Biopolym. Cell. 2023; 39(3):201-208.
Genomics, Transcriptomics and Proteomics
Variation in highly repetitive DNA composition in rye and wild relatives discovered by FISH
1Alkhimova O. G., 1Twardovska M. O., 2Portova P. A., 1Kunakh V. A.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03143
  2. Sofware development company MacPaw
    100, Velyka Vasylkivska Str., Kyiv, Ukraine, 03150

Abstract

Aim. Determination of the sequence organization of the chromosomes terminal regions in Secale cereale L. varieties and some of its wild relatives for further identification of individual chromosomes with the use of appropriate probes. Methods. Fluorescence in situ hybridization, microscopy. Results. FISH analysis revealed 26–28 sites of the pSc200 sequence at the ends of all 14 pairs of chromosomes and 18 signals of the pSc250 sequence on the chromosomes of S. cereale in four accessions. Repeats were differently localized on the chromosomes of the closely related species Dasypyrum villosum and Dasypyrum breviaristatum, so it can be assumed that the tetraploid D. breviaristatum has an allopolyploid origin, may not be a descendant of D. villosum. Conclusions. A characteristic distribution of pSc200 and pSc250 tandem repeats of the tribe Triticeae was established, which allows revealing the evolutionary relationships between the studied species and the directions of their divergence.
Keywords: Secale cereale L., Dasypyrum species, Agropyron cristatum L., subtelomeres, tandem repeats, fluorescence in situ hybridization

References

[1] Van de Peer Y, Mizrachi E, Marchal K. The evolutionary significance of polyploidy. Nat Rev Genet. 2017; 18(7):411-24.
[2] Aguilar M, Prieto P. Telomeres and Subtelomeres Dynamics in the Context of Early Chromosome Interactions During Meiosis and Their Implications in Plant Breeding. Front Plant Sci. 2021; 12:672489.
[3] Luo J, Liao R, Duan Y, Fu S, Tang Z. Variations of subtelomeric tandem repeats and rDNA on chromosome 1RS arms in the genus Secale and 1BL.1RS translocations. BMC Plant Biol. 2022; 22(1):212.
[4] Evtushenko EV, Elisafenko EA, Vershinin AV. Organization and evolution of the subtelomeric regions of the rye chromosomes. Tsitologiia. 2013; 55(4):230-3.
[5] Mehrotra S, Goyal V. Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function. Genomics Proteomics Bioinformatics. 2014; 12(4):164-71.
[6] Ågren JA, Wright SI. Selfish genetic elements and plant genome size evolution. Trends Plant Sci. 2015; 20(4):195-6.
[7] Plohl M. Those mysterious sequences of satellite DNAs. Period Biol. 2010; 112(4): 403-10.
[8] Saxena RK, Edwards D, Varshney RK. Structural variations in plant genomes. Brief Funct Genomics. 2014; 13(4):296-307.
[9] Alkhimova OG, Zimina OV. Identification of rye chromosomes by flow cytogenetics. Byopolym Cell. 2017; 33(2):116-23.
[10] Evtushenko EV, Levitsky VG, Elisafenko EA, Gunbin KV, Belousov AI, Šafář J, Doležel J, Vershinin AV. The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements. BMC Genomics. 2016; 17:337.
[11] Vershinin AV, Schwarzacher T, Heslop-Harrison JS. The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes. Plant Cell. 1995; 7(11):1823-33.
[12] Schwarzacher T, Heslop-Harrison JS. Practical in situ Hybridization. – Oxford: BIOS, 2000; 250p.
[13] Alkhimova OG, Mazurok NA, Potapova TA, Zakian SM, Heslop-Harrison JS, Vershinin AV. Diverse patterns of the tandem repeats organization in rye chromosomes2004; 113(1):42-52.
[14] Uslu E, Reader SM, Miller TE. Characterization of Dasypymm villosum (L.) Candargy chromosomes by fluorescent in situ hybridization. Hereditas. 1999; 131(2):129-34.
[15] Li G, Gao D, Zhang H, Li J, Wang H, La S, Ma J, Yang Z. Molecular cytogenetic characterization of Dasypyrum breviaristatum chromosomes in wheat background revealing the genomic divergence between Dasypyrum species. Mol Cytogenet. 2016; 9:6.
[16] Gupta PK, Fedak G, Molnar SJ, Wheatcroft R. Distribution of a Secale cereale DNA repeat sequence among 25 Hordeum species. Genome. 1989; 32(3):383-8.
[17] Dover G. Molecular drive: a cohesive mode of species evolution. Nature. 1982; 299(5879):111-7.
[18] Vershinin AV, Elisafenko EA, Evtushenko EV. Genetic Redundancy in Rye Shows in a Variety of Ways. Plants (Basel). 2023; 12(2):282.
[19] Alkhimova AG, Heslop-Harrison JS, Shchapova AI, Vershinin AV. Rye chromosome variability in wheat-rye addition and substitution lines. Chromosome Res. 1999; 7(3):205-12.
[20] Vershinin AV, Alkhimova EG, Heslop-Harrison JS. Molecular diversification of tandemly organized DNA sequences and heterochromatic chromosome regions in some Triticeae species. Chromosome Res. 1996; 4(7):517-25.
[21] Šafář J, Šimková H, Doležel J. Construction of BAC Libraries from Flow-Sorted Chromosomes. Methods Mol Biol. 2016; 1429:135-49.
[22] Palazzo AF, Koonin EV. Functional Long Non-coding RNAs Evolve from Junk Transcripts. Cell. 2020; 183(5):1151-61.
[23] van Emden TS, Braun S. TASks for subtelomeres: when nucleosome loss and genome instability are favored. Curr Genet. 2019; 65(5):1153-60.
[24] Calderón MC, Rey MD, Martín A, Prieto P. Homoeologous Chromosomes From Two Hordeum Species Can Recognize and Associate During Meiosis in Wheat in the Presence of the Ph1 Locus. Front Plant Sci. 2018; 9:585.
[25] Naranjo T. Forcing the shift of the crossover site to proximal regions in wheat chromosomes. Theor Appl Genet. 2015; 128(9):1855-63.
[26] Xi W, Tang Z, Luo J, Fu S. Physical Location of New Stripe Rust Resistance Gene(s) and PCR-Based Markers on Rye (Secale cereale L.) Chromosome 5 Using 5R Dissection Lines. Agronomy. 2019; 9(9):498.