SUMMARY. The wavy hair-grass, Avenella flexuosa (L.) Drejer (also known as Deschampsia flexuosa (L.) Trin. or Lerchenfeldia flexuosa (L.) Schur), is a species of perennial herbaceous plants of the Poaceae family that is widespread in Eurasia, Africa, North and South America. Whether this species belongs to the Deschampsia genus has long been an open question. Taking into account that the 5S rDNA comparison is a convenient tool in the molecular taxonomy of plants, we cloned and sequenced this region of the A. flexuosa genome and evaluated the genetic distances between this species and other species of the Poeae tribe. It has been found that at least two structural classes of 5S rDNA repeats are present in the A. flexuosa genome. The spacer regions in the 5S rDNA of A. flexuosa and D. antarctica have a low level of similarity that does not exceed the level of similarity with representatives of several other genera of the Poeae tribe. The 5S rDNA clones of A. flexuosa and D. antarctica form two distinct clades on the phyllodendogram. Taking together, our results support the idea that A. flexuosa belongs to a separate genus Avenella.
Keywords: molecular evolution and taxonomy, intergenic spacer of 5S rDNA, Avenella, Deschampsia, Poeae
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References
1. Linnaeus, C., Species Plantarum, Holmiae: Impensis Laurentii Salvii, 1753. https://doi.org/10.5962/bhl.title.669
2. Palisot de Beauvois, A.M.F.J., Essai d’une nouvelle Agrostographie; ou nouveau genres des Graminées; avec figures représentant les caracters de tous les genres, Paris: Chez l’auteur, Rue de Turenne, 1812.
3. Mosyakin, S.L. and Fedoronchuk, M.M., Vascular Plants of Ukraine. A Nomenclatural Checklist, Kiev: M.G. Kholodny Institute of Botany, 1999. https://doi.org/10.13140/2.1.2985.0409
4. Chiapella, J., A molecular phylogenetic study of De-schampsia (Poaceae: Aveneae) inferred from nuclear ITS and plastid trnL sequence data: support for the recognition of Avenella and Vahlodea, Taxon, 2007, vol. 56, no. 1, p. 55–64. https://doi.org/10.2307/25065735
5. Albers, F., Cytotaxonomie und B-Chromosomen bei Deschampsia cespitosa (L.) P.B. und verwandten Arten, Beitr. Biol. Pflanzen, 1972, vol. 48, pp. 1–62.
6. Albers, F., Cytosystematische Untersuchungen in der Subtribus Deschampsiineae Holub (Tribus Aveneae Nees). II. Die Gattungen Vahlodea Fr. und Avenella Koch, Ber. Deutsch. Bot. Ges., 1972, vol. 85, pp. 279–285.
7. Albers, F. Vergleichende Karyologie der Gräser-Subtriben Aristaveninae und Airinae (Poaceae-Aveneae), Plant Syst. Evol., 1980, vol. 136, pp. 137–167.
8. Quintanar, A., Castroviejo, S., and Catalán, P. Phylogeny of the tribe Aveneae (Pooideae, Poaceae) inferred from plastid trnT-F and nuclear ITS sequences, Am. J. Bot., 2007, vol. 94, no. 9, pp. 1554–1569. https://doi.org/10.3732/ajb.94.9.1554
9. Chiapella, J. and Zuloaga, F.O., A revision of Deschampsia, Avenella, and Vahlodea (Poaceae, Poeae, Airinae) in South America, Ann. Missouri Bot. Garden, 2010, vol. 97, no. 2, pp. 141–162.https://doi.org/10.3417/2008115
10. Volkov, R.A., Panchuk, I.I., Borisjuk, L.G., and Borisjuk M.V. Plant rDNA: organization, evolution, and using, Cytol. Genet., 2003, vol. 37, no. 1, pp. 68–72.
11. Davis, J.I. and Soreng, R.J., A preliminary phylogenetic analysis of the grass subfamily Pooideae (Poaceae), with attention to structural features of the plastid and nuclear genomes, including an intron loss in GBSSI, Aliso, 2007, vol. 23, pp. 335–348.
