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Hu Y, Ye T, Zou H, Wang GT, Li WX, Zhang D. Complete mitochondrial genome and phylogenetic analysis of Dollfustrema vaneyi (Trematoda: Bucephalidae). BMC Genomics 2024; 25:862. [PMID: 39278945 PMCID: PMC11403940 DOI: 10.1186/s12864-024-10740-1] [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: 06/11/2024] [Accepted: 08/26/2024] [Indexed: 09/18/2024] Open
Abstract
BACKGROUND The Bucephalidae is a large family of digenean trematodes but most previous analyses of its phylogenetic position have relied on a single mitochondrial gene or morphological features. Mitochondrial genomes (mitogenomes) remain unavailable for the entire family. To address this, we sequenced the complete mitogenome of Dollfustrema vaneyi and analyzed the phylogenetic relationships with other trematodes. RESULTS The circular genome of Dollfustrema vaneyi spanned 14,959 bp and contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a major non-coding region. We used concatenated amino acid and nucleotide sequences of all 36 genes for phylogenetic analyses, conducted using MrBayes, IQ-TREE and PhyloBayes. We identified pronounced topological instability across different analyses. The addition of recently sequenced two mitogenomes for the Aspidogastrea subclass along with the use of a site-heterogeneous model stabilized the topology, particularly the positions of Azygiidae and Bucephalidae. The stabilized results indicated that Azygiidae was the closest lineage to Bucephalidae in the available dataset, and together, they clustered at the base of the Plagiorchiida. CONCLUSIONS Our study provides the first comprehensive description and annotation of the mitochondrial genome for the Bucephalidae family. The results indicate a close phylogenetic relationship between Azygiidae and Bucephalidae, and reveal their basal placement within the order Plagiorchiida. Furthermore, the inclusion of Aspidogastrea mitogenomes and the site-heterogeneous model significantly improved the topological stability. These data will provide key molecular resources for future taxonomic and phylogenetic studies of the family Bucephalidae.
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Affiliation(s)
- Ye Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Tong Ye
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Hong Zou
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Gui-Tang Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Wen-Xiang Li
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.
| | - Dong Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
- Key Laboratory of Biodiversity and Environment On the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, 850011, China.
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Atopkin DM, Semenchenko AA, Solodovnik DA, Ivashko YI. A report on the complete mitochondrial genome of the trematode Azygia robusta Odhner, 1911, its new definitive host from the Russian Far East, and unexpected phylogeny of Azygiidae within Digenea, as inferred from mitogenome sequences. J Helminthol 2023; 97:e69. [PMID: 37655787 DOI: 10.1017/s0022149x23000500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
New data on the complete mitochondrial genome of Azygia robusta (Azygiidae) were obtained by the next-generation sequencing (NGS) approach. The mitochondrial DNA (mtDNA) of A. robusta had a length of 13 857 bp and included 12 protein-coding genes, two ribosomal genes, 22 transfer RNA genes, and two non-coding regions. The nucleotide sequences of the complete mitochondrial genomes of two A. robusta specimens differed from each other by 0.12 ± 0.03%. Six of 12 protein-coding genes demonstrated intraspecific variation. The difference between the nucleotide sequences of the complete mitochondrial genomes of A. robusta and Azygia hwangtsiyui was 26.95 ± 0.35%; the interspecific variation of protein-coding genes between A. robusta and A. hwangtsiyui ranged from 20.5 ± 0.9% (cox1) to 30.7 ± 1.2% (nad5). The observed gene arrangement in the mtDNA sequence of A. robusta was identical to that of A. hwangtsiyui. Codon usage and amino acid frequencies were highly similar between A. robusta and A. hwangtsiyui. The results of phylogenetic analyses based on mtDNA protein-coding regions showed that A. robusta is closely related to A. hwangtsiyui (belonging to the same suborder, Azygiida) that formed a distinct early-diverging branch relative to all other Digenea. A preliminary morphological analysis of paratypes of the two azygiid specimens studied showed visible morphological differences between them. The specimen extracted from Sakhalin taimen (Parahucho perryi) was most similar to A. robusta. Thus, we here provide the first record of a new definitive host, P. perryi, for A. robusta and also molecular characteristics of the trematode specimens.
