TSitologiya i Genetika 2021, vol. 55, no. 5, 3-12
Cytology and Genetics 2021, vol. 55, no. 5, 405–413, doi: https://www.doi.org/10.3103/S0095452721050108

Molecular organization and polymorphism of 5S rDNA in carpathian bees

Roshka N.M., Cherevatov O.V., Volkov R.А.

  • Yuriy Fedkovych Chernivtsi National University Kotsiubynsky str. 2, 58012 Chernivtsi, Ukraine

SUMMARY. The natural distribution area of the western honey bee, Apis mellifera L., covers Europe, West Asia and Africa. Adaptation to local environmental conditions resulted in the formation of numerous subspecies and ecotypes of western honey bee, which represent a convenient model for studying the microevolution of insects. Genomic region encoding 5S rRNA (5S rDNA) is a popular tool for investigation of the molecular evolution and phylogeny of closely related animal and plant taxa. In this article, we present the results of the analysis of 5S rDNA polymorphism in two breeding races, Rakhiv and Hoverla, of the Carpathian breed of western honey bee, which represents the local ecotype of the subspecies A. m. carnica, and compare them with the data available in the Genbank database for this subspecies and the Asian species A. cerana. It was found that in the genome of A. m. carnica there are at least two classes of 5S rDNA, each of which includes several structural variants. The genomes of the two studied races of the Carpathian breed and that of the A. m. carnica from Genbank differ in the sets of such variants, while the 5S rDNA repeated units of the of A. cerana are identical within the genome. The obtained results indicate a high intra- and intergenomic polymorphism of 5S rDNA in A. m. carnica.

Keywords: 5S rDNA, Carpathian bee, molecular markers, repeated sequences, Apis mellifera

TSitologiya i Genetika
2021, vol. 55, no. 5, 3-12

Current Issue
Cytology and Genetics
2021, vol. 55, no. 5, 405–413,
doi: 10.3103/S0095452721050108

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1. Abou-Shaara, H.F., Abbas, A.S., et al., Exploring the non-coding regions in the mtDNA of some honey bee species and subspecies, Saudi J. Bio. Sci., 2021, vol. 28, no. 1, pp. 204–209. https://doi.org/10.1016/j.sjbs.2020.09.047

2. Allendorf, F.W., Leary, R.F., et al., The problems with hybrids: setting conservation guidelines, Trends Ecol. Evol., 2001, vol. 16, pp. 613–622. https://doi.org/10.1016/S0169-5347(01) 02290-X

3. Altschul, S.F., Gish, W., et al., Basic local alignment search tool, J. Mol. Biol., 1990, vol. 215, pp. 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

4. Bardella, V.B. and Cabral-de-Mello, D.C., Uncovering the molecular organization of unusual highly scattered 5S rDNA: the case of Chariesterus armatus (Heteroptera), Gene, 2018, vol. 646, pp. 153–158. https://doi.org/10.1016/j.gene.2017.12.030

5. Barman, A.S., Singh, M., et al., Evidence of birth-and-death evolution of 5S rRNA gene in Channa species (Teleostei, Perciformes), Genetica, 2016, vol. 144, no. 6, pp. 723–732. https://doi.org/10.1007/s10709-016-9938-6

6. Boardman, L., Eimanifar, A., et al., The complete mitochondrial genome of the West African honey bee Apis mellifera adansonii (Insecta: Hymenoptera: Apidae), Mitochondrial DNA, Part B, 2020a, vol. 5, no. 1, pp. 11–12. https://doi.org/10.1080/23802359.2019.1693308

7. Boardman, L., Eimanifar, A., et al., The mitochondrial genome of Apis mellifera simensis (Hymenoptera: Apidae), an Ethiopian honey bee, Mitochondrial DNA, Part B, 2020b, vol. 5, no. 1, pp. 9–10. https://doi.org/10.1080/23802359.2019.1693307

8. Brown, P, Newstrom-Lloyd, L.E., et al., Winter 2016 honey bee colony losses in New Zealand, J. Apic. Res., 2018, vol. 57, no. 2, pp. 278–291. https://doi.org/10.1080/00218839.2018.1430980

9. Bueno, D., Palacios-Gimenez, O.M., et al., The 5S rDNA in two Abracris grasshoppers (Ommatolampidinae: Acrididae): molecular and chromosomal organization, Mol. Gen. Genomics, 2016, vol. 291, no. 4, pp. 1607–1613. https://doi.org/10.1007/s00438-016-1204-1

