Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Acta Parasitologica

4 Issues per year


IMPACT FACTOR 2016: 1.160
5-year IMPACT FACTOR: 1.185

CiteScore 2016: 1.24

SCImago Journal Rank (SJR) 2016: 0.532
Source Normalized Impact per Paper (SNIP) 2016: 0.721

Online
ISSN
1896-1851
See all formats and pricing
More options …
Volume 63, Issue 2

Issues

Characterization of the complete mitochondrial genome of Metastrongylus salmi (M. salmi) derived from Tibetan pigs in Tibet, China

Kun Li
  • College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Muhammad Shahzad
  • College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
  • University College of Veterinary & Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Hui Zhang
  • College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Khalid Mehmood
  • College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
  • University College of Veterinary & Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Xiong Jiang
  • College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Houqiang Luo
  • College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Lihong Zhang
  • College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Xiaoqian Dong
  • Animal husbandry and Veterinary Bureau of Taishan district, Taian, People’s Republic of China
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Jiakui Li
  • Corresponding author
  • College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
  • Laboratory of Detection and Monitoring of Highland Animal Disease, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, People’s Republic of China
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2018-04-13 | DOI: https://doi.org/10.1515/ap-2018-0032

Abstract

The present study was designed to determine and analyze the mt genomes of Metastrongylus salmi (M. salmi), and reveal the phylogenetic relationships of this parasite using mt DNA sequences. Results showed that the complete mt genome of M. salmi was 13722 bp containing 12 protein-coding genes (cox1-3, nad1-6, nad4L, atp6 and cytb), 22 transfer RNA genes, and 2 ribosomal RNA genes (rrnL and rrnS). The overall A+T content was 73.54% and the nucleotide composition was A (23.52%), C (6.14%), G (19.60%), T (50.02%), and N (UCAG) (0.73%). A total of 4237 amino acids are encoded from the Tibetan isolates of M. salmi mt genomes. The ATA was predicted as the most common starting codon with 41.7% (5/12 protein genes); and 11 of the 12 protein genes were found to have a TAG or TAA translation termination codon. By clustering together the phylogenetic trees of Tibetan M. salmi and Austrian M. salmi, the M. salmi isolated from Tibetan pigs was found to be highly homological with that stemmed from Austrian one. This information provides meaningful insights into the phylogenetic position of the M. salmi China isolate and represents a useful resource for selecting molecular markers for diagnosis and population studies.

Keywords: Lungworm; Tibetan pigs; mitochondrial genome; Metastrongylus salmi

References

  • Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410PubMedCrossrefGoogle Scholar

  • Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. 2000. Gene Ontology: tool for the unification of biology. Nature Genetics, 25, 25–29CrossrefPubMedGoogle Scholar

  • Benson G. 1999 Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27, 573–580CrossrefGoogle Scholar

  • Borgstrom E., Lundin S., Lundeberg J. 2011. Large scale library generation for high throughput sequencing. PLoS One, 6, e19119. DOI: 10.1371/journal.pone.0019119Web of ScienceCrossrefPubMedGoogle Scholar

  • Chiaromonte F., Yap V.B., Miller W. 2002. Scoring pairwise genomic sequence alignments. Pacific Symposium on Biocomputing, 7, 115–126Google Scholar

  • Cronn R., Liston A., Parks M., Gernandt D.S., Shen R.K. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Research, 36, e122Web of ScienceCrossrefPubMedGoogle Scholar

  • Durent L., Mouchiroud D. 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila and Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 96, 4482–4487CrossrefPubMedGoogle Scholar

  • García-González Á.M., Pérez-Martín J.E., Gamito-Santos J.A., Calero-Bernal R., Alonso M.A., Carrión E.M. 2013. Epidemiologic study of lung parasites (Metastrongylus spp.) in wild boar (Sus scrofa) in southwestern Spain. Journal of Wildlife Disease, 49, 157–162. CrossrefGoogle Scholar

