gusang Q, Tso S, Xue S, Zhu WJ, Li Z, Wu J, Wang GT. Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea. Int J Parasitol 2024; 54:213-223. [PMID: 38185351 DOI: 10.1016/j.ijpara.2024.01.001] [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: 08/11/2023] [Revised: 12/03/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3'-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China.
| | - Ivan Jakovlić
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fei Liu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Institute of Aquatic Sciences, Tibet Academy of Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850032, China
| | - Chuan-Yu Xiang
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qunzong Gusang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Sonam Tso
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Shenggui Xue
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Wen-Jin Zhu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Zhenxin Li
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Jihua Wu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Gui-Tang Wang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Wang L, Hu Z, Wang Z, Zhu P, Wei G, Fan X, Huang J, Wang R, Wang H, Xie Y. Complete Mitogenome sequencing of the fish louse Argulus japonicus (Crustacea: Branchiura): Comparative analyses and phylogenetic implications. Front Vet Sci 2024; 11:1376898. [PMID: 38590542 PMCID: PMC10999652 DOI: 10.3389/fvets.2024.1376898] [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: 01/26/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024] Open
Abstract
The fish louse Argulus japonicus, a branchiuran crustacean of the Argulidae family, is attracting increasing attention because of its parasitic tendencies and significant health threats to global fish farming. The mitogenomes can yield a foundation for studying epidemiology, genetic diversity, and molecular ecology and therefore may be used to assist in the surveillance and control of A. japonicus. In this study, we sequenced and assembled the complete mitogenome of A. japonicus to shed light on its genetic and evolutionary blueprint. Our investigation indicated that the 15,045-bp circular genome of A. japonicus encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs) with significant AT and GC skews. Comparative genomics provided an evolutionary scenario for the genetic diversity of 13 PCGs: all were under purifying selection, with cox1 and nad6 having the lowest and highest evolutionary rates, respectively. Genome-wide phylogenetic trees established a close relationship between species of the families Argulidae (Arguloida) and Armilliferidae (Porocephalida) within Crustacea, and further, A. japonicus and Argulus americanus were determined to be more closely related to each other than to others within the family Argulidae. Single PCG-based phylogenies supported nad1 and nad6 as the best genetic markers for evolutionary and phylogenetic studies for branchiuran crustaceans due to their similar phylogenetic topologies with those of genome-based phylogenetic analyses. To sum up, these comprehensive mitogenomic data of A. japonicus and related species refine valuable marker resources and should contribute to molecular diagnostic methods, epidemiological investigations, and ecological studies of the fish ectoparasites in Crustacea.
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Affiliation(s)
- Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zun Hu
- Department of Food Technology and Science, College of Food Science, Shanghai Ocean University, Shanghai, China
| | - Zhao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Pengchen Zhu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Guoshan Wei
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinyi Fan
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jiali Huang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ruixi Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hui Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Huang Y, Feng JM, Liu W, Sun BL, Shu XJ, Li WX, Wang GT, Hua CJ. Comprehensive molecular characterisation of the complete mitogenome of Ergasilus tumidus and phylogenetic relationships of Copepoda inferred from mitogenomes. Folia Parasitol (Praha) 2024; 71:2024.002. [PMID: 38440897 DOI: 10.14411/fp.2024.002] [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: 07/29/2023] [Accepted: 01/05/2024] [Indexed: 03/06/2024]
Abstract
Although parasitic copepods of the genus Ergasilus von Nordmann, 1832 are globally distributed parasites of fish, their phylogenetic relationships with other Copepoda are not clear, and the characteristics of their mitochondrial genomes (mitogenomes) are not thoroughly understood. The objective of this study was to address these knowledge gaps by sequencing the complete mitogenome of Ergasilus tumidus Markevich, 1940. The complete mitogenome (GenBank Acc. No. OQ596537) was 14,431 bp long and it comprised 13 protein-coding genes (PCGs), 22 tRNAs, two tRNAs, and two control regions (CRs). Phylogenetic analyses, conducted using concatenated nucleotide and amino acid sequences of 13 protein-coding genes, produced two partially incongruent topologies. While the order Calanoida was consistently resolved as the sister lineage to the other three orders, topological instability was observed in the relationships of the orders Cyclopoida, Siphonostomatoida and Harpacticoida. Siphonostomatoida clustered with Cyclopoida in the nucleotide-based phylogeny, but with Harpacticoida in the amino acid-based phylogeny. The latter topology conforms to the widely accepted relationships, but we speculate that the former topology is more likely to be the correct one. Our study provides a complete mitogenome sequence of E. tumidus, which helps us better understand the molecular evolution of the genus Ergasilus. Additionally, we suggest a different perspective on the controversial phylogenetic relationships among Siphonostomatoida, Cyclopoida and Harpacticoida, diverging from previously accepted views.