12. Soreng, R.J., Davis, J.I., and Voionmaa, M. A. A phylogenetic analysis of Poaceae tribe Poeae sensu lato based on morphological characters and sequence data from three plastid-encoded genes: evidence for reticulation, and a new classification for the tribe, Kew Bull., 2007, vol. 62, no. 3, pp. 425–454.
13. Soreng, R.J., Peterson, P.M., Romschenko, K., Davidse, G., Zuloaga, F.O., Judziewicz, E.J., Filgueiras, T.S., Davis, J.I., and Morrone, O.A., A worldwide phylogenetic classification of the Poaceae (Gramineae), J. Syst. Evol., 2015, vol. 53, no. 2, pp. 117–137. https://doi.org/10.1111/jse.12150
14. Tkach, N., Schneider, J., Döring, E., Wölk, A., Hochbach, A., Nissen, J., Winterfeld, G., Meyer, S., Gabriel, J., Hoffmann M.H., and Röser, M. Phylogeny, morphology and the role of hybridization as driving force of evolution in grass tribes Aveneae and Poeae (Poaceae), bioRvix, 2019, 707588. https://doi.org/10.1101/707588
15. Döring, E., Schneider, J., Hilu, K., and Röser, M., Phylogenetic relationships in the Aveneae/Poeae complex (Pooideae, Poaceae), Kew Bull., 2007, vol. 62, no 3, pp. 407–424.
16. Saarela, J.M., Liu, Q., Peterson, P.M., Soreng, R.J., and Paszko, B., Phylogenetics of the grass ‘Aveneae-type plastid DNA clade’ (Poaceae: Pooideae, Poeae) based on plastid and nuclear ribosomal DNA sequence data, in Diversity, Phylogeny, and Evolution in the Monocotyledons, Aarhus: Aarhus University Press, 2010.
17. Garcia-Suarez, R., Alonso-Blanco, C., Fernandez-Carvajal, M.C., Fernandez-Prieto, J.A., Roca, A., and Giraldez, R., Diversity and systematics of Deschampsia sensu lato (Poaceae), inferred from karyotypes, protein electrophoresis, total genomic DNA hybridization and chloroplast DNA analysis, Plant Syst. Evol., 1997, vol. 205, pp. 99–110. https://doi.org/10.1007/BF00982800
18. Souto, D.P.F., Catalano, S.A., Tosto, D., Bernasconi, P., Sala, A., Wagner, M., and Corach, D., Phylogenetic relationships of Deschampsia antarctica (Poaceae): insights from nuclear ribosomal ITS, Plant Syst. Evol., 2006, vol. 261, pp. 1–9. https://doi.org/10.1007/s00606-006-0425-x
19. Andreev, I.O., Spiridonova, E.V., Kyryachenko, S.S., Parnikoza, I.Yu., Maidanyuk D.N., Volkov, R.A., Kozeretska, I.A., and Kunakh, V.A., Population-genetic analysis of Deschampsia antarctica from two regions of Maritime Antarctica, Moscow Univ. Biol. Sci. Bull., 2010, vol. 65, no. 4, pp. 208–210. https://doi.org/10.3103/S0096392510040243
20. Volkov, R.A., Kozeretska, I.A., Kyryachenko, S.S., Andreev, I.O., Maidanyuk, D.N., Parnikoza, I.Yu., and Kunakh, V.A., Molecular evolution and variability of ITS1 and ITS2 in populations of Deschampsia antarctica from two regions of the Maritime Antarctic, Polar Sci., 2010, vol. 4, no. 3, pp.469–478. https://doi.org/10.1016/j.polar.2010.04.011
21. Amosova, A.V., Bolsheva, N.L., Zoshchuk, S.A., Twardovska, M.O., Yurkevich, O.Yu., Andreev, I.O., Samatadze, T.E., Badaeva, E.D., Kunakh, V.A., and Muravenko, O.V., Comparative molecular cytogenetic characterization of seven Deschampsia (Poaceae) species, PLoS One, 2017, vol. 12, no. 4, e0138878. https://doi.org/10.1371/journal.pone.0175760
