Skip to main content
SpringerLink
Log in

Variability of Nucleotide Sequences in the ITS1–5.8S rRNA–ITS2a–2S rRNA–ITS2 Region of rRNA Gene Cluster in Species of the Family Chironomidae

  • GENERAL GENETICS
  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

The variability of nucleotide sequences of ribosomal genes and internal transcribed spacers located in the ITS1–5.8S rRNA–ITS2a–2S rRNA–ITS2 region separating the 18S and 28S rRNA genes in the rRNA gene cluster was studied in order to estimate the possibility of using these sequences as molecular markers for species identification and reconstruction of the phylogeny of the family Chironomidae. It was established that, in species of the family Chironomidae, the content of AT base pairs in the sequences of the 5.8S rRNA and 2S rRNA genes is lower (50–57%) than in the sequences of the ITS1, ITS2a, and ITS2 transcribed spacers (64–71%). The sizes of nucleotide sequences of the 5.8S rRNA (123 bp) and 2S rRNA (30 bp) genes in species of the family Chironomidae are conservative, while the sizes of the ITS1, ITS2a, and ITS2 internal transcribed spacers vary both within the species and between species. Neither intraspecific, nor interspecific, nor intergeneric nucleotide differences were found in the sequences of the 2S rRNA gene in 27 species from five genera of the family Chironomidae. Nucleotide sequences of the 5.8S rRNA gene are identical in most studied species of the Chironomus genus. Fixed interspecific nucleotide substitutions were found only in two sites of this gene sequence in three species: C. piger, C. riparius (473С>T), and C. annularius (474A>G). The number of insertions, deletions, and nucleotide substitutions in the sequences of the ITS1, ITS2a, and ITS2 internal transcribed spacers and the whole ITS1–5.8S rRNA–ITS2a–2S rRNA–ITS2 region is generally low within species and increases 5–6 times in sibling species and more than 10 times in morphologically distinct species; that is, it increases in accordance with the growth of taxonomic status of species from the family Chironomidae. The data obtained indicate that nucleotide sequences of ribosomal genes and internal transcribed spacers from the ITS1–5.8S rRNA–ITS2a–2S rRNA–ITS2 region of the rRNA gene cluster can be used as molecular markers for species identification and reconstruction of the phylogeny of the family Chironomidae.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.

Similar content being viewed by others

REFERENCES

  1. Ferrington, L.C., Global diversity of non-biting midges (Chironomidae; Insecta—Diptera) in freshwater, Hydrobiologia, 2008, vol. 595, no. 1, pp. 447—455. https://doi.org/10.1007/s10750-007-9130-1

    Article  Google Scholar 

  2. Saether, O.A., Phylogeny of the subfamilies of Chironomidae (Diptera), Syst. Entomol., 2000, vol. 25, no. 3, pp. 393—403. https://doi.org/10.1046/j.1365-3113.2000.00111.x

    Article  Google Scholar 

  3. Wiederholm, T., Chironomidae of the Holarctic Region: Keys and Diagnoses, Part 1: Larvae, in Ent. Scand. Suppl., 1983, vol. 19.

  4. Shobanov, N.A., Shilova, A.I., and Belyanina, S.I., Volume and structure of the genus Chironomus Meig. (Diptera, Chironomidae): a review of the world’s fauna, in Ekologiya, evolyutsiya i sistematika khironomid (Ecology, Evolution, and Taxonomy of Chironomids), Tol’yatti: Inst. Biol. Vnutrennikh Vod and Inst. Ekol. Volzh. Basseina Russ. Akad. Nauk, 1996, pp. 44—96.

    Google Scholar 

  5. Lindeberg, B. and Wiederholm, T., Notes on the taxonomy of European species of Chironomus (Diptera Chironomidae), Ent. Scand. Suppl., 1979, vol. 10, pp. 99—116.

    Google Scholar 

  6. Keyl, H.-G., Chromosomenevolution bei Chironomus: II. Chromosomenumbauten und phylogenetische Beziehungen der Arten, Chromosoma, 1962, vol. 13, no. 4, pp. 464—514. https://doi.org/10.1007/BF00327342

    Article  Google Scholar 

  7. Kiknadze, I.I., Shilova, A.I., Kerkis, I.E., et al., Kariotipy i morfologiya lichinok triby Chironomini: atlas (Karyotypes and Larval Morphology of the Midges of the Tribe Chironomini: An Atlas), Novosibirsk: Nauka, 1991.

    Google Scholar 

  8. Kiknadze, I., Istomina, A., Golygina, V., and Gunderina, L., Karyotypes of Palearctic and Holarctic Species of the Genus Chironomus, Novosibirsk: GEO, 2016.

