蟾蜍棒线虫线粒体全基因组特征分析

doi:10.16431/j.cnki.1671-7236.2025.07.020

Abstract

Abstract: 【Objective】 The aim of this experiment was to obtain the complete mitochondrial genome of Rhabdias bufonis and analyze its characteristics. 【Method】 The mitochondrial genes of Rhabdias bufonis were amplified by PCR,and the whole mitochondrial genome of Rhabdias bufonis was obtained by sequencing,annotation,assembly and spliceover,and the sequence analysis was performed.Using Camallanus lacustris as an outgroup,based on the amino acid series of 12 protein-coding genes (PCGs) in mitochondria.The phylogenetic tree was constructed by Neighbor-Joining (NJ) and Bayesian inference (BI) method for evolutionary analysis. 【Result】 The mitochondrial genome of Rhabdias bufonis was a circular structure with a total length of 14 208 bp,consisting of 12 PCGs,22 tRNAs,2 rRNAs and 2 non-coding control regions.The base composition of the mitochondrial genome，AT content was 75%,GC content was 25%,AT-skew was 0.26,GC-skew was -0.36,showing obvious AT bias.PCGs used ATG and GTG as start codons and TGA,TAA and incomplete TA- as stop codon.Secondary structure analysis of tRNAs showed that the trnS2 and trnH genes lacked dihydroouracil (DHU) arm,and the rest were typical clover structures.Phylogenetic tree analysis showed that Tylenchina was divided into two large clades,Cephaloboidea and Tylenchoidea formed clade Ⅰ,Strongyloidoidea,Steinernematoidea,Aphelenchoidea and Panagrolaimoidea formed clade Ⅱ.In clade Ⅱ,Steinernematidae and Rhabdiasidae gathered together to form a branch and grouped to another sisters branch formed by Aphelenchoidiae and Panagrolaimidae.Howerver,Strongyloididae independently formed another large branch.In Rhabdiasidae,Rhabdias bufonis from forest frog in this study and the Rhabdias bufonis (OR725306) from toad gathered together,and it was more closely to two strains of Rhabdias kafunata.The amphibian-parasitic Rhabdias sp.and the insect-associated Steinernema sp.clustered together,which exhibited more closer to the plant-parasitic Aphelenchoididae than to the mammalian-parasitic Strongyloididae. 【Conclusion】 In this study,the complete mitochondrial genome sequence of Rhabdias bufonis from forest frog was obtained. The phylogenetic relationship between Steinernematidae and Rhabdiasidae was obviously close to that of Strongyloididae,supporting the validity of Steinernematoidea as an independent taxonomic order,and Steinernematidae should be included in Steinernematoidea.The results provided basic information for the taxonomy,population genetics and phylogeny of Rhabdiasidae.

Key words: Rhabdias bufonis; mitochondrial genome; sequence analysis; genetic evolutionary analysis

CLC Number:

S852.73^＋1

YANG Yan, HU Yanming, DING Jian, LI Ben, HE Yutong, LIU Xuewei, WANG Jiawen, LAN Zhuo, QIU Hongyu, GAO Junfeng, WANG Chunren. Characterization Analysis of Complete Mitochondrial Genome of Rhabdias bufonis[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(7): 3190-3201.

