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Aldamigh MA, Alahmadi AA, Al-Turaiki IM, Hassan AH. Morphological, ultrastructural, and phylogenetic analysis of Ascaridia columbae infecting domestic pigeons ( Columba livia domestica). Helminthologia 2024; 61:174-183. [PMID: 39040808 PMCID: PMC11260315 DOI: 10.2478/helm-2024-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/16/2024] [Indexed: 07/24/2024] Open
Abstract
Ascaridia species are the most common nematodes infecting pigeons. The current study investigated specific identity of nematode parasites collected from domestic pigeons (Columba livia domestica) in Al-Qassim Region, Saudi Arabia. Out of 354 pigeons, 13.3 % were infected with nematode parasites. The morphological structure and genetic relationship of nematode worms were studied using conventional methods (Light and scanning electron microscopes) coupled with the newly introduced molecular method. Microscopical and ultrastructure observations showed that the present nematode worms belong to the genus Ascaridia and have all the characteristic features of Ascaridia columbae. Moreover, Random Amplifier morphometric (RAPD) PCR analysis revealed that the present A. columbae had a close identity of up to 98.3 % to Ascaridia columbae JX624729 for Cox-1 gene regions, and up to 98.3 % to Ascaridia nymphii LC057210, and Ascaridia galli EF180058 for ITS1-5.8s- ITS2 rDNA gene regions. Phylogenetic analysis supported the placement of this Ascaridia species within Ascaridiidae family with close relationships to other nematode species obtained from GenBank. Finally, our study recommends using molecular analysis in helminths identification as the main methodology for correct identification especially in closely related species.
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Affiliation(s)
- M. A. Aldamigh
- Department of Biology, College of Science, Majmaah University, Majmaah11952, Saudi Arabia
| | - A. A. Alahmadi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah21589, Saudi Arabia
| | - I. M. Al-Turaiki
- Department of Computer Science, College of Computer and information Sciences, King Saud University, Riyadh11653, Saudi Arabia
| | - A. H. Hassan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah21589, Saudi Arabia
- Zoology Department, Faculty of Science, Sohag University, Sohag52824, Egypt
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Huo C, Bao F, Long H, Qin T, Zhang S. The complete mitochondrial genome of Wellcomia compar (Spirurina: Oxyuridae) and its genome characterization and phylogenetic analysis. Sci Rep 2023; 13:14426. [PMID: 37660220 PMCID: PMC10475117 DOI: 10.1038/s41598-023-41638-9] [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: 03/27/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023] Open
Abstract
Wellcomia compar (Spirurina: Oxyuridae) is a pinworm that infects wild and captive porcupines. Despite clear records of its morphological structure, its genetics, systematics, and biology are poorly understood. This study aimed to determine the complete mitochondrial (mt) genome of W. compar and reconstruct its phylogenetic relationship with other nematodes. We sequenced the complete mt genome of W. comparand conducted phylogenetic analyses using concatenated coding sequences of 12 protein-coding genes (PCGs) by maximum likelihood and Bayesian inference. The complete mt genome is 14,373 bp in size and comprises 36 genes, including 12 protein-coding, two rRNA and 22 tRNA genes. Apart from 28 intergenic regions, one non-coding region and one overlapping region also occur. A comparison of the gene arrangements of Oxyuridomorpha revealed relatively similar features in W. compar and Wellcomia siamensis. Phylogenetic analysis also showed that W. compar and W. siamensis formed a sister group. In Oxyuridomorpha the genetic distance between W. compar and W. siamensis was 0.0805. This study reports, for the first time, the complete W. compar mt genome sequence obtained from Chinese porcupines. It provides genetic markers for investigating the taxonomy, population genetics, and phylogenetics of pinworms from different hosts and has implications for the diagnosis, prevention, and control of parasitic diseases in porcupines and other animals.
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Affiliation(s)
- Chunmao Huo
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Fengyun Bao
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Hong Long
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Tingyang Qin
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Shibin Zhang
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China.
