Advertisement

Acta Parasitologica

, Volume 63, Issue 2, pp 280–286 | Cite as

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

  • Kun Li
  • Muhammad Shahzad
  • Hui Zhang
  • Khalid Mehmood
  • Xiong Jiang
  • Houqiang Luo
  • Lihong Zhang
  • Xiaoqian Dong
  • Jiakui LiEmail author
Article

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 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410CrossRefGoogle Scholar
  2. 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, 25–29CrossRefGoogle Scholar
  3. Benson G. 1999 Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27, 573–580CrossRefGoogle Scholar
  4. Borgstrom, E., Lundin, S., Lundeberg J. 2011. Large scale library generation for high throughput sequencing. PLoS One, 6, e19119. DOI: 10.1371/journal.pone.0019119CrossRefGoogle Scholar
  5. Chiaromonte, F., Yap, V.B., Miller W. 2002. Scoring pairwise genomic sequence alignments. Pacific Symposium on Biocomputing, 7, 115–126Google Scholar
  6. 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, e122CrossRefGoogle Scholar
  7. 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, 4482–4487CrossRefGoogle Scholar
  8. 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. DOI: 10.7589/2011-07-217CrossRefGoogle Scholar
  9. 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. DOI: 10.1007/s00436-014-4001-yCrossRefGoogle Scholar
  10. 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, 1734–1744CrossRefGoogle Scholar
  11. 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
  12. 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
  13. 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, 522–533CrossRefGoogle Scholar
  14. Kanehisa M. 1997. A database for post-genome analysis. Trends in Genetics, 13, 375CrossRefGoogle Scholar
  15. 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
  16. 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
  17. 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, R12CrossRefGoogle Scholar
  18. 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, 2078–2079CrossRefGoogle Scholar
  19. Li, K., Lan, Y.F., Luo, H.Q., Shahzad, M., Zhang, H., Wang, L., et al. 2017a. Prevalence of three Oesophagostomum spp. from Tibetan pigs analyzed by genetic markers of nad1, cox3 and ITS1. Acta Parasitologica, 62, 90–96. DOI: 10.1515/ap-2017-0010PubMedGoogle Scholar
  20. 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. DOI: 10.1016/j.vetpar.2016.04.036CrossRefGoogle Scholar
  21. 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. DOI: 10.1016/j.actatropica.2017.06.019CrossRefGoogle Scholar
  22. 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, 224CrossRefGoogle Scholar
  23. 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, 265–272CrossRefGoogle Scholar
  24. Li X.R. (Ed.) 2011. Color atlas of animal parasitosis (2nd Edition). Beijing: China Agriculture PressGoogle Scholar
  25. 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: c haracterization of the complete mitochondrial genome sequences of the two pig nodule worms. Experimental Parasitology 131, 1–7. DOI: 10.1016/j.exppara.2012.02.015CrossRefGoogle Scholar
  26. 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
  27. Magrane M. 2011. UniProt. Knowledgebase: a hub of integrated protein data. Databases-Oxford, 2011, 9. DOI: 10.1093/database/bar009Google Scholar
  28. 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. DOI: 10.1016/j.rvsc.2011.05.016CrossRefGoogle Scholar
  29. 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
  30. Saha, S., Bridges, S., Magbanua, Z.V., Peterson D.G. 2008. Empirical comparison of ab initio repeat finding programs. Nucleic Acids Research, 36, 2284–2294CrossRefGoogle Scholar
  31. 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, 1581–1588CrossRefGoogle Scholar
  32. 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, 339–347CrossRefGoogle Scholar
  33. 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, 1–15Google Scholar
  34. 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, 41CrossRefGoogle Scholar
  35. Tatusov, R.L., Koonin, E.V., Lipman D.J. 1997. A genomic perspective on protein families. Science, 278, 631–637CrossRefGoogle Scholar
  36. Wyman, S.K., Jansen, R.K., Boore J.L. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20, 3252–3255CrossRefGoogle Scholar
  37. 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. DOI: 10.1016/j.actatropica.2013.12.021CrossRefGoogle Scholar
  38. 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. DOI: 10.1186/1756-3305-7-319CrossRefGoogle Scholar

Copyright information

© Witold Stefański Institute of Parasitology, Polish Academy of Sciences 2018

Authors and Affiliations

  • Kun Li
    • 1
  • Muhammad Shahzad
    • 1
    • 3
  • Hui Zhang
    • 1
  • Khalid Mehmood
    • 1
    • 3
  • Xiong Jiang
    • 1
  • Houqiang Luo
    • 1
  • Lihong Zhang
    • 1
  • Xiaoqian Dong
    • 4
  • Jiakui Li
    • 1
    • 2
    Email author
  1. 1.College of Veterinary MedicineHuazhong Agricultural UniversityWuhanPeople’s Republic of China
  2. 2.Laboratory of Detection and Monitoring of Highland Animal DiseaseTibet Agriculture and Animal Husbandry CollegeLinzhi, TibetPeople’s Republic of China
  3. 3.University College of Veterinary & Animal SciencesThe Islamia University of BahawalpurBahawalpurPakistan
  4. 4.Animal husbandry and Veterinary Bureau of Taishan districtTaianPeople’s Republic of China

Personalised recommendations