10. Bustos, A., Figueroa, R.I., et al., The 5S rRNA genes in Alexandrium: their use as a FISH chromosomal marker in studies of the diversity, cell cycle and sexuality of dinoflagellates, Harmful Algae, 2020, vol. 98. doi.org/https://doi.org/10.1016/j.hal.2020.101903

11. Cavalcante, M.G., Nagamachi, C.Y., et al., Evolutionary insights in Amazonian turtles (Testudines, Podocnemididae): co-location of 5S rDNA and U2 snRNA and wide distribution of Tc1/Mariner, Biol. Open, 2020, vol. 9, no. 4, art. bio049817. https://doi.org/10.1242/bio.049817

12. Cherevatov, O.V. and Volkov, R.A., Molecular organization of 5S ribosomal DNA of Polyommatus icarus, Bull. Vavilov Soc. Genet. Breed. Ukr., 2010, vol. 8, no. 2, pp. 271–278.

13. Cherevatov, O.V. and Volkov, R.A., Molecular organization of 5S rDNA of Satyrus drias (Lepidoptera), Rep. Natl. Acad. Sci. Ukr., 2011a, no. 1, pp. 140–145.

14. Cherevatov, O.V. and Volkov, R.A., Organization of 5S ribosomal DNA of Melitaea trivia, Cytol. Genet., 2011b, vol. 45, no. 2, pp. 115–120. https://doi.org/10.3103/S0095452711020034

15. Cherevatov, O.V., Statna, A.P., and Volkov, R.A., Novel structural subclass of Lycaena tityrus 5S ribosomal DNA, Bull. Vavilov Soc. Genet. Breed. Ukr., 2012, vol. 10, no. 2, pp. 202–207.

16. Cherevatov, O.V., Panchuk, I.I., et al., Molecular diversity of the CoI-CoII spacer region in the mitochondrial genome and the origin of the Carpathian bee, Cytol. Genet., 2019, vol. 53, no. 4, pp. 276–281. https://doi.org/10.3103/S009 5452719040030

17. Cherevatov, O.V., Melnik, E.O., and Volkov, R.A., Polymorphism of COI gene in honey bees from different regions of Ukraine, Bull. Vavilov Soc. Genet. Breed. Ukr., 2020, vol. 18, nos. 1–2, pp. 22–28.

18. Ding, Q., Li, R., et al., Genomic architecture of 5S rDNA cluster and its variations within and between species, bioRxiv, 2021. https://doi.org/10.1101/2021.02.17.431734

19. Fedoriak, M.M., Tymochko, L.I., et al., Winter losses of honey bee (Apis mellifera L.) colonies in Ukraine (monitoring results of 2015–2016), Ukr. J. Ecol., 2017, vol. 7, no. 4, pp. 604–613. https://doi.org/10.15421/2017_167

20. Ferher, J., Skavikova, R., et al., Molecular evolution and organization of ribosomal DNA in the Hawkweed tribe Hieraciinae (Cichorieae, Asteraceae), Front. Plant Sci., 2021, vol. 12, p. 647375. https://doi.org/10.3389/fpls.2021.647375

21. Francoso, E., Araujo, N., et al., Evolutionary perspectives on bee mtDNA from mito-OMICS analyses of a solitary species, Apidologie, 2020, vol. 51, pp. 531– 544. https://doi.org/10.1007/s13592-020-00740-x

22. Garnery, L., Cornuet, J.M., et al., Evolutionary history of the honey bee Apis mellifera inferred from mitochondrial DNA analysis, Mol. Ecol., 1992, vol. 1, pp. 145–154. https://doi.org/10.1111/j.1365-294X.1992.tb00170

23. Garsia, S., Kovarik, A., et al., Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database, Plant J., 2017, vol. 89, pp. 1020–1030.https://doi.org/10.1111/tpj.13442

24. Gray, A., Adjlane, N., et al., Honey bee colony winter loss rates for 35 countries participating in the COLOSS survey for winter 2018–2019, and the effects of a new queen on the risk of colony winter loss, J. Apic. Res., 2020, vol. 59, no. 5, pp. 744–751. https://doi.org/10.1080/002188 39.2020.1797272

25. Gupta, R.K., Reybroeck, W., et al., Beekeeping for Poverty Alleviation and Livelihood Security, vol. 1: Technological Aspects of Beekeeping, Netherlands: Springer, 2014.