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Zhang Y, Wang LD, Hasegawa K, Nagae S, Chen HX, Li LW, Li L. Molecular identification of a new species of Rhigonema (Nematoda: Rhigonematidae) and phylogenetic relationships within the infraorder Rhigonematomorpha. Parasit Vectors 2022; 15:427. [PMID: 36380389 PMCID: PMC9664589 DOI: 10.1186/s13071-022-05544-9] [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: 08/18/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Background The infraorder Rhigonematomorpha comprises a group of obligate parasitic nematodes of millipedes (Arthropoda: Diplopoda). The current species identification of Rhigonematomorpha nematodes remains mainly based on morphological features, with molecular-based identification still in its infancy. Also, current knowledge of the phylogeny of Rhigonematomorpha is far from comprehensive. Methods The morphology of Rhigonematomorpha nematodes belonging to the genus Rhigonema, collected from the millipede Spirobolus bungii Brandt (Diplopoda: Spirobolida) in China, was studied in detail using light and scanning electron microscopy. Five different genetic markers, including the nuclear small ribosomal subunit (18S), internal transcribed spacer (ITS) and large ribosomal subunit (28S) regions and the mitochondrial cox1 and cox2 genes of these Rhigonematomorpha nematodes collected from China and Rhigonema naylae collected from Japan were sequenced and analyzed using Bayesian inference (BI) and Assemble Species by Automatic Partitioning (ASAP) methods. Phylogenetic analyses that included the most comprehensive taxa sampling of Rhigonematomorpha to date were also performed based on the 18S + 28S genes using maximum likelihood (ML) and BI methods. Results The specimens of Rhigonema collected from S. bungii in China were identified as a new species, Rhigonema sinense n. sp. Striking variability in tail morphology was observed among individuals of R. sinense n. sp. ASAP analyses based on the 28S, ITS, cox1 and cox2 sequences supported the species partition of R. sinense n. sp. and R. naylae, but showed no evidence that the different morphotypes of R. sinense n. sp. represent distinct genetic lineages. BI analyses also indicated that R. sinense n. sp. represents a separated species from R. naylae based on the cox1 and cox2 genes, but showed that R. naylae nested in samples of R. sinense n. sp. based on the ITS and 28S data. Phylogenetic results showed that the representatives of Rhigonematomorpha formed two large clades. The monophyly of the families Carnoyidae and Ichthyocephalidae and the genus Rhigonema was rejected. The representatives of the family Ransomnematidae clustered together with the family Hethidae with strong support. Conclusions A new species of Rhigonematomorpha, R. sinense n. sp. is described based on morphological and molecular evidence. ASAP analyses using 28S, ITS, cox1 and cox2 data indicate the striking variability in tail morphology of R. sinense n. sp. as intraspecific variation, and also suggest that partial 28S, ITS, cox1 and cox2 markers are effective for molecular identification of Rhigonematomorpha nematodes. The phylogenetic results support the traditional classification of Rhigonematomorpha into the two superfamilies Rhigonematoidea and Ransomnematoidea, and indicate that the families Carnoyidae and Ichthyocephalidae and the genus Rhigonema are non-monophyletic. The present phylogeny strongly supports resurrection of the family Brumptaemiliidae, and also indicates that the family Ransomnematidae is sister to the family Hethidae. Graphical Abstract ![]()
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HODDA M. Phylum Nematoda: a classification, catalogue and index of valid genera, with a census of valid species. Zootaxa 2022; 5114:1-289. [DOI: 10.11646/zootaxa.5114.1.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 11/04/2022]
Abstract
A classification of the entire Phylum Nematoda is presented, based on current molecular, developmental and morphological evidence. The classification reflects the evolutionary relationships within the phylum, as well as significant areas of uncertainty, particularly related to the early evolution of nematodes. It includes 3 classes, 8 subclasses, 12 superorders, 32 orders, 53 suborders, 101 superfamilies, 276 families, 511 subfamilies, 3030 genera, and 28537 species. All valid species named from the time of publication of the previous classification and census (2010) to the end of 2019 are listed, along with the number of valid species in each genus. Taxonomic authorities are provided for taxon names of all ranks. The habitats where the species in each genus are found are listed, and an alphabetic index of genus names is provided. The systematics of nematodes is reviewed, along with a history of nematode classification; evolutionary affinities and origins of nematodes; and the current diagnosis of the group. Short overviews of the general biology, ecology, scientific and economic importance of the group are presented.
