Panteleev S. V., Mozharovskaya L. V., Baranov O. Yu., Yarmolovich V. A., Padutov V. Е. Genetic Polymorphism of mtCOI Locus in Belarussian Populations of Pine Bark Beetle Ips acuminatus Gyll.
1 Institute of Forest, National Academy of Sciences of Belarus
Proletarskaya str., 71, Gomel, 246050 Republic of Belarus
2 Belarusian State Technological University
Sverdlov str., 13а, Minsk, 220006 Republic of Belarus
E-mail: stasikdesu@mail.ru, milamozh@yandex.ru, betula-belarus@mail.ru, yarm@belstu.by,
Abstract
UDC 631.523.5
How to cite: Panteleev S. V.1, Mozharovskaya L. V.1, Baranov O. Yu.1, Yarmolovich V. A.2, Padutov V. Е.1 Genetic polymorphism of mtCOI locus in belarussian populations of pine bark beetle Ips acuminatus Gyll. // Sibirskij Lesnoj Zurnal (Sib. J. For. Sci.). 2020. N 4. P. 15–29 (in Russian with English abstract and references).
DOI: 10.15372/SJFS20200403
© Panteleev S. V., Mozharovskaya L. V., Baranov O. Yu., Yarmolovich V. A., Padutov V. Е., 2020
Sequencing and annotation of the pine bark beetle mitochondrial genome (registration number in NCBI GenBank MK988441), including the insect barcoding marker – the part of the subunit I of mitochondrial cytochrome oxidase gene (mtCOI), were carried out. A comparative assessment of the level of polymorphism among mtDNA loci revealed that mtcoI has moderate level of variability. A preliminary study of the Belarusian populations of the pine bark beetle showed 18 haplotype variants at the mtCOI marker locus (mtcoI gene fragment). Significant portion of the studied individuals (50 %) were heteroplasmic – contained at least two mtCOI haplotypes in the genome together. Studying the level of genetic differentiation between haplotypes using the Jukes-Cantor (JC) and Kimura (K80) models revealed a wide range of variation in the values of the evolutionary distance indicator D - from 0.001 to 0.066, which corresponded to 1–46 nucleotide substitutions for the studied region (690 nr) in individual haplotypes. Analysis of the peptide sequences of the pine bark beetle mtCOI locus using 3D modeling technology, as well as using Ramachandran maps and the NCBI CDART database, showed that the domain architecture of the protein remains unchanged for the majority (94 %) of haplotypes and the functionality of allozymes is not violated, that indicates the relatively selectively neutral nature of the detected polymorphism. Based on the obtained total molecular genetic data, it was concluded that the degree of informational content of the mtCOI marker (based on mtcoI) is sufficient to carry out population-genetic studies of the pine bark beetle, including an assessment of its migration activity.
Article
СПИСОК ЛИТЕРАТУРЫ (REFERENCES)
Падутов В. Е., Баранов О. Ю., Воропаев Е. В. Методы молекулярно-генетического анализа. Минск: Юнипол, 2007. 176 с. [Padutov V. Е., Baranov O. Yu., Voropaev Е. V. Metody molekulyarno-geneticheskogo analiza (Methods of molecular-genetic analysis). Minsk: Yunipol, 2007. 176 p. (in Russian)].
Сазонов А. А., Звягинцев В. Б. «Биологический пожар» соснового леса // Лесн. и охотн. хоз-во. 2016. № 6. С. 9–13 [Sazonov A. A., Zvyagintsev V. B. «Biologicheskiy pozhar» sosnovogo lesa («Biological fire» of a pine forest) // Lesn. i okhotn. khoz-vo (Forest and hunting economy). 2016. N. 6. P. 9–13 (in Russian)].
Alfonzo J. D., Thiemann O. H., Simpson L. W. The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria // Nucl. Acids Res. 1997. V. 25. Iss. 19. P. 3751–3759.
Avtzis D. N., Lakatos F., Gallego D., Pernek M., Faccoli M., Wegensteiner R., Stauffer C. Shallow genetic structure among the European populations of the six-toothed bark beetle Ips sexdentatus (Coleoptera, Curculionidae, Scolytinae) // Forests. 2019. V. 10. Iss. 2. P. 1–10.