References

[1] 唐仲璋,唐崇惕.人畜线虫学[M].北京:科学出版社,2009.TANG Z Z,TANG C T.Human-Animal Nematodeology[M].Beijing:Science Press,2009.(in Chinese)
[2] WANG Y,WANG M,ZHANG Y,et al.Efficient control of root-knot nematodes by expressing Bt nematicidal proteins in root leucoplasts[J].Molecular Plant,2024,17(10):1504-1519.
[3] DUBEY J P,THOMPSON P C,FOURNET V,et al.Over a century of progress on Trichinella research in pigs at the United States Department of Agriculture:Challenges and solutions[J].Food and Waterborne Parasitology,2024,36:e00239.
[4] KELEHEAR C,BROWN G P,SHINE R.Influence of lung parasites on the growth rates of free-ranging and captive adult cane toads[J].Oecologia,2011,165(3):585-592.
[5] 谢沛璇.黑龙江两种林蛙线虫感染调查及优势虫种遗传多样性分析[D].大庆：黑龙江八一农垦大学,2022.XIE P X.Investigation of nematode infection of two species of forest frog in Heilongjiang and analysis of genetic diversity of dominant species[D].Daqing:Heilongjiang Bayi Agricultural University,2022.(in Chinese)
[6] BOORE J L.Animal mitochondrial genomes[J].Nucleic Acids Research, 1999,27:1767-1780.
[7] GYLLENSTEN U,WHARTON D,WILSON A C.Maternal inheritance of mitochondrial DNA during backcrossing of two species of mice[J]. The Journal of Heredity,1985,76(5):321-324.
[8] HU M,GASSER R B.Mitochondrial genomes of parasitic nematodes-progress and perspectives[J]. Trends in Parasitology,2006,22(2):78-84.
[9] XIE Y,WANG L,CHEN Y,et al.The complete mitogenome of Toxocara vitulorum:Novel in-sights into the phylogenetics in Toxocaridae[J].Animals,2022,12(24),3546.
[10] YAMAGUTI S.Systerma Heminthum Vol Ⅱ:The Nnematodes of Vertebrates Part 1,Part2[M].New York:Interscience Publ Inc,1961.
[11] DE LEY P,BLAXTER M L.A new system for Nematoda:Combining morphological characters with molecular trees,and translating clades into ranks and taxa[J].Proceedings of the Fourth International Congress of Nematology,2022,2:8-13.
[12] HODDA M.Phylum nematoda[J]. Zootaxa,2007,1668:265-293.
[13] ZENG J L,CHEN H X,NI X F,et al.Molecular phylogeny of the family Rhabdiasidae (Nematoda:Rhabditida),with morphology,genetic characterization and mitochondrial genomes of Rhabdias kafunata and R.bufonis[J].Parasit Vectors,2024,17(1):100.
[14] GASSER R B,BOTT N J,CHILTON N B,et al.Toward practical,DNA-based diagnostic methods for parasitic nematodes of livestock--bionomic and biotechnological implications[J].Biotechnology Advances，2008,26(4):325-334.
[15] 汪溥钦,汪彦愔,赵玉如,等.梅花山自然保护区及其周围的脊椎动物寄生蠕虫[J].武夷科学,1992,1:31-48.WANG F Q,WANG Y Y,ZHAO Y R,et al.The parasitic helminthes of vertebrates from Meihuashan Nature Mountain Reserve and adjacent area[J].Wuyi Science Journaly,1992,1:31-48.(in Chinese)
[16] MENG G,LI Y,YANG C,et al.MitoZ:A toolkit for animal mitochondrial genome assembly,annotation and visualization[J].Nucleic Acids Research,2019,47:e63.
[17] LOWE TM,CHAN P P.tRNAscan-SE on-line:Integrating search and contextual analysis of transfer RNA genes[J].Nucleic Acids Research,2016,44:W54-W57.