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Affiliation(s)
- Yan Huang
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Jin-Mei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, China
| | - Wei Liu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Bin-Lian Sun
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Xi-Ji Shu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Wen-Xiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China
| | - Gui-Tang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China
| | - Cong-Jie Hua
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, China
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6
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Struck TH, Golombek A, Hoesel C, Dimitrov D, Elgetany AH. Mitochondrial Genome Evolution in Annelida-A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution. Syst Biol 2023; 72:925-945. [PMID: 37083277 PMCID: PMC10405356 DOI: 10.1093/sysbio/syad023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/22/2023] Open
Abstract
The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA, and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene order variability including, among others, increased substitution rates, base composition differences, structure of noncoding regions, parasitism, living in extreme habitats, short generation times, and biomineralization. However, these analyses were neither done systematically nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits, and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best-predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, variability of the gene order does not predict if a taxon is difficult to place in molecular phylogenetic reconstructions using sequence data or not. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why the canonical views do not always fit to the observed patterns without making some adjustments. [Annelida; compositional biases; ecology; gene order; life history; macroevolution; mitochondrial genomes; substitution rates.].
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Affiliation(s)
- Torsten H Struck
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
- Centre of Molecular Biodiversity Research, Zoological Research Museum Alexander KoenigBonn 53113, Germany
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Anja Golombek
- Centre of Molecular Biodiversity Research, Zoological Research Museum Alexander KoenigBonn 53113, Germany
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Christoph Hoesel
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway
| | - Asmaa Haris Elgetany
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
- Zoology Department, Faculty of Science, Damietta University, New Damietta, Central zone, 34517, Egypt
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He J, Zhou Z, Huang Y, Feng J, Li W, Wang G, Hua C. Evolutionary Rates, Divergence Rates, and Performance of Individual Mitochondrial Genes Based on Phylogenetic Analysis of Copepoda. Genes (Basel) 2023; 14:1496. [PMID: 37510402 PMCID: PMC10379994 DOI: 10.3390/genes14071496] [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: 06/22/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Copepoda is a large and diverse group of crustaceans, which is widely distributed worldwide. It encompasses roughly 9 orders, whose phylogeny remains unresolved. We sequenced the complete mitochondrial genome (mitogenome) of Sinergasilus major (Markevich, 1940) and used it to explore the phylogeny and mitogenomic evolution of Copepoda. The mitogenome of S. major (14,588 bp) encodes the standard 37 genes as well as a putative control region, and molecular features are highly conserved compared to other Copepoda mitogenomes. Comparative analyses indicated that the nad2 gene has relatively high nucleotide diversity and evolutionary rate, as well as the largest amount of phylogenetic information. These results indicate that nad2 may be a better marker to investigate phylogenetic relationships among closely related species in Copepoda than the commonly used cox1 gene. The sister-group relationship of Siphonostomatoida and Cyclopoida was recovered with strong support in our study. The only topological ambiguity was found within Cyclopoida, which might be caused by the rapid evolution and sparse taxon sampling of this lineage. More taxa and genes should be used to reconstruct the Copepoda phylogeny in the future.
