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Deng YP, Suleman, Zhang XL, Li R, Li LY, Fu YT, Liu GH, Yao C. Aonchotheca (Nematoda: Capillariidae) is validated as a separated genus from Capillaria by both mitochondrial and nuclear ribosomal DNA. Parasit Vectors 2022; 15:493. [PMID: 36585724 PMCID: PMC9805247 DOI: 10.1186/s13071-022-05609-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/03/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The family Capillariidae is a group of thread-like nematodes of 27 genera and over 300 species that infect a great variety of hosts including humans. Among these, some taxa such as the genus Aonchotheca have remained controversial regarding their systematic status for decades. The aim of the current study was to verify Aonchotheca's systemic status and to further determine whether it is a distinct genus from Capillaria using molecular and phylogenetic analyses. RESULTS We sequenced the mitochondrial (mt) genome and nuclear small subunit (18S) rRNA gene of Aonchotheca putorii, a representative species of the genus, and investigated its systematic status in Trichinellida using maximum likelihood and Bayesian inference. The differences in amino acid sequences of 13 protein-coding genes were 12.69-67.35% among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillaria with cox1 (12.69%) and atp8 (67.35%) as the most and the least conserved gene, respectively, and the difference of two mt rRNAs was 18.61-34.15%. Phylogenetic analyses of the complete mt genome and 18S rRNAs unequivocally showed that Aonchotheca was a distinct genus from Capillaria. CONCLUSIONS Large difference exists among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillarias. Aonchotheca putorii is the first species in the genus Aonchotheca for which a complete mitogenome has been sequenced. These data are useful for phylogenetics, systematics and the evolution of Capillariidae.
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Affiliation(s)
- Yuan-Ping Deng
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Suleman
- grid.502337.00000 0004 4657 4747Department of Zoology, University of Swabi, Swabi, 23561 Khyber Pakhtunkhwa Pakistan
| | - Xue-Ling Zhang
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Rong Li
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Le-Yan Li
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Yi-Tian Fu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Guo-Hua Liu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Chaoqun Yao
- grid.412247.60000 0004 1776 0209Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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Wu T, Ma X, Wang F, Xie L, Lv Q, Zeng M, Xu Y, Qin S, Chang Q. First Description of the Mitogenome Features of Neofoleyellides Genus (Nematoda: Onchocercidae) Isolated from a Wild Bird (Pyrrhocorax pyrrhocorax). Animals (Basel) 2022; 12:ani12202854. [PMID: 36290239 PMCID: PMC9597759 DOI: 10.3390/ani12202854] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Filarioidea, a superfamily of nematodes, presently includes 42 species divided into six genera, mainly in the family Onchocercidae, which have been reported to infect a wide range of hosts, including reptiles, birds, and mammals. Current limitations in molecular characterization methods and species identification are the main obstacles to a better understanding of the biology of Onchocercidae species, particularly in wildlife. Thus, the objective of the present study was to sequence and analyze the complete mt genome of Neofoleyellides sp. isolated from a wild bird (Pyrrhocorax pyrrhocorax) and to assess its phylogenetic position in the Onchocercidae family. The evaluated Neofoleyellides sp. mt genome was consistent with the molecular pattern of the Onchocercidae family: 36 subunits consisting of 12 PCGs, 2 rRNAs, and 22 tRNAs. Phylogenetic analyses based on the 18S rRNA gene, cox1 gene, and 12 PCGs showed consistent results, which strongly supported monophyly of the genus Neofoleyellides. These findings enriched the gene database and improved our knowledge of the molecular characteristics of the Onchocercidae family, which provide useful genetic markers to study the population genetics, molecular biology, and phylogenetics of these Onchocercidae nematodes. Abstract The Onchocercidae family is composed of more than 30 valid nematode species with notable zoonotic potential. Current limitations in molecular characterization methods and species identification are the main obstacles to a better understanding of the biology of Onchocercidae species, particularly in wildlife. This study describes for the first time the complete mitochondrial (mt) genome sequence of Neofoleyellides sp. isolated from a wild bird (Pyrrhocorax pyrrhocorax) and belonging to the Neofoleyellides genus (Nematoda: Onchocercidae). The mt genome of Neofoleyellides sp. (GenBank accession number: ON641583) was a typical circular DNA molecule of 13,628 bp in size with an AT content of 76.69%. The complete mt genome comprised 36 functional subunits, including 12 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. The most common start codon was ATT/ATG except for nad2 with TTG, and TAA was the termination codon for all protein-coding genes (PCGs). Phylogenetic analysis of the concatenated and aligned amino acid sequences of the 12 PCGs showed that the trees generated using different methods (Bayesian inference and maximum likelihood) with different partition schemes shared similar topologies. The isolated Neofoleyellides sp. was placed in the Onchocercidae family and formed a sister branch with the genera Onchocerca and Dirofilaria. The entire mt genome of Neofoleyellides sp. presented in this study could provide useful data for studying the population genetics and phylogenetic relationships of Onchocercidae species.