26. Henriques, D., Chavez-Galarza, J., et al., From the popular tRNAleu-COX2 intergenic region to the mitogenome: insights from diverse honey bee populations of Europe and North Africa, Apidologie, 2019, vol. 50, pp. 215–229. https://doi.org/10.1007/s13592-019-00632-9

27. Higgins, D.G., Bleasby, A.J., and Fuchs, R., CLUSTAL V: improved software for multiple sequence alignment, Bioinformatics, 1992, vol. 8, no. 2, pp. 189–191. https://doi.org/10.1093/bioinformatics/8.2.189

28. Ishchenko, O.O., Panchuk, I.I., et al., Molecular organization of 5S ribosomal DNA of Deschapmpsia antarctica, Cytol. Genet., 2018, vol. 52, pp. 416–421. https://doi.org/10.3103/S0095452718060105

29. Ishchenko, O.O., Bednarska, O.I., and Panchuk, I.I., Application of 5S ribosomal DNA for molecular taxonomy of subtribe Loliinae (Poaceae), Cytol. Genet., 2021, vol. 55, no. 1, pp. 10–18. https://doi.org/10.3103/S0095452721010096

30. Kek, S.P., Chin, N.L., et al., Molecular identification of honey entomological origin based on bee mitochondrial 16S rRNA and COI gene sequences, Food Control, 2017. https://doi.org/10.1016/j.foodcont.2017.02.025

31. Kotthoff, U., Wappler, T., and Engel, M.S., Greater past disparity and diversity hints at ancient migrations of European honey bee lineages into Africa and Asia, J. Biogeogr., 2013, vol. 40, pp. 1832–1838. https://doi.org/10.1111/jbi.12151

32. Kulhanek, K., Steinhauer, N., et al., A national survey of managed honey bee 2015–2016 annual colony losses in the USA, J. Apic. Res., 2017, vol. 56, no. 4, pp. 328–340. https://doi.org/10.1080/00218839.2017.1344496

33. Layat, E., Saez-Vasquez, J., and Tourmente, S., Regulation of Pol I-transcribed 45S rDNA and Pol III-transcribed 5S rDNA in Arabidopsis, Plant Cell Phys., 2012, vol. 53, no. 2, pp. 267–276. https://doi.org/10.1093/pcp/pcr177

34. Layat, E., Probst, A.V., and Tourmente, S., Structure, function and regulation of transcription factor IIIA: from Xenopus to Arabidopsis, Biochim. Biophys. Acta, 2013, vol. 1829, pp. 274–282. https://doi.org/10.1016/j.bbagrm.2012.10.013

35. Martins, C. and Galetti, P.M., Two 5S rDNA arrays in Neotropical fish species: is it a general rule for fishes?, Genetica, 2001, vol. 111, pp. 439–446.

36. Morton, D.G. and Sprague, K.U., In vitro transcription of a silkworm 5S RNA gene requires an upstream signal, Proc. Natl. Acad. Sci. U. S. A., 1984, vol. 81, pp. 5519–5522.

37. Nelson, D.W., Linning, R.M., et al., 5'-Flanking sequences required for efficient transcription in vitro of 5S RNA genes, in the related nematodes Caenorhabditis elegans and Caenorhabditis briggsae, Gene, 1998, vol. 218, pp. 9–16.

38. Neumann, P., Norman, L.C., et al., Honey bee colony losses, J. Api. Res., 2010, vol. 49, no. 1, pp. 1–6. https://doi.org/10.3896/IBRA.

39. Oliveira, N.L., Cabral-de-Mello, D.V., et al., Chromosomal mapping of rDNAs and H3 histone sequences in the grasshopper Rhammatocerus brasiliensis (Acrididae, Gomphocerinae): extensive chromosomal dispersion and co-localization of 5S rDNA/H3 histone clusters in the A complement and B chromosome, Mol. Cytogenet., 2011, vol. 4, p. 24. https://doi.org/10.1186/1755-8166-4-24

40. Oliveira, S.G., Cabral-de-Mello, D.C., et al., Heterochromatin, sex chromosomes and rRNA gene clusters in Coprophanaeus beetles (Coleoptera, Scarabaeidae), Cytogenet. Genome Res., 2012, vol. 138, pp. 46–55. https://doi.org/10.1159/000339648