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Nagae S, Sato K, Tanabe T, Hasegawa K. Symbiosis of the millipede parasitic nematodes Rhigonematoidea and Thelastomatoidea with evolutionary different origins. BMC Ecol Evol 2021; 21:120. [PMID: 34118872 PMCID: PMC8199837 DOI: 10.1186/s12862-021-01851-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 06/04/2021] [Indexed: 11/15/2022] Open
Abstract
Background How various host–parasite combinations have been established is an important question in evolutionary biology. We have previously described two nematode species, Rhigonema naylae and Travassosinema claudiae, which are parasites of the xystodesmid millipede Parafontaria laminata in Aichi Prefecture, Japan. Rhigonema naylae belongs to the superfamily Rhigonematoidea, which exclusively consists of parasites of millipedes. T. claudiae belongs to the superfamily Thelastomatoidea, which includes a wide variety of species that parasitize many invertebrates. These nematodes were isolated together with a high prevalence; however, the phylogenetic, evolutionary, and ecological relationships between these two parasitic nematodes and between hosts and parasites are not well known. Results We collected nine species (11 isolates) of xystodesmid millipedes from seven locations in Japan, and found that all species were co-infected with the parasitic nematodes Rhigonematoidea spp. and Thelastomatoidea spp. We found that the infection prevalence and population densities of Rhigonematoidea spp. were higher than those of Thelastomatoidea spp. However, the population densities of Rhigonematoidea spp. were not negatively affected by co-infection with Thelastomatoidea spp., suggesting that these parasites are not competitive. We also found a positive correlation between the prevalence of parasitic nematodes and host body size. In Rhigonematoidea spp., combinations of parasitic nematode groups and host genera seem to be fixed, suggesting the evolution of a more specialized interaction between Rhigonematoidea spp. and their host. On the other hand, host preference of Thelastomatoidea spp. was not specific to any millipede species, indicating a non-intimate interaction between these parasites and their hosts. Conclusions The two nematode superfamilies, Rhigonematoidea and Thelastomatoidea, have phylogenetically distinct origins, and might have acquired xystodesmid millipede parasitism independently. Currently, the two nematodes co-parasitize millipedes without any clear negative impact on each other or the host millipedes. Our study provides an example of balanced complex symbioses among parasitic nematodes and between parasitic nematodes and host millipedes, which have been established over a long evolutionary history. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01851-4.
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Affiliation(s)
- Seiya Nagae
- Department of Environmental Biology, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto, Kasugai, Aichi, 487-8501, Japan
| | - Kazuki Sato
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tsutomu Tanabe
- Faculty of Advanced Science and Technology, Kumamoto University, 2-40-1 Kurokami, Kumamoto, 860-8555, Japan
| | - Koichi Hasegawa
- Department of Environmental Biology, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto, Kasugai, Aichi, 487-8501, Japan.
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Deng YP, Zhang XL, Li LY, Yang T, Liu GH, Fu YT. Characterization of the complete mitochondrial genome of the swine kidney worm Stephanurus dentatus (Nematoda: Syngamidae) and phylogenetic implications. Vet Parasitol 2021; 295:109475. [PMID: 34062343 DOI: 10.1016/j.vetpar.2021.109475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 11/26/2022]
Abstract
Swine stephanuriasis caused by kidney worm Stephanurus dentatus is a parasitic disease in tropical and subtropical countries, leading to economic losses. Despite its significance as a pathogen, the phylogenetic position and taxonomic status of this nematode remain poorly understood. Mitochondrial (mt) genome sequences are known to provide useful genetic markers for investigations in these areas, but mt genome sequences are lacking for S. dentatus. In the present study, we determined the complete mt genome sequences of S. dentatus with an Illumina platform and compared it with the mt genomes of other closely related species. The circular mt genome was 13,735 bp in size with 36 genes. All genes are transcribed in the same direction and the mt gene arrangement is identified as a GA3 pattern, that is the most common pattern of gene arrangement observed in nematodes to date. Phylogenetic analysis using concatenated amino acid sequences of 12 protein-coding genes supported the hypothesis that S. dentatus was closely related to the family Chabertiidae. Our results provided insights into the phylogenetic relationship of the family Syngamidae within the superfamily Strongyloidea.
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Affiliation(s)
- Yuan-Ping Deng
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Xue-Ling Zhang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Le-Yan Li
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Tian Yang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Guo-Hua Liu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China; Hunan Co-Innovation Center of Animal Production Safety, Changsha, Hunan Province, 410128, China.
| | - Yi-Tian Fu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China.
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Kim T, Lee Y, Kil HJ, Park JK. The mitochondrial genome of Acrobeloides varius (Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda). PeerJ 2020; 8:e9108. [PMID: 32440374 PMCID: PMC7229770 DOI: 10.7717/peerj.9108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023] Open
Abstract
The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.