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Affiliation(s)
- Tingting Wu
- School of Public Health, Shantou University, Shantou 515063, China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaoxiao Ma
- School of Public Health, Shantou University, Shantou 515063, China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Fengfeng Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Linhong Xie
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Qingbo Lv
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Minhao Zeng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Yu Xu
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Siyuan Qin
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Qiaocheng Chang
- School of Public Health, Shantou University, Shantou 515063, China
- Correspondence:
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Kim KS, Kang DW, Kim KY, Heo JS, Song HY, Yoon JD. Characterization of the complete mitogenome of the endangered freshwater fish Gobiobotia naktongensis from the Geum River in South Korea: evidence of stream connection with the Paleo-Huanghe. Genes Genomics 2022; 44:945-956. [PMID: 35674881 PMCID: PMC9273560 DOI: 10.1007/s13258-022-01265-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/03/2022] [Indexed: 11/27/2022]
Abstract
Background The freshwater fish Gobiobotia naktongensis (Teleostei, Cypriniformes, and Gobionidae) is an endangered class I species whose population size has been greatly reduced. Objective To successfully protect and restore the highly endangered freshwater fish G. naktongensis from the Geum River in South Korea. Methods The mitogenome was characterized using the primer walking method with phylogenetic relationships. Results The complete mitogenome of G. naktongensis Geum River was 16,607 bp, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA (tRNA) genes. Seventeen substitutions were found by comparing the tRNA regions between G. naktongensis Geum and Nakdong Rivers and G. pappenheimi; most were specific to G. naktongensis Nakdong River, with changes in their secondary structures. The comparison between G. naktongensis Geum River and G. pappenheimi revealed differences in the lengths of the D-loop and two tRNAs (tRNAArg and tRNATrp) and the secondary structures in the TΨC-arm of tRNAHis. In the phylogenetic tree, G. naktongensis Geum River did not cluster with its conspecific specimen from the Nakdong River in South Korea, but showed the closest relationship to G. pappenheimi in mainland China. Conclusions Our results support the existence of the Paleo-Huanghe River connecting the Korean peninsula and mainland China, suggesting that G. naktongensis in the Geum River should be treated as a different evolutionarily significant unit separated from that in the Nakdong River. The complete mitogenome of G. naktongensis Geum River provides essential baseline data to establish strategies for its conservation and restoration.
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Affiliation(s)
- Keun-Sik Kim
- Restoration Research Team (Fishes/Amphibians & Reptiles), Research Center for Endangered Species, National Institute of Ecology, 23 Gowol-gil, Yeongyang-gun, Gyeongsangbuk-do, 36531, Republic of Korea
| | - Dong-Won Kang
- Restoration Research Team (Fishes/Amphibians & Reptiles), Research Center for Endangered Species, National Institute of Ecology, 23 Gowol-gil, Yeongyang-gun, Gyeongsangbuk-do, 36531, Republic of Korea
| | - Keun-Yong Kim
- Department of Genetic Analysis, AquaGenTech Co., Ltd, 48300, Busan, Republic of Korea
| | - Jung Soo Heo
- Department of Genetic Analysis, AquaGenTech Co., Ltd, 48300, Busan, Republic of Korea
| | - Ha-Yoon Song
- Inland Fisheries Research Institute, National Institute of Fisheries Science, 32762, Geumsan, Republic of Korea
| | - Ju-Duk Yoon
- Restoration Research Team (Fishes/Amphibians & Reptiles), Research Center for Endangered Species, National Institute of Ecology, 23 Gowol-gil, Yeongyang-gun, Gyeongsangbuk-do, 36531, Republic of Korea.