[18] ROZAS J,FERRER-MATA A,LIBRADO P,et al.DnaSP 6:DNA sequence polymorphism analysis of large data sets[J].Molecular Biology and Evolution,2017,34:3299-3302.
[19] GRANT J R,STOTHARD P.The CGView Server:A comparative genomics tool for circular genomes[J].Nucleic Acids Research,2008,36:W181-W184.
[20] BALAKRISHNAN S,SHENGHAN G,LERCHER M J,et al.Evolview v3:A webserver for visualization,annotation,and management of phylogenetic trees[J].Nucleic Acids Research,2019,47:W270-W275.
[21] CAO K,FENG Z,GAO F,et al.Mitoepigenetics:An intriguing regulatory layer in aging and metabolic-related diseases[J].Free Radical Biology Medicine,2021,177:337-346.
[22] CHATTERJEE D,DAS P,CHAKRABARTI O.Mitochondrial epigenetics regulating inflammation in cancer and aging[J].Frontiers in Cell and Developmental Biology,2022,10:929708.
[23] 徐其放,陈嘉昌,朱世杰,等.动物线粒体DNA的特异结构及应用分子系统学分析的方法[J].中国比较医学杂志,2005,5:315-319.XU Q F,CHEN J C,ZHU S J,et al.Structural characteristics of animal’s mitochondrial DNA and its application on molecular systematics[J]. Chinese Journal of Comparative Medicine,2005,5:315-319.(in Chinese)
[24] AN Q,QIU Y Y,WANG C R,et al.Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda:Diplodiscidae):Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication[J].International Journal for Parasitology. Parasites and Wildlife,2022,19:9-17.
[25] GAO J F,HOU M R,CUI Y C,et al.The complete mitochondrial genome sequence of Drepanidotaenia lanceolata (Cyclophyllidea:Hymenolepididae)[J].Mitochondrial DNA,2017,28(3):317-318.
[26] MASTA S E,BOORE J L.The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs[J].Molecular Biology and Evolution,2004,21(5):893-902.
[27] LAVROV D V,BROWN W M.Trichinella spiralis mtDNA:A nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAs and has a gene arrangement relatable to those of coelomate metazoans[J]. Genetics,2001,157(2):621-637.
[28] LIU G H,WANG Y,XU M J,et al.Characterization of the complete mitochondrial genomes of two whipworms Trichuris ovis and Trichuris discolor (Nematoda:Trichuridae)[J].Infection, Genetics and Evolution,2012,12(8):1635-1641.
[29] LI M W,LIN R Q,SONG H Q,et al.The complete mitochondrial genomes for three Toxocara species of human and animal health significance[J].BMC Genomics,2008,9:224.
[30] KIKUCHI T,AFRIN T,YOSHIDA M.Complete mitochondrial genomes of four entomopathogenic nematode species of the genus Steinernema[J].Parasit Vectors,2016,9(1):430.
[31] SUN L,ZHUO K,LIN B,et al.The complete mitochondrial genome of Meloidogyne graminicola (Tylenchina):A unique gene arrangement and its phylogenetic implications[J].Public Library of Science One,2014,9(6):e98558.
[32] LIU Z X,ZHANG Y,LIU Y T,et al.Complete mitochondrial genome of Echinostoma hortense (Digenea:Echinostomatidae)[J].Korean Journal of Parasitology,2016,54:173-179.
[33] GUO D H,ZHANG Y,FU X,et al.Complete mitochondrial genomes of Dermacentor silvarum and comparative analyses with another hard tick Dermacentor nitens[J].Experimental Parasitology,2016,169:22-27.