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Affiliation(s)
- Taeho Kim
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Yucheol Lee
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Hyun-Jong Kil
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
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Morphological and Molecular Characteristics of the Gastro-Intestinal Nematode Parasite Ascaridia columbae Infecting the Domestic Pigeon Columba livia domestica in Saudi Arabia. Acta Parasitol 2020; 65:208-224. [PMID: 31832920 DOI: 10.2478/s11686-019-00151-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 11/25/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND Parasitism is a complex problem that is often ignored in companion animals, including birds, unless it develops into a severe clinical disorder. The present study was, therefore, aimed to investigate the presence of the gastrointestinal nematode infecting the domestic pigeon and provide a complete morphological description and clarify its taxonomic position through phylogenetic analysis of the ITS1-5.8s-ITS2 rDNA gene region. MATERIALS AND METHODS During the current study, a total of twenty-six domestic pigeons, Columba livia domestica, were collected and internal organs examined for helminth detection. Using light and scanning electron microscopy, the recovered parasite species are studied. In addition, the selected gene region was obtained and sequenced using appropriate primers that aid in the formation of the phylogenetic dendrogram for the recovered parasite species with others retrieved from GenBank. RESULTS Morphological examination showed that this nematode parasite belongs to the Ascaridiidae family within the genus Ascaridia. The material was assigned to the previously described Ascaridia columbae by providing all the characteristic features as the presence of a mouth opening surrounded by three tri-lobed lips; each lip has two triangular teeth with a spoon-like structure, cephalic papillae and amphidal pores on lips surface, presence of lateral cuticular alae and pre-cloacal sucker, 10 pairs of caudal papillae, and two equal spicules in male worms. The morphological investigations of this species were supplemented by molecular analysis of ITS1-5.8s-ITS2 rDNA gene region. The data showed that the present A. coulmbae is deeply embedded in the Ascaridia genus with a 74-99% sequence similarity to other species in the Chromadorea class. Ascaridiidae appears as monophyly and represented as a sister group to Heterakidae. The ascaridiid species examined belong to the Ascaridia genus and displaced a close relationship with the previously described A. coulmbae (gb| KF147909.1, gb| AJ001509.1, gb| KC905082.1, gb| JQ995321.1, gb| JX624729.1) as putative sister taxa. CONCLUSION The present study revealed that the species Ascaridia is the first account of this genus as an endoparasite from the domestic pigeon inhabiting Saudi Arabia. Therefore, the combination of morphological and molecular studies helps to identify this species correctly and identified as Ascaridia columbae.
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Prevalence, Morphological and Molecular Phylogenetic Analyses of the Rabbit Pinworm, Passalurus ambiguus Rudolphi 1819, in the Domestic Rabbits Oryctolagus cuniculus. Acta Parasitol 2019; 64:316-330. [PMID: 30941669 DOI: 10.2478/s11686-019-00047-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/12/2019] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Passalurus ambiguus, a pinworm nematode parasite, infects domestic and wild rabbits, hares, and rodents worldwide. MATERIALS AND METHODS The current parasitological study was performed during January-December 2016, to investigate helminth parasites infecting the domestic rabbit species Oryctolagus cuniculus at the Department of Animal Production, Faculty of Agriculture, Cairo University, Cairo, Egypt. RESULTS Of the twenty rabbit specimens examined for gastrointestinal nematodes, 75% were infected with adult oxyurid species, which were morphologically characterized using light and scanning electron microscopy studies. The oxyurid species had a triangular mouth opening surrounded by simple lips with four cephalic papillae and a pair of lateral amphidial pores with three teeth-like structures, an esophagus divided into a cylindrical corpus and globular bulb supported internally with tri-radiate valvular apparatus, and four caudal papillae distributed on the posterior end of males with a single short protruding spicule and ovijector apparatus opening ventrally by the vulva, surrounded by protruded lips in female worms. The species were compared morphometrically with other Passalurus species described previously; light differences were found in different body part sizes. Molecular characterization based on 18 small subunit (SSU) rDNA sequences showed ~ 85% similarity with other Chromadorea species. A preliminary genetic comparison between the 18S rDNA sequences of the isolated parasite and those of other oxyurid species suggested that it belonged to Passalurus ambiguus. The 18S rDNA sequence of the parasite was deposited in GenBank (accession no., MG310151.1). CONCLUSION The 18S rDNA gene of P. ambiguus was shown to yield a unique genetic sequence that confirms its taxonomic position within the Oxyuridae family.