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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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Pan T, Miao JS, Zhang HB, Yan P, Lee PS, Jiang XY, Ouyang JH, Deng YP, Zhang BW, Wu XB. Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa074] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Abstract
Species of the order Crocodylia are mostly large, predatory and semi-aquatic reptiles. Crocodylia, the closest living relatives of birds, first appeared in the Late Cretaceous period. In the present study, the complete mitochondrial (mt) genomes of 19 Crocodylia species, including two species (Melanosuchus niger and Caiman yacare) that have not been previously sequenced for mitogenomes, were processed through Illumina sequencing to offer genetic resources and compare with the mitogenomes of Crocodylia species reported previously. In addition, a high-resolution phylogenetic tree of nearly all current recognized species of Crocodylia is constructed based on mitogenomic data. Phylogenetic analyses support monophyly of three families: Alligatoridae (four genera: Alligator, Caiman, Melanosuchus and Paleosuchus), Crocodylidae (three genera: Crocodylus, Mecistops and Osteolaemus) and Gavialidae (two genera: Gavialis and Tomistoma). The tree topology is generally similar to previous studies. Molecular dating suggests that the first split within Crocodylia date back to the Upper Cretaceous (approx. 86.75 Mya). The estimated time to the most recent common ancestor (TMRCA) of Alligatoridae is 53.33 Mya and that of Crocodylidae and Gavialidae is 50.13 Mya, which might be closely linked to climate changes during the Late Palaeocene and Early Eocene. Additionally, this study proves that the diversification rate within Crocodylia began to increase from the Late Eocene (about 36 Mya) and two diversification peak periods of Crocodylia (0–10 Mya and 10–20 Mya) are disclosed, which is roughly consistent with the estimated crocodylian species richness through time. Combining all these clues, we can suggest that climate fluctuation may have played a decisive role in the speciation of Crocodylia.
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Affiliation(s)
- Tao Pan
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Jia-Shun Miao
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hua-Bin Zhang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Peng Yan
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Ping-Shin Lee
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xin-Yue Jiang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Jia-Hui Ouyang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - You-Peng Deng
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Bao-Wei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xiao-Bing Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
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Fu YT, Jin YC, Liu GH. The Complete Mitochondrial Genome of the Caecal Fluke of Poultry, Postharmostomum commutatum, as the First Representative from the Superfamily Brachylaimoidea. Front Genet 2019; 10:1037. [PMID: 31708971 PMCID: PMC6823182 DOI: 10.3389/fgene.2019.01037] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022] Open
Abstract
Postharmostomum commutatum (Platyhelminthes: Brachylaimoidea), a parasite of the caeca of poultry, has been frequently reported from many countries and regions, including China. However, the molecular epidemiology, population genetics and phylogenetics of this parasite are poorly understood. In the present study, we determined and characterized the complete mitochondrial (mt) genome of P. commutatum, as the first representative from the superfamily Brachylaimoidea. The mt genome of P. commutatum is a circular DNA molecule of 13,799 bp in size and encodes the complete set of 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as a typical control region. The mt genome of P. commutatum presents a clear bias in nucleotide composition with a negative AT-skew on average (-0.306) and a positive GC-skew on average (0.466). Phylogenetic analyses showed that P. commutatum (superfamily Brachylaimoidea) and other ten members of the order Diplostomida were recovered as sister groups of the order Plagiorchiida, indicating that the order Diplostomida is paraphyletic. This is the first mt genome of any member of the superfamily Brachylaimoidea and should represent a rich source of genetic markers for molecular epidemiological, population genetic and phylogenetic studies of parasitic flukes of socio-economic importance in poultry.
