1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Solórzano-García B, Hernández-Mena DI, Choudhury A, Pérez-Ponce de León G. The complete mitochondrial genome of 3 species of allocreadiids (Digenea, Allocreadiidae): characterization and phylogenetic position within the order Plagiorchiida. Parasitology 2024; 151:309-318. [PMID: 38223986 PMCID: PMC11007277 DOI: 10.1017/s0031182024000064] [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: 12/19/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
Trematodes of the family Allocreadiidae are primarily found in the intestines of freshwater fishes around the world. The family includes 15 genera and c. 130 species. The last 2 decades have witnessed an increase in the genetic library of its species. Molecular data have been crucial for species delimitation and species description within Allocreadiidae and for understanding their evolutionary and biogeographical history and classification. Here, the mitogenomes of 3 species of allocreadiids were obtained using high throughput sequencing methods. Mitogenomes were compared with other members of the order Plagiorchiida to determine their molecular composition, gene rearrangement and phylogenetic interrelationships. The complete circular mitogenomes of Allocreadium lobatum, Creptotrematina aguirrepequenoi and Wallinia mexicana were 14 424, 13 769 and 13 924 bp long respectively, comprising 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions. Gene arrangements were identical to other Xiphidiatan trematodes. Phylogenetic analyses using the mitogenomes revealed Allocreadiidae as a monophyletic group closely related to other members of the suborder Xiphidiata; A. lobatum was yielded as the sister taxon of C. aguirrepequenoi + W. mexicana. Our study increases the complete mitochondrial genome library of trematodes and strengthens our understanding of the phylogenetic relationships and classification of this parasite group.
Collapse
Affiliation(s)
- Brenda Solórzano-García
- Escuela Nacional de Estudios Superiores unidad Mérida (ENES-Mérida, UNAM), Mérida, Yucatán, Mexico
| | - David I. Hernández-Mena
- Escuela Nacional de Estudios Superiores unidad Mérida (ENES-Mérida, UNAM), Mérida, Yucatán, Mexico
| | | | | |
Collapse
|
3
|
Moguel-Chin WI, Panti-May JA, García-García BA, Hernández-Mena DI. Description of new species of Trematoda from bats of Southeastern Mexico and a new classification for Brachylecithum rileyi n. comb. (Dicrocoeliidae). Syst Parasitol 2023; 101:4. [PMID: 38105370 PMCID: PMC10725855 DOI: 10.1007/s11230-023-10127-y] [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: 06/28/2023] [Accepted: 10/26/2023] [Indexed: 12/19/2023]
Abstract
To date, 23 species of trematodes have been reported in bats from Mexico. However, in some regions of Mexico, such as the Yucatan Peninsula, many species of bats do not have helminthological records. Here, we sampled bats in four localities in Southeastern Mexico from April 2017 to February 2022. Parasites were collected from the intestine of four species of bats: Pteronotus fulvus, Eumops nanus, Noctilio leporinus and Nyctinomops laticaudatus. Conventional morphological techniques and molecular tools with the 28S ribosomal gene were used to describe the helminths. We discovered that our parasites represent three new species and a new combination of trematodes. We found that the new species have morphological differences with their congeneric species, and we complement this information whit molecular data. Furthermore, we found morphological and molecular evidence that places Dicrocoelium rileyi within the genus Brachylecithum. This study points out the importance of comparing morphological and phylogenetic information.
Collapse
Affiliation(s)
- Wilson I Moguel-Chin
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, Campus de Ciencias Biológicas y Agropecuarias, km 15.5 carretera Mérida-Xmatkuil, 97135, Mérida, Yucatán, Mexico.
| | - Jesús Alonso Panti-May
- Centro de Investigaciones Regionales 'Dr. Hideyo Noguchi', Universidad Autónoma de Yucatán, Av. Itzáes, Centro, 97000, Mérida, Yucatán, Mexico
| | - Brenda Atziri García-García
- Instituto de Biología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 3000, CU, 04510, Coyoacán, CDMX, Mexico
| | - David I Hernández-Mena
- Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Unidad Mérida, Carretera Mérida-Progreso, Loma Bonita, 97205, Mérida, Yucatán, Mexico.
- Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de Mexico, Carretera Mérida-Tetiz Km4, 97357, Ucú, Yucatán, Mexico.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
The complete mitochondrial genome of Prosthogonimus cuneatus and Prosthogonimus pellucidus (Trematoda: Prosthogonimidae), their features and phylogenetic relationships in the superfamily Microphalloidea. Acta Trop 2022; 232:106469. [PMID: 35430263 DOI: 10.1016/j.actatropica.2022.106469] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/22/2022]
Abstract
Prosthogonimus cuneatus and Prosthogonimus pellucidus (Trematoda: Prosthogonimidae) are common flukes of poultry and other birds which can cause severe impacts on animal health and losses to the poultry industry. However, there are limited studies on the molecular epidemiology, population genetics, and systematics of Prosthogonimus species. In the present study, the complete mitochondrial (mt) genomes of P. cuneatus and P. pellucidus were determined to be 14,829 bp and 15,013 bp in length, respectively. Both mt genomes contain 12 protein-coding genes (PCGs) (cox1-3, nad1-6, nad4L, cytb, and atp6), 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding region. Our comparative analysis shows that the atp6 genes of P. cuneatus and P. pellucidus are longer than any previously published atp6 genes of other trematodes. The lengths of the atp6 genes of P. cuneatus and P. pellucidus in this study seem unusual, and should therefore be studied further. The mt genes of P. cuneatus and P. pellucidus are transcribed in the same direction, and the gene arrangements are identical to those of Plagiorchis maculosus, Tamerlania zarudnyi, and Tanaisia sp., but different from those of Eurytrema pancreaticum, Dicrocoelium chinensis, and Brachycladium goliath. The mt genome A + T contents of P. cuneatus and P. pellucidus are 64.47% and 65.34%, respectively. In the 12 PCGs, ATG is the most common initiation codon, whereas TAG is the most common termination codon. The sequence identity of the same 12 PCGs among the eight trematodes (P. cuneatus, P. pellucidus, Pl. maculosus, D. chinensis, E. pancreaticum, B. goliath, T. zarudnyi, Tanaisia sp.) of Xiphidiata are 55.5%-81.7% at the nucleotide level and 43.9%-82.5% at the amino acid level. The nucleotide similarities among the complete mt genomes of the eight trematodes range from 54.1%-81.5%. Phylogenetic analysis based on the aligned concatenated amino acid sequences of the 12 PCGs shows that P. cuneatus and P. pellucidus cluster together and are sister to T. zarudnyi and Tanaisia sp., and this clade is more closely related to E. pancreaticum, Dicrocoelium spp. and Lyperosomum longicauda in the family Dicrocoeliidae, than it is to species in the families Plagiorchiidae and Brachycladiidae. These are the first reported complete mt genomes of Prosthogonimidae, and these data will provide additional molecular resources for further studies of Prosthogonimidae taxonomy, population genetics, and systematics.
Collapse
|
6
|
Chelatrematidae n. fam., a new family of digenetic trematodes from the South Western Ghats, India, erected on the basis of morphological and molecular studies. J Helminthol 2022; 96:e47. [PMID: 35833304 DOI: 10.1017/s0022149x22000396] [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: 11/07/2022]
Abstract
On the basis of the morphological characterization of Chelatrema neilgherriensis Manjula & Janardanan, 2006 recovered from the freshwater fish Barilius gatensis (Valenciennes, 1844) in the Wayanad region of the Western Ghats, the diagnostic features of the genus Chelatrema Gupta & Kumari, 1973 have been modified. Based on the phylogenetic analysis of C. neilgherriensis and comparative morphology studies relative to members of other families of Gorgoderoidea Looss, 1901, this genus is placed in a new family Chelatrematidae n. fam. The studies revealed the molecular and morphological closeness of Chelatrema with Paracreptatrematina limi Amin & Myer, 1982, and the latter is transferred to this new family. Hence the new family Chelatrematidae n. fam. comprises the genera Chelatrema and Paracreptatrematina.