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Affiliation(s)
- D M Atopkin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Department of Cell Biology and Genetics, Far Eastern Federal University, Vladivostok, Russia
| | - A A Semenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - D A Solodovnik
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Y I Ivashko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
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Gao JF, Zhang AH, Wei W, Jia B, Zhang J, Li B, Chen YY, Sun YY, Hou MR, Liu XW, Wang JW, Zhang XH, Wang CR. The complete mitochondrial genome of Ogmocotyle ailuri: gene content, composition and rearrangement and phylogenetic implications. Parasitology 2023; 150:661-671. [PMID: 37051880 PMCID: PMC10410389 DOI: 10.1017/s0031182023000379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023]
Abstract
Trematodes of the genus Ogmocotyle are intestinal flukes that can infect a variety of definitive hosts, resulting in significant economic losses worldwide. However, there are few studies on molecular data of these trematodes. In this study, the mitochondrial (mt) genome of Ogmocotyle ailuri isolated from red panda (Ailurus fulgens) was determined and compared with those from Pronocephalata to investigate the mt genome content, genetic distance, gene rearrangements and phylogeny. The complete mt genome of O. ailuri is a typical closed circular molecule of 14 642 base pairs, comprising 12 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions. All genes are transcribed in the same direction. In addition, 23 intergenic spacers and 2 locations with gene overlaps were determined. Sequence identities and sliding window analysis indicated that cox1 is the most conserved gene among 12 PCGs in O. ailuri mt genome. The sequenced mt genomes of the 48 Plagiorchiida trematodes showed 5 types of gene arrangement based on all mt genome genes, with the gene arrangement of O. ailuri being type I. Phylogenetic analysis using concatenated amino acid sequences of 12 PCGs revealed that O. ailuri was closer to Ogmocotyle sikae than to Notocotylus intestinalis. These data enhance the Ogmocotyle mt genome database and provide molecular resources for further studies of Pronocephalata taxonomy, population genetics and systematics.
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Affiliation(s)
- Jun-Feng Gao
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Ai-Hui Zhang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Wei Wei
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Bin Jia
- Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Jun Zhang
- Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Ben Li
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Ying-Yu Chen
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Yun-Yi Sun
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Mei-Ru Hou
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xue-Wei Liu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Jia-Wen Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xin-Hui Zhang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Chun-Ren Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
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Li R, Wang HM, Liu GH, Tu Y, Deng YP. Characterization of the complete mitochondrial genome of the fluke of turdus, Plagiorchis elegans, and phylogenetic implications. Exp Parasitol 2022; 242:108387. [PMID: 36170911 DOI: 10.1016/j.exppara.2022.108387] [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: 04/23/2022] [Revised: 09/03/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022]
Abstract
Plagiorchis elegans (Trematoda: Digenea) is mainly parasitic in the intestines of vertebrate animals, including humans, causing irreversible pathological damage and herd-spherical influences. However, little information is available about its molecular epidemiology, population genetics, and phylogeny. In the present study, we sequenced, assembled, and annotated the complete mitochondrial (mt) genome of P. elegans. Combining with the available mitochondrial data of subclass Digenea, phylogenetic analysis was performed based on Bayesian inference (BI). The results showed that the complete length of P. elegans is 13,862 bp, including 12 PCGs, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and one non-coding gene (NCR). There was an obvious A + T content from 61.0% to 71.3% and the values of the Ka/Ks ratio ranged from 0.119 (cox1) to 1.053 (nad6). In the BI analysis, different from previous studies, phylogenetic analysis showed genus Glypthelmins was paraphyletic rather than monophyletic and had a closer relationship with Plagiorchis and Orientocreadium. Additionally, the BI tree also presented that the genus Echinostoma was monophyletic. Our results provided molecular data in the family Plagiorchiidae proposing new insight within Xiphidiata and Echinostomata.
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Affiliation(s)
- Rong Li
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan province, 410128, China
| | - Hui-Mei Wang
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan province, 410128, China
| | - Guo-Hua Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan province, 410128, China
| | - Ya Tu
- Beijing Wildlife Rescue and Rehabilitation Center, Beijing, 101300, China.
| | - Yuan-Ping Deng
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan province, 410128, China.