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Affiliation(s)
- Junzong He
- School of Life Science, Jianghan University, Wuhan 430056, China
| | - Zhihao Zhou
- School of Life Science, Jianghan University, Wuhan 430056, China
| | - Yan Huang
- School of Life Science, Jianghan University, Wuhan 430056, China
| | - Jinmei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Wenxiang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430056, China
| | - Guitang Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430056, China
| | - Congjie Hua
- Wuhan Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan 430056, China
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Hao C, Liu Y, Wei N, Arken K, Shi C, Yue C. The complete mitochondrial genomes of the Leuciscus baicalensis and Rutilus rutilus: a detailed genomic comparison among closely related species of the Leuciscinae subfamily. Gene 2023:147535. [PMID: 37328078 DOI: 10.1016/j.gene.2023.147535] [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: 01/09/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023]
Abstract
Cyprinidae is the largest family in the order of freshwater fish Cypriniformes. Increased subfamily members of Cyprinidae have been suggested to be re-classified for decades. In this study, we sequenced the mitochondrial genomes (mitogenomes) of Leuciscus baicalensis and Rutilus rutilus collected from northwest China and compared with other closely related species to determine their associated family or subfamily. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of Leuciscus baicalensis and Rutilus rutilus and characterized the mitogenomes by the gene structure, gene order, and the secondary structures of the 22 tRNA genes. We compared mitogenome features of Leuciscinae with other subfamilies in Cyprinidae. We used the analytic Bayesian Information and Maximum Likelihood methods to determine phylogenetic trees of 13 PCGs. The mitogenomes of Leuciscus baicalensis and Rutilus rutilus were 16,607 bp and 16,606 bp, respectively. Organization and location of these genes were consistent with already studied Leuciscinae fishes. Synonymous codon usage was conservative in Leuciscinae as compared with other subfamilies in Cyprinidae. Phylogenetic analysis indicated that Leuciscinae was a monophyletic group, and genus Leuciscus was a paraphyletic group. Our approach, for the first time, of studying comparative mitochondrial genomics and phylogenetics together provided a supportive platform to the analysis of population genetics and phylogeny for Leuciscinae. Our results indicated a promising potential of comparative mitochondrial genomics in the manifestation of phylogenetic relationships between fishes, leading us to a suggestion that mitogenomes should be routinely considered in clarifying phylogenetics of family and subfamily members of fish.
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Affiliation(s)
- Cuilan Hao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China.
| | - Yanjun Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Nianwen Wei
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Kadirden Arken
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Caixia Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Cheng Yue
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
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Hao CL, Wei NW, Liu YJ, Shi CX, Arken K, Yue C. Mitochondrial phylogenomics provides conclusive evidence that the family Ancyrocephalidae is deeply paraphyletic. Parasit Vectors 2023; 16:83. [PMID: 36859280 PMCID: PMC9979435 DOI: 10.1186/s13071-023-05692-6] [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: 11/21/2022] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Unresolved taxonomic classification and paraphyly pervade the flatworm class Monogenea: the class itself may be paraphyletic and split into Polyopisthocotylea and Monopisthocotylea; there are some indications that the monopisthocotylean order Dactylogyridea may also be paraphyletic; single-gene markers and some morphological traits indicate that the family Ancyrocephalidae is paraphyletic and intertwined with the family Dactylogyridae. METHODS To attempt to study the relationships of Ancyrocephalidae and Monopisthocotylea using a phylogenetic marker with high resolution, we sequenced mitochondrial genomes of two fish ectoparasites from the family Dactylogyridae: Dactylogyrus simplex and Dactylogyrus tuba. We conducted phylogenetic analyses using three datasets and three methods. Datasets were ITS1 (nuclear) and nucleotide and amino acid sequences of almost complete mitogenomes of almost all available Monopisthocotylea mitogenomes. Methods were maximum likelihood (IQ-TREE), Bayesian inference (MrBayes) and CAT-GTR (PhyloBayes). RESULTS Both mitogenomes exhibited the ancestral gene order for Neodermata, and both were compact, with few and small intergenic regions and many and large overlaps. Gene sequences were remarkably divergent for nominally congeneric species, with only trnI exhibiting an identity value > 80%. Both mitogenomes had exceptionally low A + T base content and AT skews. We found evidence of pervasive compositional heterogeneity in the dataset and indications that base composition biases cause phylogenetic artefacts. All six mitogenomic analyses produced unique topologies, but all nine analyses produced topologies that rendered Ancyrocephalidae deeply paraphyletic. Mitogenomic data consistently resolved the order Capsalidea as nested within the Dactylogyridea. CONCLUSIONS The analyses indicate that taxonomic revisions are needed for multiple Polyopisthocotylea lineages, from genera to orders. In combination with previous findings, these results offer conclusive evidence that Ancyrocephalidae is a paraphyletic taxon. The most parsimonious solution to resolve this is to create a catch-all Dactylogyridae sensu lato clade comprising the current Ancyrocephalidae, Ancylodiscoididae, Pseudodactylogyridae and Dactylogyridae families, but the revision needs to be confirmed by another marker with a sufficient resolution.