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Affiliation(s)
- Yi-Tian Fu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Yuan-Chun Jin
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Guo-Hua Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China.,Hunan Co-Innovation Center of Animal Production Safety, Changsha, China
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Mitochondrial genome of Pteronotus personatus (Chiroptera: Mormoopidae): comparison with selected bats and phylogenetic considerations. Genetica 2016; 145:27-35. [PMID: 27995348 DOI: 10.1007/s10709-016-9943-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 12/02/2016] [Indexed: 12/14/2022]
Abstract
We described the complete mitochondrial genome (mitogenome) of the Wagner's mustached bat, Pteronotus personatus, a species belonging to the family Mormoopidae, and compared it with other published mitogenomes of bats (Chiroptera). The mitogenome of P. personatus was 16,570 bp long and contained a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). Most of the genes were encoded on the H-strand, except for eight tRNA and the ND6 genes. The order of protein-coding and rRNA genes was highly conserved in all mitogenomes. All protein-coding genes started with an ATG codon, except for ND2, ND3, and ND5, which initiated with ATA, and terminated with the typical stop codon TAA/TAG or the codon AGA. Phylogenetic trees constructed using Maximum Parsimony, Maximum Likelihood, and Bayesian inference methods showed an identical topology and indicated the monophyly of different families of bats (Mormoopidae, Phyllostomidae, Vespertilionidae, Rhinolophidae, and Pteropopidae) and the existence of two major clades corresponding to the suborders Yangochiroptera and Yinpterochiroptera. The mitogenome sequence provided here will be useful for further phylogenetic analyses and population genetic studies in mormoopid bats.
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Hao S, Yu D, Ping J, Zhou H, Zhang Y. Complete mitochondrial genomes of two gecko species, Gekko hokouensis and Gekko japonicus (Squamata, Gekkonidae). Mitochondrial DNA B Resour 2016; 1:346-347. [PMID: 33473477 PMCID: PMC7800641 DOI: 10.1080/23802359.2015.1137809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The Gekkonidae is the second-most-numerous Family in Sauria and widely distributed around the world. In this paper, the complete mitochondrial genomes of two gecko species, Gekko hokouensis and Gekko japonicas, were sequenced. The lengths of the two mitochondrial genomes (G. hokouensis and G. japonicus) are 17 956 bp and 17 769 bp, respectively. These mitochondrial genomes both contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region (control region). The overall base compositions of the H-strand of G. hokouensis and G. japonicus are 32.1% A, 26.7% T, 27.0% C, 14.2% G and 31.6% A, 25.2% T, 28.6% C, 14.7% G, respectively. Phylogenetic analysis showed that G. hokouensis is a sister clade with G. swinhonis. G. japonicus has a close phylogenetic relationship to the clade of G. hokouensis and G. swinhonis.
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Affiliation(s)
- Shuangli Hao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Danna Yu
- Institute of Ecology, Zhejiang Normal University, Jinhua, China
| | - Jun Ping
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Huabin Zhou
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Yongpu Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
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Srikulnath K, Thapana W, Muangmai N. Role of Chromosome Changes in Crocodylus Evolution and Diversity. Genomics Inform 2015; 13:102-11. [PMID: 26865840 PMCID: PMC4742319 DOI: 10.5808/gi.2015.13.4.102] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/03/2015] [Accepted: 11/16/2015] [Indexed: 01/21/2023] Open
Abstract
The karyotypes of most species of crocodilians were studied using conventional and molecular cytogenetics. These provided an important contribution of chromosomal rearrangements for the evolutionary processes of Crocodylia and Sauropsida (birds and reptiles). The karyotypic features of crocodilians contain small diploid chromosome numbers (30~42), with little interspecific variation of the chromosome arm number (fundamental number) among crocodiles (56~60). This suggested that centric fusion and/or fission events occurred in the lineage, leading to crocodilian evolution and diversity. The chromosome numbers of Alligator, Caiman, Melanosuchus, Paleosuchus, Gavialis, Tomistoma, Mecistops, and Osteolaemus were stable within each genus, whereas those of Crocodylus (crocodylians) varied within the taxa. This agreed with molecular phylogeny that suggested a highly recent radiation of Crocodylus species. Karyotype analysis also suggests the direction of molecular phylogenetic placement among Crocodylus species and their migration from the Indo-Pacific to Africa and The New World. Crocodylus species originated from an ancestor in the Indo-Pacific around 9~16 million years ago (MYA) in the mid-Miocene, with a rapid radiation and dispersion into Africa 8~12 MYA. This was followed by a trans-Atlantic dispersion to the New World between 4~8 MYA in the Pliocene. The chromosomes provided a better understanding of crocodilian evolution and diversity, which will be useful for further study of the genome evolution in Crocodylia.