Collapse
|
7
|
Shumenko PG, Tatonova YV. Assessing the population structure of trematode Metagonimus suifunensis using three mitochondrial markers. Parasitol Res 2022; 121:915-923. [PMID: 35133488 DOI: 10.1007/s00436-022-07456-0] [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: 09/24/2021] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
In this work, for the first time, the genetic variability of the Metagonimus suifunensis population in the Russian southern Far East was estimated based on the full-length sequences of the nad1 gene of mitochondrial DNA. In addition, for a sample of the same size, the sequences of cox1 and cytb genes, previously used for population studies for M. suifunensis, were reanalysed. Three markers were combined to a common sequence, and the obtained data were studied. Despite the higher level of variability, nad1 and cox1 mtDNA genes did not reveal subdivisions within the population. The combined dataset made it possible to determine that the sample from the Odyr River was the centre of the species' range formation and clarified the continental migration route of the parasite from south to north. According to the data obtained, it was presumed that piscivorous birds participate in the life cycle of the parasite. The subdivision within population revealed that using all three mitochondrial markers is consistent with the features of differentiation within populations of related species, but the reasons for its formation remain unclear due to the insufficient amount of data and the use of different markers in studies of different species.
Collapse
Affiliation(s)
- Polina G Shumenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, 100-letiya Street, 159, Vladivostok, 690022, Russia
| | - Yulia V Tatonova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, 100-letiya Street, 159, Vladivostok, 690022, Russia. .,School of Biomedicine, Far Eastern Federal University, Sukhanova Street, 8, Vladivostok, 690091, Russia.
| |
Collapse
|
8
|
Chan AHE, Saralamba N, Saralamba S, Ruangsittichai J, Thaenkham U. The potential use of mitochondrial ribosomal genes (12S and 16S) in DNA barcoding and phylogenetic analysis of trematodes. BMC Genomics 2022; 23:104. [PMID: 35130837 PMCID: PMC8822746 DOI: 10.1186/s12864-022-08302-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Genetic markers like the nuclear ribosomal RNA (rRNA) genes, internal transcribed spacer regions, mitochondrial protein-coding genes, and genomes have been utilized for molecular identification of parasitic trematodes. However, challenges such as the design of broadly applicable primers for the vast number of species within Digenea and the genetic markers’ ability to provide sufficient species-level resolution limited their utility. This study presented novel and broadly applicable primers using the mitochondrial 12S and 16S rRNA genes for Digenea and aimed to show their suitability as alternative genetic markers for molecular identification of orders Plagiorchiida, Echinostomida, and Strigeida. Results Our results revealed that the mitochondrial 12S and 16S rRNA genes are suitable for trematode molecular identification, with sufficient resolution to discriminate closely related species and achieve accurate species identification through phylogenetic placements. Moreover, the robustness of our newly designed primers to amplify medically important parasitic trematodes encompassing three orders was demonstrated through successful amplification. The convenience and applicability of the newly designed primers and adequate genetic variation of the mitochondrial rRNA genes can be useful as complementary markers for trematode molecular-based studies. Conclusions We demonstrated that the mitochondrial rRNA genes could be alternative genetic markers robust for trematode molecular identification and potentially helpful for DNA barcoding where our primers can be widely applied across the major Digenea orders. Furthermore, the potential of the mitochondrial rRNA genes for molecular systematics can be explored, enhancing their appeal for trematode molecular-based studies. The novelty of utilizing the mitochondrial rRNA genes and the designed primers in this study can potentially open avenues for species identification, discovery, and systematics in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08302-4.
Collapse
Affiliation(s)
- Abigail Hui En Chan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Naowarat Saralamba
- Department of Molecular Tropical Medicine and Genetics, Mahidol University, Bangkok, Thailand
| | - Sompob Saralamba
- Mathematical and Economic Modelling (MAEMOD), Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jiraporn Ruangsittichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Urusa Thaenkham
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| |
Collapse
|
9
|
Duan DY, Chen Z, Fu YT, Liu GH, Cheng TY. Characterization of the complete mitochondrial genomes of two Ixodes ticks, I. nipponensis and Ixodes (Pholeoixodes) sp. MEDICAL AND VETERINARY ENTOMOLOGY 2021; 35:513-522. [PMID: 33931902 DOI: 10.1111/mve.12523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 04/10/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
In this study, the authors sequenced and characterized the complete mitochondrial (mt) genomes of two hard ticks of the genus Ixodes, I. nipponensis and Ixodes (Pholeoixodes) sp., which were 14 505 and 14 543 bp in length, respectively. Their mt genomes encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes and two ribosomal RNA genes, and have only one non-coding region. The gene order in their mt genomes was the same as that of other Ixodes spp. mt genomes. The average sequence identity, combined nucleotide diversity, non-synonymous/synonymous substitutions ratio analyses consistently demonstrated that cox1, rrnS, cox2, cox3 and cytb were the most conserved and atp8, nad6 and nad2 were the most variable genes across Ixodes mitogenomes. Phylogeny of the present Ixodes spp., and other selected hard tick species, based on concatenated amino acid sequences of PCGs, confirmed their position within the genus Ixodes and sub-family Ixodinae. The novel mt markers described herein will be useful for further studies of the population genetics, molecular epidemiology and systematics of hard ticks.