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Affiliation(s)
- Cui-Lan Hao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Nian-Wen Wei
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Yan-Jun Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Cai-Xia Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Kadirden Arken
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Cheng Yue
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China.
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Montaña-Lozano P, Balaguera-Reina SA, Prada-Quiroga CF. Comparative analysis of codon usage of mitochondrial genomes provides evolutionary insights into reptiles. Gene 2023; 851:146999. [DOI: 10.1016/j.gene.2022.146999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/30/2022] [Accepted: 10/18/2022] [Indexed: 11/04/2022]
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11
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Gao JW, Yuan XP, Wu H, Xiang CY, Xie M, Song R, Chen ZY, Wu YA, Ou DS. Mitochondrial phylogenomics of Acanthocephala: nucleotide alignments produce long-branch attraction artefacts. Parasit Vectors 2022; 15:376. [PMID: 36261865 PMCID: PMC9583589 DOI: 10.1186/s13071-022-05488-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Classification of the Acanthocephala, a clade of obligate endoparasites, remains unresolved because of insufficiently strong resolution of morphological characters and scarcity of molecular data with a sufficient resolution. Mitochondrial genomes may be a suitable candidate, but they are available for a small number of species and their suitability for the task has not been tested thoroughly. METHODS Herein, we sequenced the first mitogenome for the large family Rhadinorhynchidae: Micracanthorhynchina dakusuiensis. These are also the first molecular data generated for this entire genus. We conducted a series of phylogenetic analyses using concatenated nucleotides (NUC) and amino acids (AAs) of all 12 protein-coding genes, three different algorithms, and the entire available acanthocephalan mitogenomic dataset. RESULTS We found evidence for strong compositional heterogeneity in the dataset, and Micracanthorhynchina dakusuiensis exhibited a disproportionately long branch in all analyses. This caused a long-branch attraction artefact (LBA) of M. dakusuiensis resolved at the base of the Echinorhynchida clade when the NUC dataset was used in combination with standard phylogenetic algorithms, maximum likelihood (ML) and Bayesian inference (BI). Both the use of the AA dataset (BI-AAs and ML-AAs) and the CAT-GTR model designed for suppression of LBA (CAT-GTR-AAs and CAT-GTR-NUC) at least partially attenuated this LBA artefact. The results support Illiosentidae as the basal radiation of Echinorhynchida and Rhadinorhynchidae forming a clade with Echinorhynchidae and Pomporhynchidae. The questions of the monophyly of Rhadinorhynchidae and its sister lineage remain unresolved. The order Echinorhynchida was paraphyletic in all of our analyses. CONCLUSIONS Future studies should take care to attenuate compositional heterogeneity-driven LBA artefacts when applying mitogenomic data to resolve the phylogeny of Acanthocephala.
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Affiliation(s)
- Jin-Wei Gao
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
| | - Xi-Ping Yuan
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
| | - Hao Wu
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
| | - Chuan-Yu Xiang
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Min Xie
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
| | - Rui Song
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China.