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Affiliation(s)
- Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Watcharaporn Thapana
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
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A 454 sequencing approach to dipteran mitochondrial genome research. Genomics 2015; 105:53-60. [DOI: 10.1016/j.ygeno.2014.10.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 01/14/2023]
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Suh A, Churakov G, Ramakodi MP, Platt RN, Jurka J, Kojima KK, Caballero J, Smit AF, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J. Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biol Evol 2014; 7:205-17. [PMID: 25503085 PMCID: PMC4316615 DOI: 10.1093/gbe/evu256] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians.
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Affiliation(s)
- Alexander Suh
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany Department of Evolutionary Biology (EBC), Uppsala University, Sweden
| | - Gennady Churakov
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany
| | - Meganathan P Ramakodi
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Present address: Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA Present address: Department of Biology, Temple University, Philadelphia, PA
| | - Roy N Platt
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Biological Sciences, Texas Tech University
| | - Jerzy Jurka
- Genetic Information Research Institute, Mountain View, California
| | - Kenji K Kojima
- Genetic Information Research Institute, Mountain View, California
| | | | - Arian F Smit
- Institute for Systems Biology, Seattle, Washington
| | | | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | - Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany
| | - Richard E Green
- Department of Biomolecular Engineering, University of California
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida
| | - David A Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Biological Sciences, Texas Tech University
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany
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12
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Bloor P, Ibáñez C, Viloria-Lagares TA. Mitochondrial DNA analysis reveals hidden genetic diversity in captive populations of the threatened American crocodile (Crocodylus acutus) in Colombia. Ecol Evol 2014; 5:130-40. [PMID: 25628870 PMCID: PMC4298440 DOI: 10.1002/ece3.1307] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 10/04/2014] [Accepted: 10/08/2014] [Indexed: 01/10/2023] Open
Abstract
Identification of units within species worthy of separate management consideration is an important area within conservation. Mitochondrial DNA (mtDNA) surveys can potentially contribute to this by identifying phylogenetic and population structure below the species level. The American crocodile (Crocodylus acutus) is broadly distributed throughout the Neotropics. Its numbers have been reduced severely with the species threatened throughout much of its distribution. In Colombia, the release of individuals from commercial captive populations has emerged as a possible conservation strategy that could contribute to species recovery. However, no studies have addressed levels of genetic differentiation or diversity within C. acutus in Colombia, thus complicating conservation and management decisions. Here, sequence variation was studied in mtDNA cytochrome b and cytochrome oxidase I gene sequences in three Colombian captive populations of C. acutus. Two distinct lineages were identified: C. acutus-I, corresponding to haplotypes from Colombia and closely related Central American haplotypes; and C. acutus-II, corresponding to all remaining haplotypes from Colombia. Comparison with findings from other studies indicates the presence of a single "northern" lineage (corresponding to C. acutus-I) distributed from North America (southern Florida), through Central America and into northern South America. The absence of C. acutus-II haplotypes from North and Central America indicates that the C. acutus-II lineage probably represents a separate South American lineage. There appears to be sufficient divergence between lineages to suggest that they could represent two distinct evolutionary units. We suggest that this differentiation needs to be recognized for conservation purposes because it clearly contributes to the overall genetic diversity of the species. All Colombian captive populations included in this study contained a mixture of representatives of both lineages. As such, we recommend against the use of captive-bred individuals for conservation strategies until further genetic information is available.
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Affiliation(s)
- Paul Bloor
- Grupo de Biodiversidad y Recursos Genéticos, Instituto de Genética, Universidad Nacional de Colombia Bogotá, DC, Colombia
| | - Carolina Ibáñez
- Grupo de Biodiversidad y Recursos Genéticos, Instituto de Genética, Universidad Nacional de Colombia Bogotá, DC, Colombia
| | - Thomas A Viloria-Lagares
- Grupo de Biodiversidad y Recursos Genéticos, Instituto de Genética, Universidad Nacional de Colombia Bogotá, DC, Colombia
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13
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Meganathan PR, Dubey B, Jogayya KN, Haque I. Identification of Indian crocodile species through DNA barcodes. J Forensic Sci 2013; 58:993-8. [PMID: 23718785 DOI: 10.1111/1556-4029.12129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 03/06/2012] [Accepted: 05/06/2012] [Indexed: 12/27/2022]
Abstract
The biodiversity of India includes three crocodile species, Crocodylus palustris, Crocodylus porosus, and Gavialis gangeticus, whose status is threatened due to bushmeat crisis and illegal hunting. The crocodilian conservation management requires novel techniques to help forensic analysts to reveal species identity. DNA barcoding is a species identification technique, where a partial cytochrome c oxidase subunit 1 gene is used as a marker for species identification. Herein, the DNA barcoding technique is evaluated for three Indian crocodiles by analyzing an approximately 750-bp barcode region. The alignment result shows interspecific variations between sequences for discrimination of the three Indian crocodiles leading to species identification. The phylogenetic analyses also substantiate the established crocodilian relationships, which add further advantage to use this DNA barcoding approach for Indian crocodiles. This study provides preliminary evidences for the use of DNA barcoding technique in the identification of Indian crocodile species.