Bark beetles: Biology and ecology of native and invasive species / F. E. Vega, and R. W. Hofstetter (Eds.). Elsevier Acad. Press, 2015. P. 351–359.
Bentz B. J., Regniere J., Fettig C. J., Hansen E. M., Hayes J. L., Hicke J. A.; Kelsey R. G., Negron J. F., Seybold S. J. Climate change and bark beetles of the western United States and Canada: direct and indirect effects // Bioscience. 2010. V. 60. N. 8. P. 602–613.
Bernt M., Donath A., Juhling F., Externbrink F., Florentz C., Fritzsch G., Putz J., Middendorf M., Stadler P. F. MITOS: Improved de novo metazoan mitochondrial genome annotation // Mol. Phylogenet. Evolut. 2013. V. 69. Iss. 2. P. 313–319.
Castle J. C. SNPs occur in regions with less genomic sequence conservation // PLoS One. 2011. V. 6. Iss. 6. Article number: e20660. P. 1–12.
Clare E. L., Lim B. K., Engstrom M. D., Eger J. L., Hebert P. D. DNA barcoding of Neotropical bats: species identification and discovery within Guyana // Mol. Ecol. Notes. 2007. V. 7. Iss. 2. P. 184–190.
Clement M. D., Posada D., Crandall K. A. TCS: a computer program to estimate gene genealogies // Mol. Ecol. 2000. V. 9. Iss. 10. P. 1657–1659.
Colombari F., Schroeder M. L., Battisti A., Faccoli M. Spatio‐temporal dynamics of an Ips acuminatus outbreak and implications for management // Agr. For. Entomol. 2013. V. 15. Iss. 1. P. 34–42.
Dayama G., Emery S. B., Kidd J. M., Mills R. E. The genomic landscape of polymorphic human nuclear mitochondrial insertions // Nucl. Acids Res. 2014. V. 42. N. 20. P. 12640–12649.
DNA barcodes: methods and protocols / W. J. Kress, and D. L. Erickson (Eds.). Humana Press, 2012. 370 p.
Fearnley I. M., Walker J. E. Initiation codons in mammalian mitochondria: differences in genetic code in the organelle // Biochemistry. 1987. V. 26. P. 8247–8251.
Folmer O., Black M., Hoeh W., Lutz R., Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates // Mol. Marine Biol. Biotechnol. 1994. V. 3. N. 5. P. 294–299.
Freeland J. R., May M., Lodge R., Conrad K. F. Genetic diversity and widespread haplotypes in a migratory dragonfly, the common green darner Anax junius // Ecol. Entomol. 2003. V. 28. N. 4. P. 413–421.
Fu Y. X., Li W. H. Statistical tests of neutrality of mutations // Genetics. 1993. V. 133. N. 3. P. 693–709.
Glasel J. A. Validity of nucleic acid purities monitored by 260nm/280nm absorbance ratios // BioTechn. 1995. V. 18. N. 1. P. 62–63.
Hlaing T., Tun-Lin W., Somboon P., Socheat D., Setha T., Min S., Chang M. S., Walton C. Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes: implications for the past and future population genetic studies // BMC Genet. 2009. V. 10. N. 11. P. 1–12.
Hlasny T., Krokene P., Liebhold A., Montagne-Huck C., Muller J., Qin H., Raffa K., Schelhaas M-J., Seidl R., Svoboda M., Viiri H. Living with bark beetles: impacts, outlook and management options. From Science to Policy 8. Joensuu, Finland: EFI, 2019. 52 p.
Jukes T. H., Cantor C. R. Evolution of protein molecules In Mammalian Protein Metabolism / H. N. Munro (Ed.). New York: Acad. Press, 1969. P. 21–132.
Kang A. R., Kim M. J., Park I. A., Kim K. Y., Kim I. Extent and divergence of heteroplasmy of the DNA barcoding region in Anapodisma miramae (Orthoptera: Acrididae) // Mitochondrial DNA. A DNA Mapp. Seq. Anal. 2016. V. 27. N. 5. P. 3405–3414.