22. Volkov, R.A., Zanke, C., Panchuk, I.I., and Hemleben, V. Molecular evolution of 5S rDNA of Solanum species (sect. Petota): application for molecular phylogeny and breeding, Theor. Appl. Genet., 2001, vol. 103, no. 8, pp. 1273–1282. https://doi.org/10.1007/s001220100670
23. Saini, A. and Jawali, N., Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications, Plant Syst. Evol., 2009, vol. 280, nos. 3–4, p. 187–206. https://doi.org/10.1007/s00606-009-0178-4
24. Garcia, S., Panero, J.L., Siroky, J., and Kovarik, A. Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family, BMC Plant Biol., 2010, vol. 10, no. 1, pp. 176–195. https://doi.org/10.1186/1471-2229-10-176
25. Garcia, S., Garnatje, T., and Kovarik, A., Plant rDNA database: ribosomal DNA loci information goes online, Chromosoma, 2012, vol. 121, no. 4, pp. 389–394. https://doi.org/10.1007/s00412-012-0368-7
26. Rusak, O.O., Petrashchuk, V.I., Panchuk, I.I., and Volkov, R.A., Molecular organization of 5S rDNA in two Ukrainian populations of Sycamore (Acer pseudoplatanus), Bull. Vavilov Soc. Genet. Breed. Ukr., 2016, vol. 14, no. 2, pp. 216–220.
27. Volkov, R.A., Panchuk, I.I., Borisjuk, N.V., Hosiawa-Baranska, M., Maluszynska, J., and Hemleben, V. Evolutional dynamics of 45S and 5S ribosomal DNA in ancient allohexaploid Atropa belladonna, BMC Plant Biol., 2017, vol. 17, no. 1, pp. 1–15. https://doi.org/10.1186/s12870-017-0978-6
28. Baum, B.R. and Johnson, D.A., Lophopyrum Á. Löve (1980), Thinopyrum Á. Löve (1980), Trichopyrum Á. Löve (1986): one, two or three genera? A study based on the nuclear 5S DNA, Genet. Resour. Crop. Evol., 2018, vol. 65, pp. 161–186. https://doi.org/10.1007/s10722-017-0519-z
29. Vaio, M., Mazzella, C., Guerra, M., and Speranza, P., Effects of the diploidisation process upon the 5S and 35S rDNA sequences in the allopolyploid species of the Dilatata group of Paspalum (Poaceae, Paniceae), Aust. J. Bot., 2019, vol. 67, no. 7, pp 521–530. https://doi.org/10.1071/BT18236
30. Cloix, C., Tutois, S., Mathieu, O., Cuvillier, C., Espagno, M.C., Picard, C., and Tourmente, S., Analysis of 5S rDNA arrays in Arabidopsis thaliana: physical mapping and chromosome-specific polymorphisms, Genome Res., 2000, vol. 10, no 5, pp. 679–690. https://doi.org/10.1101/gr.10.5.679
31. Simeone, M.C., Cardoni, S., Piredda, R., Imperatori, F., Avishai, M., Grimm, G.W., and Denk, T., Comparative systematics and phylogeography of Quercus section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation, PeerJ., 2018, vol. 6, e5793. https://doi.org/10.7717/peerj.5793
32. Kolano, B.M., Cann, J., Oskędra, M., Chrapek, M., Rojek, M., Nobis, A., and Weiss-Schneeweiss, H., Parental origin and genome evolution of several Eurasian hexaploid species of Chenopodium (Chenopodiaceae), Phytotaxa, 2019, vol. 392, no. 3, pp. 163–185. https://doi.org/10.11646/phytotaxa.392.3.1
33. 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