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According to mitochondrial DNA evidence, Parascaris equorum and Parascaris univalens may represent the same species. J Helminthol 2018; 93:383-388. [DOI: 10.1017/s0022149x18000330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractParascarosis is caused mainly by parasitic infections with Parascaris equorum and Parascaris univalens, the most common ascarid nematodes, in the small intestine of equines. Parascarosis often causes severe illness and even death in foals and yearlings. In this study, we obtained the complete sequence of the P. equorum mitochondrial (mt) genome and compared its organization and structure with that of P. equorum Japan isolate (nearly complete), and the complete mtDNA sequences of P. univalens Switzerland and USA isolates. The complete mtDNA genome of P. equorum China isolate is 13,899 base pairs (bp), making it the smallest of the four genomes. All four Parascaris mt genomes are circular, and all genes are transcribed in the same direction. The P. equorum mtDNA genome consists of 12 protein-coding genes, two ribosomal RNA genes, 22 transfer (t) RNA genes and one non-coding region, which is consistent with P. equorum Japan isolate and P. univalens Switzerland isolate but distinct from P. univalens USA isolate, which has 20 tRNA genes. Differences in nucleotide sequences of the four entire mt genomes range from 0.1–0.9%, and differences in total amino acid sequences of protein-coding genes are 0.2–2.1%. Phylogenetic analyses showed that the four Parascaris species clustered in a clade, indicating that P. equorum and P. univalens are very closely related. These mt genome datasets provide genetic evidence that P. equorum and P. univalens may represent the same species, which will be of use in further studies of the taxonomy, systematics and population genetics of ascarids and other nematodes.
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Kim T, Kern E, Park C, Nadler SA, Bae YJ, Park JK. The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda). Sci Rep 2018; 8:7482. [PMID: 29749383 PMCID: PMC5945635 DOI: 10.1038/s41598-018-25759-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/27/2018] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial genes and whole mitochondrial genome sequences are widely used as molecular markers in studying population genetics and resolving both deep and shallow nodes in phylogenetics. In animals the mitochondrial genome is generally composed of a single chromosome, but mystifying exceptions sometimes occur. We determined the complete mitochondrial genome of the millipede-parasitic nematode Ruizia karukerae and found its mitochondrial genome consists of two circular chromosomes, which is highly unusual in bilateral animals. Chromosome I is 7,659 bp and includes six protein-coding genes, two rRNA genes and nine tRNA genes. Chromosome II comprises 7,647 bp, with seven protein-coding genes and 16 tRNA genes. Interestingly, both chromosomes share a 1,010 bp sequence containing duplicate copies of cox2 and three tRNA genes (trnD, trnG and trnH), and the nucleotide sequences between the duplicated homologous gene copies are nearly identical, suggesting a possible recent genesis for this bipartite mitochondrial genome. Given that little is known about the formation, maintenance or evolution of abnormal mitochondrial genome structures, R. karukerae mtDNA may provide an important early glimpse into this process.
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Affiliation(s)
- Taeho Kim
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Elizabeth Kern
- Division of EcoScience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Steven A Nadler
- Department of Entomology and Nematology, University of California, Davis, CA, 95616, USA
| | - Yeon Jae Bae
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, Seoul, 03760, Republic of Korea.
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Mejia-Madrid HH. A molecular phylogeny of the Rhigonematomorpha De Ley & Blaxter, 2002 as inferred from SSU and LSU rDNA sequences. NEMATOLOGY 2018. [DOI: 10.1163/15685411-00003161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
A molecular hypothesis of the Infraorder Rhigonematomorpha is presented. The phylogeny recovered using combined SSU and LSU markers suggests that the Rhigonematomorpha is nested within a larger clade that includes Ascaridomorpha, Spiruromorpha and Oxyuridomorpha and is strongly supported by maximum likelihood (ML) bootstrap support values (BS) and Bayesian posterior probabilities (BPP). SSU and LSU ML and Bayesian analyses recovered Rhigonematomorpha as a paraphyletic clade. In the ML and Bayesian analyses of a combined matrix of complete to partial sequences of SSU and LSU, respectively, Rhigonematomorpha is recovered as a monophyletic clade with moderate BPP but low BS. Highly supported BS and BPP of a combined SSU and LSU matrix support a hypothesis of a monophyletic Superfamily Ransomnematoidea that includes the families Carnoyidae, Hethidae, Ransomnematidae plus a Brumptaemilius, Cattiena, Insulanema clade, and a monophyletic Superfamily Rhigonematoidea that probably includes the paraphyletic families Rhigonematidae and Ichthyocephalidae. It is suggested that the future inclusion of more families and genera might help resolve the monophyly of the Infraorder Rhigonematomorpha as advanced here.