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Affiliation(s)
- P R Meganathan
- Biology Division, DNA Unit, Central Forensic Science Laboratory, 30, Gorachand Road, Park Circus, Kolkata 700 014, West Bengal, India
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14
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Mitochondrial 16S ribosomal RNA gene for forensic identification of crocodile species. J Forensic Leg Med 2013; 20:334-8. [DOI: 10.1016/j.jflm.2012.09.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 07/15/2012] [Accepted: 09/07/2012] [Indexed: 02/07/2023]
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15
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Liu GH, Gasser RB, Otranto D, Xu MJ, Shen JL, Mohandas N, Zhou DH, Zhu XQ. Mitochondrial genome of the eyeworm, Thelazia callipaeda (Nematoda: Spirurida), as the first representative from the family Thelaziidae. PLoS Negl Trop Dis 2013; 7:e2029. [PMID: 23383353 PMCID: PMC3561134 DOI: 10.1371/journal.pntd.0002029] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/07/2012] [Indexed: 12/14/2022] Open
Abstract
Human thelaziosis is an underestimated parasitic disease caused by Thelazia species (Spirurida: Thelaziidae). The oriental eyeworm, Thelazia callipaeda, infects a range of mammalian definitive hosts, including canids, felids and humans. Although this zoonotic parasite is of socio-economic significance in Asian countries, its genetics, epidemiology and biology are poorly understood. Mitochondrial (mt) DNA is known to provide useful genetic markers to underpin fundamental investigations, but no mt genome had been characterized for any members of the family Thelaziidae. In the present study, we sequenced and characterized the mt genome of T. callipaeda. This AT-rich (74.6%) mt genome (13,668 bp) is circular and contains 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes, but lacks an atp8 gene. All protein-coding genes are transcribed in the same direction; the gene order is the same as those of Dirofilaria immitis and Setaria digitata (Onchocercidae), but distinct from Dracunculus medinensis (Dracunculidae) and Heliconema longissimum (Physalopteridae). Phylogenetic analyses of the concatenated amino acid sequence data for all 12 protein-coding genes by Bayesian inference (BI) showed that T. callipaeda (Thelaziidae) is related to the family Onchocercidae. This is the first mt genome of any member of the family Thelaziidae and should represent a new source of genetic markers for studying the epidemiology, ecology, population genetics and systematics of this parasite of humans and other mammals. Human thelaziosis is an underestimated parasitic disease caused by the eyeworm Thelazia callipaeda (Spirurida: Thelaziidae). Although this parasite is of significance in humans in many Asian countries, its genetics, epidemiology and biology are poorly understood. Mitochondrial (mt) DNA can provide useful genetic markers for fundamental investigations, but no mt genome had been characterized for any members of the family Thelaziidae. In this study, we sequenced and characterized the mt genome of T. callipaeda. This circular mt genome is 13,668 bp long and contains 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes, but lacks an atp8 gene. Phylogenetic analyses of the concatenated amino acid sequence data for all 12 protein-coding genes by Bayesian inference showed that T. callipaeda is closely related to the family Onchocercidae, consistent with previous study. This is the first mt genome of any member of the family Thelaziidae, and represents a new source of genetic markers for studies of the epidemiology, ecology, population genetics and systematics of this parasite of human and animal health significance.