  • Gassó D., Rossi L., Mentaberre G., Casas E., Velarde R., Nosal P., et al. 2014. An identification key for the five most common species of Metastrongylus. Parasitology Research, 113, 3495–3500. CrossrefPubMedWeb of ScienceGoogle Scholar

  • Helfenbein K.G., Brown W.M., Boore J.L. 2001. The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Molecular Biology and Evolution, 18, 1734–1744CrossrefPubMedGoogle Scholar

  • Hu M., Chilton N.B., Gasser R.B. 2003. The mitochondrial genome of Strongyloides stercoralis (Nematoda)-idiosyncratic gene order and evolutionary implications. International Journal of Parasitology, 33, 1393–1408CrossrefGoogle Scholar

  • Humbert J.F., Drouet J. 1990. Enquête épidémiologique sur la métastrongylose du sanglier (Sus scrofa) en France. Gibier Faune Sauvag, 7, 67–84. (In French)Google Scholar

  • Jex A.R., Hall R.S., Littlewood D.T., Gasser R.B. 2010. An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Nucleic Acids Research, 38, 522–533 Kanehisa M. 1997. A database for post-genome analysis. Trends in Genetics, 13, 375PubMedWeb of ScienceCrossrefGoogle Scholar

  • Kanehisa M., Goto S., Hattori M., Aoki-Kinoshita K.F., Itoh M., Kawashima S., et al. 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Research, 34, D354–D357CrossrefGoogle Scholar

  • Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Research, 32, D277–D280CrossrefGoogle Scholar

  • Kurtz S., Phillippy A., Delcher A.L., Smoot M., Shumway M., Antonescu C., Salzberg S.L. 2004. Versatile and open software for comparing large genomes. Genome Biology, 5, R12PubMedGoogle Scholar

  • Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., et al. 2009. The Sequence Alignment/Map (SAM) format and SAMtools. Bioinformatics, 25, 2078–2079PubMedCrossrefGoogle Scholar

  • Li K., Lan Y.F., Luo H.Q., Shahzad M., Zhang H., Wang L., et al.2017a. Prevalence of three Oesophagostomum spp. from Ti-betan pigs analyzed by genetic markers of nad1, cox3 and ITS1. Acta Parasitologica, 62, 90–96. CrossrefGoogle Scholar

  • Li K., Luo H.Q., Zhang H., Lan Y.F., Han Z.Q., Shahzad M., et al.2016. First report of Metastrongylus pudendotectus by the genetic characterization of mitochondria genome of cox1 in pigs from Tibet, China. Veterinary Parasitology, 223, 91–95. CrossrefWeb of SciencePubMedGoogle Scholar

  • Li K., Zhang L.H., Zhang H., Lei Z.X., Luo H.Q., Mehmood K., et al.2017b. Epidemiology investigation and risk factors of Echinococcus granulosus in yaks (Bos grunniens), Tibetan pigs and Tibetans on the Qinghai Tibetan plateau. Acta Tropica 173, 147–152. CrossrefGoogle Scholar

  • Li M.W., Lin R.Q., Song H.Q., Wu X.Y., Zhu X.Q. 2008. The complete mitochondrial genomes for three Toxocara species of human and animal health significance. BMC Genomics, 9, 224Web of SciencePubMedCrossrefGoogle Scholar

  • Li R., Zhu H., Ruan J., Qian W., Fang X., Shi Z., et al. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Research, 20, 265–272Web of ScienceCrossrefPubMedGoogle Scholar

  • Li X.R. (Ed.) 2011. Color atlas of animal parasitosis (2nd Edition). Beijing: China Agriculture PressGoogle Scholar

  • Lin R.Q., Liu G.H., Hu M., Song H.Q., Wu X.Y., Li M.Y., et al.2012. Oesophagostomum dentatum and Oesophagostomum quadrispinulatum: characterization of the complete mitochondrial genome sequences of the two pig nodule worms. Experimental Parasitology 131, 1–7. CrossrefPubMedWeb of ScienceGoogle Scholar