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Affiliation(s)
- Hugo H. Mejia-Madrid
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, UNAM, México D.F. C.P. 04510, Mexico
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Kim J, Kern E, Kim T, Sim M, Kim J, Kim Y, Park C, Nadler SA, Park JK. Phylogenetic analysis of two Plectus mitochondrial genomes (Nematoda: Plectida) supports a sister group relationship between Plectida and Rhabditida within Chromadorea. Mol Phylogenet Evol 2017; 107:90-102. [DOI: 10.1016/j.ympev.2016.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/08/2016] [Accepted: 10/11/2016] [Indexed: 11/28/2022]
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15
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Liu GH, Nadler SA, Liu SS, Podolska M, D'Amelio S, Shao R, Gasser RB, Zhu XQ. Mitochondrial Phylogenomics yields Strongly Supported Hypotheses for Ascaridomorph Nematodes. Sci Rep 2016; 6:39248. [PMID: 27982084 PMCID: PMC5159812 DOI: 10.1038/srep39248] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/10/2016] [Indexed: 12/03/2022] Open
Abstract
Ascaridomorph nematodes threaten the health of humans and other animals worldwide. Despite their medical, veterinary and economic importance, the identification of species lineages and establishing their phylogenetic relationships have proved difficult in some cases. Many working hypotheses regarding the phylogeny of ascaridomorphs have been based on single-locus data, most typically nuclear ribosomal RNA. Such single-locus hypotheses lack independent corroboration, and for nuclear rRNA typically lack resolution for deep relationships. As an alternative approach, we analyzed the mitochondrial (mt) genomes of anisakids (~14 kb) from different fish hosts in multiple countries, in combination with those of other ascaridomorphs available in the GenBank database. The circular mt genomes range from 13,948-14,019 bp in size and encode 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNA genes. Our analysis showed that the Pseudoterranova decipiens complex consists of at least six cryptic species. In contrast, the hypothesis that Contracaecum ogmorhini represents a complex of cryptic species is not supported by mt genome data. Our analysis recovered several fundamental and uncontroversial ascaridomorph clades, including the monophyly of superfamilies and families, except for Ascaridiidae, which was consistent with the results based on nuclear rRNA analysis. In conclusion, mt genome analysis provided new insights into the phylogeny and taxonomy of ascaridomorph nematodes.
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Affiliation(s)
- Guo-Hua Liu
- 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 Province 730046, P. R. China.,College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, P. R. China
| | - Steven A Nadler
- Department of Entomology and Nematology, University of California, Davis, CA 95616, USA
| | - Shan-Shan Liu
- 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 Province 730046, P. R. China
| | - Magdalena Podolska
- National Marine Fisheries Research Institute, Kollataja 1, 81-332 Gdynia, Poland
| | - Stefano D'Amelio
- Department of Public Health and Infectious Diseases, Section of Parasitology, Sapienza University of Rome, Rome, Italy
| | - Renfu Shao
- Genecology Research Centre, University of the Sunshine Coast, Queensland 4558, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - 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 Province 730046, P. R. China.,College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, P. R. China
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16
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Wang BJ, Gu XB, Yang GY, Wang T, Lai WM, Zhong ZJ, Liu GH. Mitochondrial genomes of Heterakis gallinae and Heterakis beramporia support that they belong to the infraorder Ascaridomorpha. INFECTION GENETICS AND EVOLUTION 2016; 40:228-235. [PMID: 26980606 DOI: 10.1016/j.meegid.2016.03.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 01/29/2016] [Accepted: 03/11/2016] [Indexed: 11/30/2022]
Abstract
Heterakis gallinae and Heterakis beramporia are the most prevalent nematode infecting native chicken breed, causing major economic losses. In the present study, the complete mitochondrial genomes (mt) of H. gallinae and H. beramporia were amplified by long-PCR and then sequenced. The complete mt genomes of H. gallinae and H. beramporia were 13,973bp and 14,012bp in size, respectively. Both mt genomes contain 12 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. All genes are transcribed in the same direction and the gene arrangement is identical to Ascaridia spp. Phylogenetic analysis based on the 12 protein-coding genes revealed that the family Heterakidae (represented by H. gallinae and H. beramporia) was more closely related to the infraorder Ascaridomorpha than it was to the infraorder Oxyuridomorpha. The present study determined the complete mt genome sequences for two Heterakis species, providing useful markers for studying the systematics, population genetics, and molecular epidemiology of these Heterakis parasites.