41. Pieler, T., Hamm, J., and Roeder, R.G., The 5S gene internal control region is composed of three distinct sequence elements, organized as two functional domains with variable spacing, Cell, 1987, vol. 48, pp. 91–100. https://doi.org/10.1016/0092-8674(87)90359-X

42. Pinhal, D., Yoshimura, T.S., et al., The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays, BMC Evol. Biol., 2011, vol. 11, p. 151. https://doi.org/10.1186/1471-2148-11-151

43. Polishchuk, V.P. and Gaidar, V.A., Apiary, Kiev, Ukraine: Perfect style, 2008.

44. Qin, Q.B., Liu, Q.W., et al., Molecular organization and chromosomal localization analysis of 5S rDNA clusters in autotetraploids derived from Carassius auratus Red Var. (♀) × Megalobrama amblycephala (♂), Front. Genet., 2019, vol. 10, p. 437. https://doi.org/10.3389/fgene.2019.00437

45. Ruttner, F., Biogeography and Taxonomy of Honeybees, Berlin: Springer-Verlag, 1988. https://doi.org/10.1007/978-3-642-72649-1

46. Ruttner, F., Naturgeschichte der Honigbienen, Munich, Germany: Ehrenwirth, 1992.

47. Schiebelhut, L.M., Abboud, S.S., et al., A comparison of DNA extraction methods for high-throughput DNA analyses, Mol. Ecol. Res., 2017, vol. 17, no. 4, pp. 721–729.

48. Sharp, S.J. and Garcia, A.D., Transcription of the Drosophila melanogaster 5S RNA gene requires an upstream promoter and four intragenic sequences elements, Mol. Cell Biol., 1988, vol. 8, no. 3, pp. 1266–1274.

49. Simon, L., Rabanal, F.A., et al., Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana, Nucleic Acids Res., 2018, vol. 46, no. 6, pp. 3019–303. https://doi.org/10.1093/nar/gky163

50. Slathia, I. and Tripathi, N.K., Genetic diversity of Apis mellifera (Hymenoptera: Insecta)—a review, J. New Biol. Rep., 2016, vol. 5, no. 3, pp. 148–164.

51. Stanimirovic, Z., Glavinic, U., et al., Looking for the causes of and solutions to the issue of honey bee colony losses, Acta Vet-Beogr., 2019, vol. 69, no. 1, pp. 1–31. https://doi.org/10.2478/acve-2019-0001

52. Tihelka, E., Cai, C., et al., Mitochondrial genomes illuminate the evolutionary history of the western honey bee (Apis mellifera), Sci. Rep., 2020, vol. 10, p. 14515. https://doi.org/10.1038/s41598-020-71393-0

53. Tynkevich, Y.O. and Volkov, R.A., 5S ribosomal DNA of distantly related Quercus species: molecular organization and taxonomic application, Cytol. Genet., 2019, vol. 53, no. 6, pp. 459–466. https://doi.org/10.3103/S0095452719060100

54. Tyler, B.M., Transcription of Neurospora crassa 5S rRNA genes requires a TATA box and three internal elements, J. Mol. Biol., 1987, vol. 196, pp. 801–811. https://doi.org/10.1016/0022-2836(87)90406-2

55. Vierna, J., Wehner, S., et al., Systematic analysis and evolution of 5S ribosomal DNA in metazoans, Heredity, 2013, vol. 111, pp. 410–421. https://doi.org/10.1038/hdy.2013.63

56. Vizoso, M., Vierna, J., et al., The 5S rDNA gene family in mollusks: characterization of transcriptional regulatory regions, prediction of secondary structures, and long-term evolution, with special attention to Mytilidae mussels, J. Hered., 2011, vol. 102, no. 4, pp. 433–447. https://doi.org/10.1093/jhered/esr046

57. Vozarova, R., Herklotz, V., et al., Ancient origin of two 5S rDNA families dominating in the genus Rosa and their behavior in the Canina-type meiosis, Front. Plant Sci., 2021, vol. 12, p. 643548. https://doi.org/10.3389/fpls.2021.643548

58. Whitfield, C.W., Behura, S.K., Berlocher, S.H., et al., Thrice out of Africa: ancient and recent expansions of the honey bee, Apis mellifera, Science, 2006, vol. 314, no. 5799, pp. 642–645. https://doi.org/10.1126/science.1132772