  • Lohse M., Drechsel O., Bock R. 2007. Organellar Genome DRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Current Genetics, 52, 267–274CrossrefGoogle Scholar

  • Magrane M. 2011. UniProt. Knowledgebase: a hub of integrated protein data. Databases-Oxford, 2011, 9. CrossrefWeb of ScienceGoogle Scholar

  • Marruchella G., Paoletti B., Speranza R., Di Guardo G. 2012. Fatal bronchopneumonia in a Metastrongylus elongatus and Porcine circovirus type 2 co-infected pig. Research in Veterinary Science, 93, 310–312. CrossrefWeb of ScienceGoogle Scholar

  • Romero H., Zavala A., Musto H. 2000. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective force. Nucleic Acids Research, 28, 2084–2090CrossrefGoogle Scholar

  • Saha S., Bridges S., Magbanua Z.V., Peterson D.G. 2008. Empirical comparison of ab initio repeat finding programs. Nucleic Acids Research, 36, 2284–2294Web of ScienceCrossrefPubMedGoogle Scholar

  • Singer G.A., Hickey D.A. 2000. Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Molecular Biology and Evolution, 17, 1581–1588CrossrefPubMedGoogle Scholar

  • Sorensen M., Sanz A., Gómez J., Pamplona R., Portero-Otín M., Gredilla R., Barja G. 2006. Effects of fasting on oxidative stress in rat liver mitochondria. Free Radical Research, 40, 339–347CrossrefPubMedGoogle Scholar

  • Tannistha N., Catherine O., Arvind P.S., Boddey J., Atkins T., Sarkar-Tyson M., et al. 2010. A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathogens, 6, 1–15Web of ScienceGoogle Scholar

  • Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41CrossrefPubMedGoogle Scholar

  • Tatusov R.L., Koonin E.V., Lipman D.J. 1997. A genomic perspective on protein families. Science, 278, 631–637CrossrefPubMedGoogle Scholar

  • Wyman S.K., Jansen R.K., Boore J.L. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20, 3252–3255CrossrefPubMedGoogle Scholar

  • Zhang N.Z., Zhou D.H., Huang S.Y., Wang M., Shi X.C., Ciren D.B., Zhu X.Q. 2014. Seroprevalence and risk factors associated with Haemophilus parasuis infection in Tibetan pigs in Tibet. Acta Tropica, 132, 94–97. CrossrefWeb of SciencePubMedGoogle Scholar

  • Zhao G.H., Hua B., Cheng W.Y., Jia Y.Q., Li H.M., Yu S.K., Liu G.H. 2013. The complete mitochondrial genomes of Oesophagostomum asperum and Oesophagostomum columbianum in small ruminants. Infection. Infection Genetics and Evolution, 19, 205–211. CrossrefWeb of ScienceGoogle Scholar

About the article

Received: 2017-07-12

Revised: 2017-12-29

Accepted: 2018-01-18

Published Online: 2018-04-13

Published in Print: 2018-06-26


Conflict of interest: The authors state that there are no competing interests.

Ethics statement: All procedures were performed in accordance with the laws, regulations, and strict guidelines of the Laboratory Animals Research Centre of Hubei province, P. R. China. Samples were collected with the permission of the relevant institutions and by following the parameters as set by the ethics committee of Huazhong Agricultural University (Permit number: 4200695757).


Citation Information: Acta Parasitologica, Volume 63, Issue 2, Pages 280–286, ISSN (Online) 1896-1851, ISSN (Print) 1230-2821, DOI: https://doi.org/10.1515/ap-2018-0032.

Export Citation

© 2018 W. Stefański Institute of Parasitology, PAS. Copyright Clearance Center

Comments (0)

Please log in or register to comment.
Log in