Collapse
Affiliation(s)
- D-Y Duan
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
- Hunan Co-Innovation Center of Animal Production Safety, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Z Chen
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Y-T Fu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| | - G-H Liu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
- Hunan Co-Innovation Center of Animal Production Safety, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| | - T-Y Cheng
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
- Hunan Co-Innovation Center of Animal Production Safety, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| |
Collapse
|
10
|
Xu G, Zhu P, Zhu W, Ma B, Li X, Li W. Characterization of the complete mitochondrial genome of Notocotylus sp. (Trematoda, Notocotylidae) and its phylogenetic implications. Parasitol Res 2021; 120:1291-1301. [PMID: 33559042 DOI: 10.1007/s00436-021-07075-1] [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: 08/14/2020] [Accepted: 01/28/2021] [Indexed: 01/20/2023]
Abstract
The parasite genus Notocotylus comprises at least 50 species colonizing mainly aquatic birds and to a lesser extent some mammals, particularly rodents. Here trematode specimens isolated from a wild black swan were characterized and identified to belong to the genus Notocotylus via morphological and molecular analyses. Phylogenetic position of the isolate among other trematodes was determined based on the ribosomal internal transcribed spacer (ITS) 1 and 2. The complete mitochondrial (mt) genome of the isolate was amplified, sequenced, assembled, analyzed, and annotated. The isolate has an AT-rich mt genome (14,317 bp in length) that comprises 12 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The Notocotylus isolate identified in this study has relatively high mt genome sequence identity and identical gene content and arrangement to a known Notocotylidae species, Ogmocotyle sikae. The isolate formed a genetic clade with O. sikae in phylogenetic analysis of the concatenated PCG amino acid sequences. Compared to the ITS, the trematode mt genome appears more informative for resolving high-level phylogenies. To the best of our knowledge, this is the first study exploring the complete mt genome for the genus Notocotylus, and it offers a novel genomic resource that has important implications for trematode phylogenetics.
Collapse
Affiliation(s)
- Guoliang Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China.,Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Peng Zhu
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Weining Zhu
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Bo Ma
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xiaoyun Li
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Wei Li
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.
| |
Collapse
|
11
|
Suleman, Muhammad N, Khan MS, Tkach VV, Ullah H, Ehsan M, Ma J, Zhu XQ. Mitochondrial genomes of two eucotylids as the first representatives from the superfamily Microphalloidea (Trematoda) and phylogenetic implications. Parasit Vectors 2021; 14:48. [PMID: 33446249 PMCID: PMC7807500 DOI: 10.1186/s13071-020-04547-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/13/2020] [Indexed: 11/10/2022] Open
Abstract
Background The Eucotylidae Cohn, 1904 (Superfamily: Microphalloidea), is a family of digeneans parasitic in kidneys of birds as adults. The group is characterized by the high level of morphological similarities among genera and unclear systematic value of morphological characters traditionally used for their differentiation. In the present study, we sequenced the complete or nearly complete mitogenomes (mt genome) of two eucotylids representing the genera Tamerlania (T. zarudnyi) and Tanaisia (Tanaisia sp.). They represent the first sequenced mt genomes of any member of the superfamily Microphalloidea. Methods A comparative mitogenomic analysis of the two newly sequenced eucotylids was conducted for the investigation of mitochondrial gene arrangement, contents and genetic distance. Phylogenetic position of the family Eucotylidae within the order Plagiorchiida was examined using nucleotide sequences of mitochondrial protein-coding genes (PCGs) plus RNAs using maximum likelihood (ML) and Bayesian inference (BI) methods. BI phylogeny based on concatenated amino acids sequences of PCGs was also conducted to determine possible effects of silent mutations. Results The complete mt genome of T. zarudnyi was 16,188 bp and the nearly complete mt genome of Tanaisia sp. was 13,953 bp in length. A long string of additional amino acids (about 123 aa) at the 5′ end of the cox1 gene in both studied eucotylid mt genomes has resulted in the cox1 gene of eucotylids being longer than in all previously sequenced digeneans. The rrnL gene was also longer