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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, PR China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, PR China
| | - Robin B. Gasser
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (RBG); (XQZ)
| | - Domenico Otranto
- Dipartimento di Sanità Pubblica e Zootecnia, Università degli Studi di Bari, Valenzano, Bari, Italy
| | - Min-Jun Xu
- 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, PR China
| | - Ji-Long Shen
- Department of Pathogen Biology, Anhui Medical University, Hefei, Anhui Province, China
| | - Namitha Mohandas
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Dong-Hui Zhou
- 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, PR 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 Province, PR China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, PR China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, PR China
- * E-mail: (RBG); (XQZ)
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16
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Bej D, Sahoo L, Das SP, Swain S, Jayasankar P, Das PC, Routray P, Swain SK, Jena JK, Das P. Complete mitochondrial genome sequence of Catla catla and its phylogenetic consideration. Mol Biol Rep 2012; 39:10347-54. [PMID: 23086264 DOI: 10.1007/s11033-012-1912-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 10/01/2012] [Indexed: 11/25/2022]
Abstract
Complete nucleotide sequence of mitochondrial genome (mitogenome) of the Catla catla (Ostariophysi: Cypriniformes: Cyprinidae) was determined in the present study. Its length is 16,594 bp and contains 13 protein coding genes, 22 transfer RNAs, two ribosomal RNAs and one non-coding control region. Most of the genes were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) genes were encoded on the L-strand. The reading frames of two pair of genes overlapped: ATPase 8 with 6 and ND4L with ND4 by seven nucleotides each. The main non-coding region was 929 bp, with three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and an unusual simple sequence repeat, (TA)(7). Phylogenetic analyses based on complete mitochondrial genome sequences were in favor of the traditional taxonomy of family Cyprinidae. In conclusion present mitogenome of Catla catla adds more information to our understanding of diversity and evolution of mitogenome in fishes.
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Affiliation(s)
- Dillip Bej
- Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002 Odisha, India
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17
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Dubey B, Meganathan PR, Haque I. Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae). Mol Biol Rep 2012; 39:7403-12. [PMID: 22331485 DOI: 10.1007/s11033-012-1572-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 01/25/2012] [Indexed: 12/18/2022]
Abstract
This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.
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Affiliation(s)
- Bhawna Dubey
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30-Gorachand Road, Kolkata, 700 014 West Bengal, India
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18
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Liu GH, Wu CY, Song HQ, Wei SJ, Xu MJ, Lin RQ, Zhao GH, Huang SY, Zhu XQ. Comparative analyses of the complete mitochondrial genomes of Ascaris lumbricoides and Ascaris suum from humans and pigs. Gene 2011; 492:110-6. [PMID: 22075400 DOI: 10.1016/j.gene.2011.10.043] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/03/2011] [Accepted: 10/20/2011] [Indexed: 12/12/2022]
Abstract
Ascaris lumbricoides and Ascaris suum are parasitic nematodes living in the small intestine of humans and pigs, and can cause the disease ascariasis. For long, there has been controversy as to whether the two ascaridoid taxa represent the same species due to their significant resemblances in morphology. However, the complete mitochondrial (mt) genome data have been lacking for A. lumbricoides in spite of human and animal health significance and socio-economic impact globally of these parasites. In the present study, we sequenced the complete mt genomes of A. lumbricoides and A. suum (China isolate), which was 14,303 bp and 14,311 bp in size, respectively. The identity of the mt genomes was 98.1% between A. lumbricoides and A. suum (China isolate), and 98.5% between A. suum (China isolate) and A. suum (USA isolate). Both genomes are circular, and consist of 36 genes, including 12 genes for proteins, 2 genes for rRNA and 22 genes for tRNA, which are consistent with that of all other species of ascaridoid studied to date. All genes are transcribed in the same direction and have a nucleotide composition high in A and T (71.7% for A. lumbricoides and 71.8% for A. suum). The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. Phylogenetic analyses of A. lumbricoides and A. suum using concatenated amino acid sequences of 12 protein-coding genes, with three different computational algorithms (Bayesian analysis, maximum likelihood and maximum parsimony) all clustered in a clade with high statistical support, indicating that A. lumbricoides and A. suum was very closely related. These mt genome data and the results provide some additional genetic evidence that A. lumbricoides and A. suum may represent the same species. The mt genome data presented in this study are also useful novel markers for studying the molecular epidemiology and population genetics of Ascaris.
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Affiliation(s)
- Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
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19
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New haplotype of the complete mitochondrial genome of Crocodylus siamensis and its species-specific DNA markers: distinguishing C. siamensis from C. porosus in Thailand. Mol Biol Rep 2011; 39:4709-17. [DOI: 10.1007/s11033-011-1263-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 09/14/2011] [Indexed: 10/17/2022]
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