| | - Zhong-Yuan Chen
- Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan, China
| | - Yuan-An Wu
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
| | - Dong-Sheng Ou
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
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12
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Yu M, Zhang D, Zhao X. Sequencing and phylogenomics of the complete mitochondrial genome of Allodiplogaster sp. (Rhabditida: Diplogasteridae): A new gene order and its phylogenetic implications. Gene 2022; 840:146761. [PMID: 35905856 DOI: 10.1016/j.gene.2022.146761] [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: 03/10/2022] [Revised: 06/13/2022] [Accepted: 07/24/2022] [Indexed: 11/18/2022]
Abstract
Gene order has been utilized as a phylogenetic signal for many taxa. However, its phylogenetic performance has not been evaluated in Nematoda. As there is only one nematode mitogenome available to date, in the Diplogasteridae family, we sequenced the mitogenome of Allodiplogaster sp. and constructed a phylogeny for Nematoda using this updated mitogenome dataset. We then compared this phylogeny to one constructed using gene order. The complete mitochondrial genome of Allodiplogaster sp. was 13,953 bp in size and included 22 tRNAs, two rRNAs, and 12 protein-coding genes. To assess how Allodiplogaster sp. is related to other nematode species, we used Bayesian inference and maximum likelihood algorithms to construct phylogenetic trees of the Nematoda. We found that: 1) The target species Allodiplogaster sp. is closely related to Allodiplogaster sudhausi. The topology of the mitogenome based phylogeny was nearly identical to previous phylogenies created using 18S rRNA data, except for the placement of the Strongyloididae family. 2) The maximum likelihood tree constructed using gene order was roughly consistent with the mitogenome-based tree at the family level, but not at the species level. 3) Protein-coding genes were ordered differently in Allodiplogaster sp. versus Allodiplogaster sudhausi; this represents the first report of such a reordering in the class Chromadorea in our study. Our study confirms that gene order represents useful phylogenetic information for the Nematoda: the maximum likelihood tree based on gene order provided additional support for the nematode phylogeny constructed using molecular data.
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Affiliation(s)
- Min Yu
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Xumao Zhao
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China.
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Inverted base composition skews and discontinuous mitochondrial genome architecture evolution in the Enoplea (Nematoda). BMC Genomics 2022; 23:376. [PMID: 35585506 PMCID: PMC9115964 DOI: 10.1186/s12864-022-08607-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 04/25/2022] [Indexed: 11/26/2022] Open
Abstract
Background Within the class Enoplea, the earliest-branching lineages in the phylum Nematoda, the relatively highly conserved ancestral mitochondrial architecture of Trichinellida is in stark contrast to the rapidly evolving architecture of Dorylaimida and Mermithida. To better understand the evolution of mitogenomic architecture in this lineage, we sequenced the mitogenome of a fish parasite Pseudocapillaria tomentosa (Trichinellida: Capillariidae) and compared it to all available enoplean mitogenomes. Results P. tomentosa exhibited highly reduced noncoding regions (the largest was 98 bp), and a unique base composition among the Enoplea. We attributed the latter to the inverted GC skew (0.08) in comparison to the ancestral skew in Trichinellidae (-0.43 to -0.37). Capillariidae, Trichuridae and Longidoridae (Dorylaimida) generally exhibited low negative or low positive skews (-0.1 to 0.1), whereas Mermithidae exhibited fully inverted low skews (0 to 0.05). This is indicative of inversions in the strand replication order or otherwise disrupted replication mechanism in the lineages with reduced/inverted skews. Among the Trichinellida, Trichinellidae and Trichuridae have almost perfectly conserved architecture, whereas Capillariidae exhibit multiple rearrangements of tRNA genes. In contrast, Mermithidae (Mermithida) and Longidoridae (Dorylaimida) exhibit almost no similarity to the ancestral architecture. Conclusions Longidoridae exhibited more rearranged mitogenomic architecture than the hypervariable Mermithidae. Similar to the Chromadorea, the evolution of mitochondrial architecture in enoplean nematodes exhibits a strong discontinuity: lineages possessing a mostly conserved architecture over tens of millions of years are interspersed with lineages exhibiting architectural hypervariability. As Longidoridae also have some of the smallest metazoan mitochondrial genomes, they contradict the prediction that compact mitogenomes should be structurally stable. Lineages exhibiting inverted skews appear to represent the intermediate phase between the Trichinellidae (ancestral) and fully derived skews in Chromadorean mitogenomes (GC skews = 0.18 to 0.64). Multiple lines of evidence (CAT-GTR analysis in our study, a majority of previous mitogenomic results, and skew disruption scenarios) support the Dorylaimia split into two sister-clades: Dorylaimida + Mermithida and Trichinellida. However, skew inversions produce strong base composition biases, which can hamper phylogenetic and other evolutionary studies, so enoplean mitogenomes have to be used with utmost care in evolutionary studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08607-4.