than previously reported in any digenean mitogenome sequenced so far. The TΨC and DHU loops of the tRNAs varied greatly between the two eucotylids while the anticodon loop was highly conserved. Phylogenetic analyses based on mtDNA nucleotide and amino acids sequences (as a separate set) positioned eucotylids as a sister group to all remaining members of the order Plagiorchiida. Both ML and BI phylogenies revealed the paraphyletic nature of the superfamily Gorgoderoidea and the suborder Xiphidiata. Conclusions The average sequence identity, combined nucleotide diversity and Kimura-2 parameter distances between the two eucotylid mitogenomes demonstrated that atp6, nad5, nad4L and nad6 genes are better markers than the traditionally used cox1 or nad1 for the species differentiation and population-level studies of eucotylids because of their higher variability. The position of the Dicrocoeliidae and Eucotylidae outside the clade uniting other xiphidiatan trematodes strengthened the argument for the need for re-evaluation of the taxonomic content of the Xiphidiata.![]()
Collapse
Affiliation(s)
- Suleman
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, People's Republic of China.,Department of Zoology, University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Nehaz Muhammad
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, People's Republic of China
| | - Mian Sayed Khan
- Department of Zoology, University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Vasyl V Tkach
- Department of Biology, University of North Dakota, Grand Forks, ND, 58202-9019, USA.
| | - Hanif Ullah
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Shanghai, 20041, People's Republic of China
| | - Muhammad Ehsan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, People's Republic of China
| | - Jun Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, People's Republic of China.
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, People's Republic of China. .,College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, People's Republic of China.
| |
Collapse
|
12
|
Achatz TJ, Cleveland DW, Carrión Bonilla C, Cronin L, Tkach VV. New dicrocoeliid digeneans from mammals in Ecuador including a highly genetically divergent new genus from an ancient marsupial lineage. Parasitol Int 2020; 78:102138. [PMID: 32428659 DOI: 10.1016/j.parint.2020.102138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 05/01/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022]
Abstract
The Dicrocoeliidae is a highly diverse and broadly distributed family of digeneans typically parasitic in the gall bladder and liver of their tetrapod hosts. So far, no study has reported dicrocoeliids, or any digeneans, from the ancient marsupial family Caenolestidae. Herein, we describe a new genus of dicrocoeliids (Otongatrema n. gen.) from Tate's shrew opossum Caenolestes fuliginosus and a new species of Metadelphis (Metadelphis cesartapiai n. sp.) from a phyllostomid bat Anoura peruana collected in Ecuador. Otongatrema can be readily distinguished from the morphologically closest dicrocoeliid genera Concinnum, Conspicuum and Canaania based on the position of the genital pore, distribution/position of the uterus and extent of vitellarium. Metadelphis cesartapiai can be easily differentiated from other Metadelphis spp. based on a combination of morphological characters including body shape and size, distribution of vitellarium, shape of the gonads as well as size of suckers and cirrus sac. In addition, we used newly generated partial sequences of the nuclear 28S rRNA gene and mitochondrial cox1 genes to examine phylogenetic affinities of the new taxa within the Dicrocoeliidae. Both the 28S and cox1 phylogenies confidently positioned Otongatrema as a sister/basal group to all other dicrocoeliids sequenced so far. The phylogenetic position of Otongatrema may be explained by a close co-evolutionary relationship with Caenolestidae, one of the most basal and most ancient groups of marsupials. In addition, our 28S phylogeny provides evidence that the complete or partial loss of intestinal structures has likely occurred independently at least 3 times in the evolutionary history of the Dicrocoeliidae.
Collapse
Affiliation(s)
- Tyler J Achatz
- Department of Biology, University of North Dakota, Grand Forks, North Dakota 58202-9019, USA.
| | - Dawn W Cleveland
- Department of Biology, University of North Dakota, Grand Forks, North Dakota 58202-9019, USA.
| | - Carlos Carrión Bonilla
- Zoological Museum, School of Biological Sciences, Universidad Católica del Ecuador, Quito, Ecuador.
| | - Lawrence Cronin
- Department of Biology, University of North Dakota, Grand Forks, North Dakota 58202-9019, USA
| | - Vasyl V Tkach
- Department of Biology, University of North Dakota, Grand Forks, North Dakota 58202-9019, USA.
| |
Collapse
|