    Google Scholar 

  9. Martin, J., Australian, North American, New Zealand and Oriental Chironomus species. http://www.chironomidae.net/Martin/JMRes.html. Accessed May 11, 2019.

  10. Wuelker, W., Devai, Gy., and Devai, I., Computer assisted studies of chromosome evolution in the genus Chironomus (Dipt.) comparative and integrated analysis of chromosome arms A, E and F, Acta Biol. Debr. Oecol. Hung., 1989, vol. 2, pp. 373—387.

    Google Scholar 

  11. Gunderina, L.I., Kiknadze, I.I., Istomina, A.G., et al., Divergence of the polytene chromosome banding sequences as a reflection of evolutionary rearrangements of the genome linear structure, Russ. J. Genet., 2005, vol. 41, no. 2, pp. 130—137. https://doi.org/10.1007/s11177-005-0036-6

    Article  CAS  Google Scholar 

  12. Shobanov, N.A., Evolution of the genus Chironomus (Diptera, Chironomidae): 2. A phylogenetic model, Zool. Zh., 2002, vol. 81, no. 6, pp. 711—718.

    Google Scholar 

  13. Kiknadze, I.I., Gunderina, L.I., Butler, M.G., et al., Chromosomes and continents, Biosphere Origin and Evolution, Dobretsov, N., Kolchanov, N., Rozanov, A., and Zavarin, G., Eds., New York: Springer-Verlag, 2008, pp. 349—369.

    Google Scholar 

  14. Guryev, V., Makarevitch, I., Blinov, A., and Martin, J., Phylogeny of the genus Chironomus (Diptera) inferred from sequences mitochondrial cytochrome b and cytochrome oxidase 1, Mol. Phylogenet. Evol., 2001, vol. 19, no.1, pp. 9—21. https://doi.org/10.1006/mpev.2001.0898

    Article  CAS  PubMed  Google Scholar 

  15. Martin, J., Guryev, V., and Blinov, A., Population variability in Chironomus (Camptochironomus) species (Diptera, Nematocera) with a Holarctic distribution: evidence of mitochondrial gene flow, Insect Mol. Biol., 2002, vol. 11, pp. 387—397. https://doi.org/10.1046/j.1365-2583.2002.00348.x27

    Article  CAS  PubMed  Google Scholar 

  16. Proulx, I., Martin, J., Carew, M., and Hare, L., Using various lines of evidence to identify Chironomus species (Diptera: Chironomidae) in eastern Canadian lakes, Zootaxa, 2013, vol. 3741, pp. 401—458. https://doi.org/10.11646/zootaxa.3741.4.1

    Article  PubMed  Google Scholar 

  17. Gunderina, L.I. and Katokhin, A.V., Variation and divergence of the rDNA ITS-1 region in species of the genus Chironomus (Diptera: Chironomidae), Contemporary Chironomid Studies (Proc. XVII Int. Symp. on Chironomidae, 2009, Nankai University, China), Nankai: Nankai University Press, 2011, pp. 22—35.

  18. Asari, H., Kasuya, S., Kobayashi, T., et al., Identification of closely related Hydrobaenus species (Diptera: Chironomidae) using the second internal transcribed spacer (ITS2) region of ribosomal DNA, Aquat. Insects, 2004, vol. 26, nos. 3—4, pp. 207—213. https://doi.org/10.1080/01650420412331327295

    Article  Google Scholar 

  19. Kaga, K., Kasuya, S., Kobayashi, T., and Ohtaka, A., Identification of chironomid species by DNA sequence—especially genus Hydrobaenus including H. sp. “Tsugaru”, in Contemporary Chironomid Studies (Proc. XVII Int. Symp. on Chironomidae, 2009, Nankai University, China), Nankai: Nankai University Press, 2011, pp. 36—40.

  20. Schlötterer, Ch., Hauser, M.-T., von Haeseler, A., and Tautz, D., Comparative evolutionary analysis of rDNA ITS regions in Drosophila, Mol. Biol. Evol., 1994, vol. 11, no. 3, pp. 513—522.

    PubMed  Google Scholar 

  21. Tautz, D., Hancock, J.M., Webb, D.A., et al., Complete sequences of the rRNA genes of Drosophila melanogaster, Mol. Biol. Evol., 1988, vol. 5, no. 4, pp. 366—376.

    CAS  PubMed  Google Scholar 

  22. Friedrich, M. and Tautz, D., An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera, Mol. Biol. Evol., 1997, vol. 14, no. 6, pp. 644—653.