Characterization Analysis of Complete Mitochondrial Genome of Rhabdias bufonis

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	SHAN Jinyan, LIAN Kaiqi, MA Jun, LIU Yuling, NIE Zhulan, LI Binshun, PENG Renhai, WEI Jie. Cloning,Sequence Analysis and Spationtemporal Expression of Runx2b Gene in Qihe Crucian Carp (Carassius auratus) [J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(6): 2717-2728.
[2]	ZHONG Weilin, YAO Jianhui, WEI Xiaoqi, YAN Guangzhi, CHEN Shengnan, LIU Mingjie, HUANG Liangzong. Diagnosis and Genetic Evolution Analysis of PCV2d Infection in a Pig Farm in Guangdong [J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(6): 2781-2789.
[3]	LI Tianxiu, LI Xinpeng, DONG Xinxing, LAN Guoxiang, YAN Dawei, ZHU Jiawei. Amplification,Sequence Analysis and Tissue Expression Study of HMOX2 Gene in Lijiang Pigs [J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(5): 2219-2231.
[4]	LI Feng, XIE Bin, ZHANG Shuai. Isolation，Identification and Genome Sequence Analysis of Two Recombinant Strains of Avian Infectious Bronchitis Virus [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(9): 3958-3969.
[5]	ZHANG Xuedi, XU Kai, YIN Shuo, LIU Jing, WANG Zhonghao, QIN Jianhua, WU Pengyuan, WANG Chuanwen. Cloning,Sequence Analysis and Expression Characteristics of Carboxylesterase 2 Gene in Dermanyssus gallinae [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(7): 2973-2983.
[6]	HUANG Liqing, DUAN Anqin, ZHENG Haiying, YANG Chunyan, SHANG Jianghua. Sequence Analysis,Eukaryotic Expression Vector Construction and Tissue Expression of SFRP1 Gene in Buffalo [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(5): 1807-1818.
[7]	HAN Hui, GUO Yajing, YAN Guangzhi, CHEN Shengnan, LIU Mingjie, MO Meilian, HUANG Liangzong. Isolation,Identification and Genetic Evolution Analysis of a Eurasian Avian-like Swine Influenza Virus [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(4): 1642-1650.
[8]	BIJunming, DONG Yaqin, CUIJin, SHA Zhou, GU Congcong, ZHENG Hui, WEI Rong, SUN Fuliang, ZHANG Feng, ZHANG Zhihong. Isolation，Identification and Genetic Evolution Analysis of a Strain of Bovine Viral Diarrhea Virus in Shandong Province [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(10): 4485-4499.
[9]	WU Aoqi, LUO Yuhang, REN Tongwei, WANG Hao, DONG Qinting, QIN Yifeng, WEI Zuzhang, OUYANG Kang, CHEN Ying, HUANG Weijian, PAN Yan, LI Fengmei, XIE Jiang. Isolation，Identification and Genetic Evolution Analysis of a Strain of Bovine Parvovirus Type 1 in Guangxi [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(10): 4540-4549.
[10]	DOU Junfeng, WANG Zui, LI Li, LU Qin, JIN Xinxin, LING Xiaochun, LUO Qingping, ZHAI Xinguo. Identification of Subgroups A, B and J Avian Leukosis Virus Co-infection and Sequence Analysis of gp85 Gene [J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(1): 302-311.
[11]	TANG Haibo, JIANG Jiajia, CHEN Fenglian, YANG Jinlan, BAI Anbin, LIU Jinfeng, QIN Shaomin, WU Jianmin. Isolation, Identification and Genomic Characterization Analysis of Parvovirus Isolate from Bamboo Rat [J]. China Animal Husbandry & Veterinary Medicine, 2023, 50(7): 2843-2853.
[12]	KANG Danju, PENG Qiuyun, ZHOU Jiaxin, CHEN Jinjun, LIN Hongying, ZHOU Guangxian. Cloning, Bioinformatics Analysis and Tissue Expression of AvBD1 and AvBD2 Genes in Yellow-feather Chickens [J]. China Animal Husbandry & Veterinary Medicine, 2023, 50(11): 4325-4337.
[13]	XING Tianqi, XU Di, YAN Gang, WANG Yubin, WANG Mengying, LIANG Jing, LAN Ganqiu. Sequence Analysis, Eukaryotic Expression Vector Construction and Tissue Expression of ABCD4 Gene in Bama Miniature Pigs [J]. China Animal Husbandry & Veterinary Medicine, 2023, 50(11): 4338-4348.
[14]	LI Nan, MENG Jinxin, WANG Jiannie, HE Yuwen, YANG Shaochang, LYU Shunyan, WANG Jinglin. Detection of Lumpy Skin Disease Virus in Cattle and Investigation of Virus Carried by Midges and Mosquitoes [J]. China Animal Husbandry & Veterinary Medicine, 2023, 50(10): 4179-4187.
[15]	PENG Caichun, LI Binqiang, WANG Yeying, SU Haijun. Genetic Diversity Analysis of Sus scrofa Population in Guizhou Based on Mitochondrial CytbGene [J]. China Animal Husbandry & Veterinary Medicine, 2022, 49(7): 2601-2612.