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Affiliation(s)
- Bao-Jian Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province 611133, PR China
| | - Xiao-Bin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province 611133, PR China.
| | - Guang-You Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province 611133, PR China
| | - Tao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province 611133, PR China
| | - Wei-Min Lai
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province 611133, PR China
| | - Zhi-Jun Zhong
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province 611133, PR China
| | - Guo-Hua Liu
- 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 Province 730046, PR China
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17
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Kim T, Kim J, Nadler SA, Park JK. The complete mitochondrial genome of Koerneria sudhausi (Diplogasteromorpha: Nematoda) supports monophyly of Diplogasteromorpha within Rhabditomorpha. Curr Genet 2015; 62:391-403. [PMID: 26581631 DOI: 10.1007/s00294-015-0536-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/29/2015] [Accepted: 10/30/2015] [Indexed: 11/29/2022]
Abstract
Testing hypotheses of monophyly for different nematode groups in the context of broad representation of nematode diversity is central to understanding the patterns and processes of nematode evolution. Herein sequence information from mitochondrial genomes is used to test the monophyly of diplogasterids, which includes an important nematode model organism. The complete mitochondrial genome sequence of Koerneria sudhausi, a representative of Diplogasteromorpha, was determined and used for phylogenetic analyses along with 60 other nematode species. The mtDNA of K. sudhausi is comprised of 16,005 bp that includes 36 genes (12 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) encoded in the same direction. Phylogenetic trees inferred from amino acid and nucleotide sequence data for the 12 protein-coding genes strongly supported the sister relationship of K. sudhausi with Pristionchus pacificus, supporting Diplogasteromorpha. The gene order of K. sudhausi is identical to that most commonly found in members of the Rhabditomorpha + Ascaridomorpha + Diplogasteromorpha clade, with an exception of some tRNA translocations. Both the gene order pattern and sequence-based phylogenetic analyses support a close relationship between the diplogasterid species and Rhabditomorpha. The nesting of the two diplogasteromorph species within Rhabditomorpha is consistent with most molecular phylogenies for the group, but inconsistent with certain morphology-based hypotheses that asserted phylogenetic affinity between diplogasteromorphs and tylenchomorphs. Phylogenetic analysis of mitochondrial genome sequences strongly supports monophyly of the diplogasteromorpha.
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Affiliation(s)
- Taeho Kim
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, Republic of Korea
| | - Jiyeon Kim
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 120-750, Republic of Korea
| | - Steven A Nadler
- Department of Entomology and Nematology, University of California, Davis, CA, 95616, USA
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 120-750, Republic of Korea.
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18
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The complete mitochondrial genome of rabbit pinworm Passalurus ambiguus: genome characterization and phylogenetic analysis. Parasitol Res 2015; 115:423-9. [PMID: 26472717 DOI: 10.1007/s00436-015-4778-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/06/2015] [Indexed: 01/13/2023]
Abstract
Passalurus ambiguus (Nematda: Oxyuridae) is a common pinworm which parasitizes in the caecum and colon of rabbits. Despite its significance as a pathogen, the epidemiology, genetics, systematics, and biology of this pinworm remain poorly understood. In the present study, we sequenced the complete mitochondrial (mt) genome of P. ambiguus. The circular mt genome is 14,023 bp in size and encodes of 36 genes, including 12 protein-coding, two ribosomal RNA, and 22 transfer RNA genes. The mt gene order of P. ambiguus is the same as that of Wellcomia siamensis, but distinct from that of Enterobius vermicularis. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes by Bayesian inference (BI) showed that P. ambiguus was more closely related to W. siamensis than to E. vermicularis. This mt genome provides novel genetic markers for studying the molecular epidemiology, population genetics, systematics of pinworm of animals and humans, and should have implications for the diagnosis, prevention, and control of passaluriasis in rabbits and other animals.
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Xu WW, Qiu JH, Liu GH, Zhang Y, Liu ZX, Duan H, Yue DM, Chang QC, Wang CR, Zhao XC. The complete mitochondrial genome of Strongylus equinus (Chromadorea: Strongylidae): Comparison with other closely related species and phylogenetic analyses. Exp Parasitol 2015; 159:94-9. [PMID: 26366671 DOI: 10.1016/j.exppara.2015.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 07/14/2015] [Accepted: 08/16/2015] [Indexed: 11/25/2022]
Abstract
The roundworms of genus Strongylus are the common parasitic nematodes in the large intestine of equine, causing significant economic losses to the livestock industries. In spite of its importance, the genetic data and epidemiology of this parasite are not entirely understood. In the present study, the complete S. equinus mitochondrial (mt) genome was determined. The length of S. equinus mt genome DNA sequence is 14,545 bp, containing 36 genes, of which 12 code for protein, 22 for transfer RNA, and two for ribosomal RNA, but lacks atp8 gene. All 36 genes are encoded in the same direction which is consistent with all other Chromadorea nematode mtDNAs published to date. Phylogenetic analysis based on concatenated amino acid sequence data of all 12 protein-coding genes showed that there were two large branches in the Strongyloidea nematodes, and S. equinus is genetically closer to S. vulgaris than to Cylicocyclus insignis in Strongylidae. This new mt genome provides a source of genetic markers for the molecular phylogeny and population genetics of equine strongyles.