Kerr K. C. R., Stoeckle M. Y., Dove C. J., Weigt L. A., Francis C. M., Hebert P. D. N. Comprehensive DNA barcode coverage of North American birds // Mol. Ecol. Notes. 2007. V. 7. Iss. 4. P. 535–543.
Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences // J. Mol. Evolut. 1980. V. 16. N. 2. P. 111–120.
Krivan V., Lewis M., Bentz B. J., Bewick S., Lenhart S. M., Liebhold A. A dynamical model for bark beetle outbreaks // J. Theor. Biol. 2016. V. 407. P. 25–37.
Latorre A., Hernandez C., Martinez D., Castro J. A., Ramon M., Moya A. Population structure and mitochondrial DNA gene flow in Old World populations of Drosophila subobscura // Heredity. 1992. V. 68. P. 15–24.
Meier R., Shiyang K., Vaidya G., Ng P. K. DNA barcoding and taxonomy in diptera: a tale of high intraspecific variability and low identification success // Syst. Biol. 2006. V. 55. Iss. 5. P. 715–728.
Meyer C. P, Paulay G. DNA barcoding: error rates based on comprehensive sampling // PLoS Biol. 2005. V. 3. Iss. 12. Article number: E422. P. 2229–2238.
National Center for Biotechnology Information, 2020. https://blast.ncbi.nlm.nih.gov/Blast.cgi
Pfeiler E., Markow T. A. Population connectivity and genetic diversity in long-distance migrating insects: divergent patterns in representative butterflies and dragonflies // Biol. J. Linnean Soc. 2017. V. 122. Iss. 2. P. 479–486.
PopART, 2020. https://popart.otago.ac.nz
Primer-BLAST. A tool for finding specific primers, 2020. https://www.ncbi.nlm.nih.gov/tools/primer-blast/
Ramachandran G. N., Ramakrishnan C., Sasisekharan V. Stereochemistry of polypeptide chain configurations // J. Mol. Biol. 1963. V. 7. P. 95–99.
Robison G. A., Balvin O., Schal C., Vargo E. L., Booth W. Extensive mitochondrial heteroplasmy in natural populations of a resurging human pest, the bed bug (Hemiptera: Cimicidae) // J. Med. Entomol. 2015. V. 52. N. 4. P. 734–738.
Rosetti N., Remis M. I. Spatial genetic structure and mitochondrial DNA phylogeography of Argentinean populations of the grasshopper Dichroplus elongatus // PLoS One. 2012 V. 7. Iss. 7. Article number: e40807. P. 1–20.
Sengupta S., Yang X., Higgs P. G. The mechanisms of codon reassignments in mitochondrial genetic codes // J. Mol. Evolut. 2007. V. 64. N. 6. P. 662–688.
Siitonen J. Ips acuminatus kills pines in southern Finland // Silva Fenn. 2014. V. 48. N. 4. P. 1–7.
Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism // Genetics. 1989. V. 123. N. 3. P. 585–595.
Tataurov A. V., You Y., Owczarzy R. Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids // Biophys. Chem. 2008. V. 133. N. 1–3. P. 66–70.
Thorsness P. E, Fox T. D. Nuclear mutations in Saccharomyces cerevisiae that affect the escape of DNA from mitochondria to the nucleus // Genetics. 1993. V. 134. N. 1. P. 21–28.
Ward R. D., Zemlak T. S., Innes B. H., Last P. R., Hebert P. D. DNA barcoding Australia’s fish species // Phil. Trans. Royal Soc. B: Biol. Sci. 2005. V. 360. Iss. 1462. P. 1847–1857.
Yeap H. L, Rasic G., Endersby-Harshman N. M., Lee S. F., Arguni E., Le Nguyen H., Hoffmann A. A. Mitochondrial DNA variants help monitor the dynamics of Wolbachia invasion into host populations // Heredity (Edinb). 2016. V. 116. Iss. 3. P. 265–276.