34. Ishchenko, O.O., Panchuk, I.I., Andreev, I.O., Kunakh, V.A., and Volkov, R.A., Molecular organization of 5S ribosomal DNA of Deschampsia antarctica, Cytol. Genet., 2018, vol. 52, no. 6, pp. 416–421. https://doi.org/10.3103/S0095452719010146
35. Röser, M., Winterfeld, G., Grebenstein, B., and Hemleben, V., Molecular diversity and physical mapping of 5S rDNA in wild and cultivated oat grasses (Poaceae: Aveneae), Mol. Phylogen. Evol., 2001, vol. 21, no. 2, pp. 198–217. https://doi.org/10.1006/mpev.2001.1003
36. Peng, Y.Y., Wei, Y.M., Baum, B.R., and Zheng, Y.L., Molecular diversity of the 5S rRNA gene and genomic relationships in the genus Avena (Poaceae: Aveneae), Genome, 2008, vol. 51, no. 2, pp. 137–154. https://doi.org/10.1139/G07-111
37. Baum, B.R., Edwards, T., Mamuti, M., and Johnson, D.A., Phylogenetic relationships among the polyploid and diploid Aegilops species inferred from the nuclear 5S rDNA sequences (Poaceae: Triticeae), Genome, 2012, vol. 55, no. 3, pp. 177–193. https://doi.org/10.1139/g2012-006
38. Volkov, A.R. and Panchuk, I.I., 5S rDNA of Dactylis glomerata (Poaceae): molecular organization and taxonomic application, Bull. Vavilov Soc. Genet. Breed. Ukr., 2014, vol. 12, no. 1, pp. 3–11.
39. Nani, T.F., Cenzi, G., Pereira, D.L., Davide, L.C., and Techio, V.H., Ribosomal DNA in diploid and polyploid Setaria (Poaceae) species: number and distribution, Comp. Cytogenet., 2015, vol., 9, no. 4, pp 645–660. https://doi.org/10.3897/CompCytogen.v9i4.5456
40. Porebski, S., Bailey, L.G., and Baum, B.R., Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components, Plant Mol. Biol. Rep., 1997, vol. 15, no. 1, pp. 8–15. https://doi.org/10.1007/BF02772108
41. Sambrook, J., Fritsch, E., and Maniatis, T. Molecular Cloning, New York: Cold Spring Harbor Laboratory, 1989.
42. Thompson, J.D., Higgins, D.G., and Gibson, T.J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 1994, vol. 22, no. 22, pp. 4673–4680. https://doi.org/10.1093/nar/22.22.4673
43. Stamatakis, A., RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 2014, vol. 30, no. 9, pp. 1312–1313. https://doi.org/10.1093/bioinformatics/btu033
44. Simon, L., Rabanal, F.A., Dubos, T., Oliver, C., Lau-ber, D., Poulet, A., Vogt, A., Mandlbauer, A., Le Goff S., Sommer A., Duborjal H., Tatout C., and Probst, A.V., Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana, Nucleic Acids Res., 2018, vol. 46, no. 6, pp. 3019–3033. https://doi.org/10.1093/nar/gky163
45. Tynkevich, Y.O. and Volkov, R.A., Structural organization of 5S ribosomal DNA in Rosa rugosa, Cytol. Genet., 2014, vol. 48, no. 1, pp. 1–6. https://doi.org/10.3103/S0095452714010095
46. Ishchenko, O.O. and Panchuk, I.I., Molecular organization of 5S rDNA of perennial ryegrass Lolium perenne L., Bull. Vavilov Soc. Genet. Breed. Ukr., 2018, vol. 16, no. 2, pp. 166–173. https://doi.org/10.7124/visnyk.utgis.16.2.1054
47. Ishchenko, O.O., Derevenko, T.O., and Panchuk, I.I. 5S rDNA of Timothy-grass Phleum pratense L., Sci. Herald Chernivtsy Univ., Biol. (Biol. Syst.), 2018, vol. 10, no. 2, pp. 107–112. https://doi.org/10.31861/biosystems2018.02.107