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Characterization of complete mitochondrial genome and ribosomal operon for Carassotrema koreanum Park, 1938 (Digenea: Haploporidae) by means of next-generation sequencing data. J Helminthol 2022; 96:e54. [PMID: 35894440 DOI: 10.1017/s0022149x22000438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We obtained new data on the complete mitochondrial DNA (mtDNA) and the ribosomal operon of the trematode Carassotrema koreanum (Digenea: Haploporata: Haploporidae), an intestinal parasite of Carassius auratus, using next-generation sequencing. The mtDNA of C. koreanum contained 13,965 bp, including 12 protein-coding genes, two ribosomal genes, 22 transport RNA (tRNA) genes and a non-coding region. The ribosomal operon of C. koreanum was 10,644 bp in length, including ETS1 (1449 bp), 18S ribosomal RNA (rRNA) gene (1988 bp), ITS1 ribosomal DNA (rDNA) (558 bp), 5.8S rRNA gene (157 bp), ITS2 rDNA (274 bp), 28S rRNA gene (4152 bp) and ETS2 (2066 bp). Phylogenetic analysis based on mtDNA protein-coding regions showed that C. koreanum was closely related to Parasaccocoelium mugili, a species from the same suborder Haploporata. Bayesian phylogenetic tree topology was the most reliable and confirmed the validity of the Haploporata. The results of sequence cluster analysis based on codon usage bias demonstrated some agreement with the results of the phylogenetic analysis. In particular, Schistosoma spp. were differentiated from the other members of Digenea and the members of Pronocephalata were localized within the same cluster. Carassotrema koreanum and P. mugili fell within different clusters. The grouping of C. koreanum and P. mugili within the same cluster was obtained on the basis of frequencies of 13 specified codons, of which three codon pairs were degenerate. A similarity was found between two haploporid species and two Dicrocoelium spp. in the presence of TTG start codon of the mitochondrial nad5 gene. Our results confirmed the taxonomical status of the Haploporata identified in the previous studies and revealed some characteristic features of the codon usage in its representatives.
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Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference. Interdiscip Sci 2022; 14:349-357. [PMID: 34817803 PMCID: PMC9124167 DOI: 10.1007/s12539-021-00493-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 10/26/2022]
Abstract
AbstractIn 2002, our research group observed a gene clustering pattern based on the base frequency of A versus T at the second codon position in the genome of Vibrio cholera and found that the functional category distribution of genes in the two clusters was different. With the availability of a large number of sequenced genomes, we performed a systematic investigation of A2–T2 distribution and found that 2694 out of 2764 prokaryotic genomes have an optimal clustering number of two, indicating a consistent pattern. Analysis of the functional categories of the coding genes in each cluster in 1483 prokaryotic genomes indicated, that 99.33% of the genomes exhibited a significant difference (p < 0.01) in function distribution between the two clusters. Specifically, functional category P was overrepresented in the small cluster of 98.65% of genomes, whereas categories J, K, and L were overrepresented in the larger cluster of over 98.52% of genomes. Lineage analysis uncovered that these preferences appear consistently across all phyla. Overall, our work revealed an almost universal clustering pattern based on the relative frequency of A2 versus T2 and its role in functional category preference. These findings will promote the understanding of the rationality of theoretical prediction of functional classes of genes from their nucleotide sequences and how protein function is determined by DNA sequence.
Graphical abstract
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Cribb TH, Cutmore SC, Bray RA. The biodiversity of marine trematodes: then, now and in the future. Int J Parasitol 2021; 51:1085-1097. [PMID: 34757087 DOI: 10.1016/j.ijpara.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 10/19/2022]
Abstract
Trematodes are the richest class of platyhelminths in the marine environment, infecting all classes of marine vertebrates as sexual adults and many phyla of marine invertebrates as part of their life cycles. Despite the cryptic nature of their existence (almost all marine trematodes are internal parasites), they have been the focus of study for almost 250 years, with the first species described in 1774. Here we review progress in the study of the "biodiversity" of these parasites, contrasting the progress made in the last 50 years (post-1971) to that in the almost 200 years before it (pre-1972). We consider an understanding of biodiversity to require knowledge of the species present in the system, an understanding of their evolutionary relationships (which informs higher classification), and, specifically for trematodes, an understanding of their complex life cycles. The fauna is now large, comprising well over 5,000 species. Although species description continues, we see evidence of a slow-down in all aspects of discovery. There has been only one completely new family identified since 1984 and the proposal of new genera is in decline as is the description of new species, especially for those of tetrapods. However, the extent to which this slow-down reflects an approach to the richness asymptote is made uncertain by changes in the field; reduced effort and difficulty of study may be important components of the effect. Regardless of how close we are to a complete description of the fauna, we infer that the outline is well-understood although the details are not. Adoption of molecular methodologies over the last 40 years have complemented morphometric analyses to facilitate objective recognition of species; however, despite these objective data, there is still inconsistency between authors on species delimitation. Molecular methodologies have also completely revolutionised inference of relationships at all levels, from within genera to between orders, and underpinned elucidation of novel life cycles. We expect the next 50 years to produce further dividends from technological innovations. The backdrop to the field will be global environmental concerns and the growing problem of funding for basic biodiversity studies.
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Affiliation(s)
- Thomas H Cribb
- The University of Queensland, School of Biological Sciences, St Lucia, Queensland 4072, Australia.
| | - Scott C Cutmore
- The University of Queensland, School of Biological Sciences, St Lucia, Queensland 4072, Australia
| | - Rodney A Bray
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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