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Affiliation(s)
- Wen-Wen Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Jian-Hua Qiu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Guo-Hua Liu
- 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 Province 730046, PR China
| | - Yan Zhang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Ze-Xuan Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Hong Duan
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Dong-Mei Yue
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Qiao-Cheng Chang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Chun-Ren Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China.
| | - Xing-Cun Zhao
- Animal and Plant Department, Quanzhou Entry-Exit Inspection and Quarantine Bureau, Quanzhou, Fujian Province, 362000, PR China.
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20
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Gnathostoma spinigerum Mitochondrial Genome Sequence: a Novel Gene Arrangement and its Phylogenetic Position within the Class Chromadorea. Sci Rep 2015; 5:12691. [PMID: 26228511 PMCID: PMC4521153 DOI: 10.1038/srep12691] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/06/2015] [Indexed: 01/21/2023] Open
Abstract
Human gnathostomiasis is an emerging food-borne parasitic disease caused by nematodes in the genus Gnathostoma. In spite of their significance as pathogens, these parasites remain poorly understood at the molecular level. In the present study, we sequenced the mitochondrial (mt) genome of G. spinigerum, which infects a range of definitive hosts including dogs, cats, tigers, leopards and humans. The mt genome of G. spinigerum is 14,079 bp in size and shows substantial changes in gene order compared to other nematodes studied to date. Phylogenetic analyses of mt genome sequences by Bayesian inference (BI) revealed that the infraorder Gnathostomatomorpha (represented by G. spinigerum) is closely related to the infraorder Ascaridomorpha. G. spinigerum is the first species from the infraorder Gnathostomatomorpha for which a complete mt genome has been sequenced. The new data will help understand the evolution, population genetics and systematics of this medically important group of parasites.
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21
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Kim J, Lee SH, Gazi M, Kim T, Jung D, Chun JY, Kim S, Seo TK, Park C, Baldwin JG, Nadler SA, Park JK. Mitochondrial genomes advance phylogenetic hypotheses for Tylenchina (Nematoda: Chromadorea). ZOOL SCR 2015. [DOI: 10.1111/zsc.12112] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiyeon Kim
- Program in Cell Biology and Genetics; College of Medicine; Chungbuk National University; Cheongju 361-763 Korea
| | - Sang-Hwa Lee
- Program in Cell Biology and Genetics; College of Medicine; Chungbuk National University; Cheongju 361-763 Korea
| | - Mohiuddin Gazi
- Program in Cell Biology and Genetics; College of Medicine; Chungbuk National University; Cheongju 361-763 Korea
| | - Taeho Kim
- Program in Cell Biology and Genetics; College of Medicine; Chungbuk National University; Cheongju 361-763 Korea
| | - Daewui Jung
- Program in Cell Biology and Genetics; College of Medicine; Chungbuk National University; Cheongju 361-763 Korea
| | - Jae-Yong Chun
- Plant Quarantine Technology Center; Animal and Plant Quarantine Agency; Suwon 443-400 Korea
| | - Sanghee Kim
- Korea Polar Research Institute; 26 Songdomirae-ro Yeonsu-gu Incheon 406-840 Korea
| | - Tae-Kun Seo
- Korea Polar Research Institute; 26 Songdomirae-ro Yeonsu-gu Incheon 406-840 Korea
| | - Chungoo Park
- School of Biological Sciences and Technology; Chonnam National University; Gwangju 500-757 Korea
| | - James G. Baldwin
- Department of Nematology; University of California; Riverside CA 92521 USA
| | - Steven A. Nadler
- Department of Entomology and Nematology; University of California; Davis CA 95616 USA
| | - Joong-Ki Park
- Division of EcoScience; Ewha Womans University; 52 Ewhayeodae-gil Seodaemun-gu Seoul 120-750 Korea
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