    Article  CAS  PubMed  Google Scholar 

  23. Stage, D.E. and Eickbush, T.H., Sequence variation within the rRNA gene loci of 12 Drosophila species, Genome Res., 2007, vol. 17, no. 12, pp. 1888—1897. https://doi.org/10.1101/gr.6376807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Matsumoto, Y., Yanase, T., Tsuda, T., and Noda, H., Characterization of internal transcribed spacer (ITS1)—ITS2 region of ribosomal RNA gene from 25 species of Culicoides biting midges (Diptera: Ceratopogonidae) in Japan, J. Med. Entomol., 2009, vol. 46, no. 5, pp. 1099—1108. https://doi.org/10.1603/033.046.0517

    Article  CAS  PubMed  Google Scholar 

  25. LaRue, B., Gaudreau, C., Bagre, H.O., and Charpentier, G., Generalized structure and evolution of ITS1 and ITS2 rDNA in black flies (Diptera: Simuliidae), Mol. Phylogenet. Evol., 2009, vol. 53, no. 3, pp. 749—757. https://doi.org/10.1016/j.ympev.2009.07.032

    Article  CAS  PubMed  Google Scholar 

  26. Tatonova, Y.V., Chelomina, G.N., and Besprosvannykh, V.V., Genetic diversity of nuclear ITS1–5.8S–ITS2 rDNA sequence in Clonorchis sinensis Cobbold, 1875 (Trematoda: Opisthorchidae) from the Russian Far East, Parasitol. Int., 2012, vol. 61, pp. 664—674. https://doi.org/10.1016/j.parint.2012.07.005

    Article  CAS  PubMed  Google Scholar 

  27. Coleman, A.W., ITS2 is a double-edged tool for eukaryote evolutionary comparisons, Trends Genet., 2003, vol. 19, no. 7, pp. 370—375. https://doi.org/10.1016/S0168-9525(03)00118-5

    Article  CAS  PubMed  Google Scholar 

  28. Coleman, A.W., Pan-eukaryote ITS2 homologies revealed by RNA secondary structure, Nucleic Acids Res., 2007, vol. 35, pp. 3322—3329. https://doi.org/10.1093/nar/gkm233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Wang, X.C., Liu, C., Huang, L., et al., ITS1: a DNA barcode better than ITS2 in eukaryotes?, Mol. Ecol. Resour., 2015, vol. 15, pp. 573—586. https://doi.org/10.1111/1755-0998.12325

    Article  CAS  PubMed  Google Scholar 

  30. Rozen, S. and Skaletsky, H.J., Primer 3 on the WWW for general users and for biologist programmers, Methods Mol. Biol., 2000, vol. 132, pp. 365—386.

    CAS  PubMed  Google Scholar 

  31. Edgar, R.C., MUSCLE: Multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 2004, vol. 32, no. 5, pp. 1792—1797. https://doi.org/10.1093/nar/gkh340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Tamura, K., Stecher, G., Peterson, D., et al., MEGA6: molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 2013, vol. 30, no. 12, pp. 2725—2729. https://doi.org/10.1093/molbev/mst197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Gunderina, L.I., Species-specific PCR primers for identification of the sibling species Chironomus plumosus (Linnaeus, 1758) and Chironomus balatonicus (Devai, Wuelker et Scholl, 1983) (Chironomidae, Diptera), Fauna Norv., 2012, vol. 32, pp. 151—157. https://doi.org/10.5324/fn.v31i0.1381

    Article  Google Scholar 

  34. Gunderina, L.I., Design of molecular markers for the identification of species of the genus Chironomus (Diptera, Chironomidae), Entmol. Rev., 2014, vol. 94, no. 1, pp. 140—148. https://doi.org/10.1134/S0013873814010151

    Article  Google Scholar 

Download references

Funding

This work was supported by the budgetary project no. 0324-2019-0042.

Author information

Authors and Affiliations

  1. Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia

    L. I. Gunderina & A. V. Katokhin

Authors
  1. L. I. Gunderina
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. V. Katokhin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to L. I. Gunderina.

Ethics declarations

The authors declare that they have no conflict of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.

Additional information

Translated by A. Barkhash

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gunderina, L.I., Katokhin, A.V. Variability of Nucleotide Sequences in the ITS1–5.8S rRNA–ITS2a–2S rRNA–ITS2 Region of rRNA Gene Cluster in Species of the Family Chironomidae. Russ J Genet 56, 916–925 (2020). https://doi.org/10.1134/S1022795420080050

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1022795420080050

Keywords:

Search

Navigation