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Hao CL, Arken K, Kadir M, Zhang WR, Rong MJ, Wei NW, Liu YJ, Yue C. The complete mitochondrial genomes of Paradiplozoon yarkandense and Paradiplozoon homoion confirm that Diplozoidae evolve at an elevated rate. Parasit Vectors 2022; 15:149. [PMID: 35477556 PMCID: PMC9044634 DOI: 10.1186/s13071-022-05275-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diplozoidae are monogenean (Monogenea: Polyopisthocotylea) fish parasites characterised by a unique life history: two larvae permanently fuse into an X-shaped "Siamese" organism. Taxonomy and phylogeny of Diplozoidae and Polyopisthocotylea remain unresolved due to the unavailability of molecular markers with sufficiently high resolution. Mitogenomes may be a suitable candidate, but there are currently only 12 available for the Polyopisthocotylea (three for Diplozoidae). The only available study of diplozoid mitogenomes found unique base composition patterns and elevated evolution rates in comparison with other Monogenean mitogenomes. METHODS To further explore their evolution and generate molecular data for evolutionary studies, we sequenced the complete mitogenomes of two Diplozoidae species, Paradiplozoon homoion and Paradiplozoon yarkandense, and conducted a number of comparative mitogenomic analyses with other polyopisthocotyleans. RESULTS We found further evidence that mitogenomes of Diplozoidae evolve at a unique, elevated rate, which was reflected in their exceptionally long branches, large sizes, unique base composition, skews, and very low gene sequence similarity levels between the two newly sequenced species. They also exhibited remarkably large overlaps between some genes. Phylogenetic analysis of Polyopisthocotylea resolved all major taxa as monophyletic, and Mazocraeidea was split into two major clades: (Diplozoidae) + (all four remaining families: Diclidophoridae, Chauhaneidae, Mazocraeidae and Microcotylidae). It also provided further confirmation that the genus Paradiplozoon is paraphyletic and requires a taxonomic revision, so the two species may have to be renamed Indodiplozoon homoion and Diplozoon yarkandense comb. nov. CONCLUSIONS Although our findings indicate that mitogenomes may be a promising tool for resolving the phylogeny of Polyopisthocotylea, elevated evolutionary rates of Diplozoidae may cause phylogenetic artefacts, so future studies should pay caution to this problem. Furthermore, as the reason for their elevated evolution remains unknown, Diplozoidae are a remarkably interesting lineage for other types of evolutionary mitogenomic studies.
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Affiliation(s)
- Cui-Lan Hao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Kadirden Arken
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Munira Kadir
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Wen-Run Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Meng-Jie Rong
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Nian-Wen Wei
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Yan-Jun Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Cheng Yue
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China.
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Jakovlić I, Zou H, Chen JH, Lei HP, Wang GT, Liu J, Zhang D. Slow crabs - fast genomes: Locomotory capacity predicts skew magnitude in crustacean mitogenomes. Mol Ecol 2021; 30:5488-5502. [PMID: 34418213 DOI: 10.1111/mec.16138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 02/05/2023]
Abstract
Base composition skews (G-C/G+C) of mitochondrial genomes are believed to be primarily driven by mutational pressure, which is positively correlated with metabolic rate. In marine animals, metabolic rate is also positively correlated with locomotory capacity. Given the central role of mitochondria in energy metabolism, we hypothesised that selection for locomotory capacity should be positively correlated with the strength of purifying selection (dN/dS), and thus be negatively correlated with the skew magnitude. Therefore, these two models assume diametrically opposite associations between the metabolic rate and skew magnitude: positive correlation in the prevailing paradigm, and negative in our working hypothesis. We examined correlations between the skew magnitude, metabolic rate, locomotory capacity, and several other variables previously associated with mitochondrial evolution on 287 crustacean mitogenomes. Weakly locomotory taxa had higher skew magnitude and ω (dN/dS) values, but not the gene order rearrangement rate. Skew and ω magnitudes were correlated. Multilevel regression analyses indicated that three competing variables, body size, gene order rearrangement rate, and effective population size, had negligible impacts on the skew magnitude. In most crustacean lineages selection for locomotory capacity appears to be the primary factor determining the skew magnitude. Contrary to the prevailing paradigm, this implies that adaptive selection outweighs nonadaptive selection (mutation pressure) in crustaceans. However, we found indications that effective population size (nonadaptive factor) may outweigh the impact of locomotory capacity in sessile crustaceans (Thecostraca). In conclusion, skew magnitude is a product of the interplay between adaptive and nonadaptive factors, the balance of which varies among lineages.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Hai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong-Peng Lei
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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