Transposable Elements in the Organization and Diversification of the Genome of Tausch (Poaceae, Triticeae)

Overview

Journal Int J Genomics

Publisher Wiley

Date 2018 Oct 26

PMID 30356408

Citations 5

Authors

Olga Raskina

Affiliations

Soon will be listed here.

Abstract

Repetitive DNA-specifically, transposable elements (TEs)-is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and intraspecific diversification in the wild. Although large amounts of data have been accumulated, the effect of TEs on the genome architecture and functioning is not fully understood. Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the genome. Individual genotypes were analyzed cytogenetically using the cloned TE fragments as the DNA probes for fluorescence in situ hybridization (FISH). The obtained TE sequences of the Ty1-, Ty3-, LINE, and CACTA superfamilies showed the relatedness of the genome to the Triticeae tribe and similarities to evolutionarily distant species. A significant number of clones consisted of intercalated fragments of TEs of various types, in which Fatima (Ty3-) sequences predominated. At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing the effect of the TE fraction on the . genome architecture and intraspecific diversification. Altogether, the obtained data highlight the current species-specific organization and patterning of the mobile element fraction and point to ancient evolutionary events in the genome of .

Citing Articles

The Influence of Edaphic Factors on DNA Damage and Repair in Wild Wheat Körn. (, Triticeae).

Raskina O, Shklyar B, Nevo E Int J Mol Sci. 2023; 24(7).

PMID: 37047823 PMC: 10094829. DOI: 10.3390/ijms24076847.

Draft Sequencing Crested Wheatgrass Chromosomes Identified Evolutionary Structural Changes and Genes and Facilitated the Development of SSR Markers.

Zwyrtkova J, Blavet N, Dolezalova A, Capal P, Said M, Molnar I Int J Mol Sci. 2022; 23(6).

PMID: 35328613 PMC: 8948999. DOI: 10.3390/ijms23063191.

Supernumerary B Chromosomes and Plant Genome Changes: A Snapshot of Wild Populations of Tausch (, Triticeae).

Shams I, Raskina O Int J Mol Sci. 2020; 21(11).

PMID: 32466617 PMC: 7312783. DOI: 10.3390/ijms21113768.

Long Tandem Arrays of Retroelements and Their Role in Genome Dynamics in Plants.

Kalendar R, Raskina O, Belyayev A, Schulman A Int J Mol Sci. 2020; 21(8).

PMID: 32331257 PMC: 7215508. DOI: 10.3390/ijms21082931.

Copy Number Variation of Transposable Elements in and Its Diploid Relative Species.

Divashuk M, Karlov G, Kroupin P Plants (Basel). 2019; 9(1).

PMID: 31877707 PMC: 7020174. DOI: 10.3390/plants9010015.

References

Kapitonov V, Jurka J . Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica. 2000; 107(1-3):27-37. View

Kashkush K, Feldman M, Levy A . Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet. 2002; 33(1):102-6. DOI: 10.1038/ng1063. View

Fransz P, de Jong H . From nucleosome to chromosome: a dynamic organization of genetic information. Plant J. 2011; 66(1):4-17. DOI: 10.1111/j.1365-313X.2011.04526.x. View

Novak P, Hribova E, Neumann P, Koblizkova A, Dolezel J, Macas J . Genome-wide analysis of repeat diversity across the family Musaceae. PLoS One. 2014; 9(6):e98918. PMC: 4059648. DOI: 10.1371/journal.pone.0098918. View

Belyayev A, Raskina O, Nevo E . Variability of the chromosomal distribution of Ty3-gypsy retrotransposons in the populations of two wild Triticeae species. Cytogenet Genome Res. 2005; 109(1-3):43-9. DOI: 10.1159/000082380. View

Middleton C, Stein N, Keller B, Kilian B, Wicker T . Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity. Plant J. 2012; 73(2):347-56. DOI: 10.1111/tpj.12048. View

Purugganan M, Wessler S . Molecular evolution of the plant R regulatory gene family. Genetics. 1994; 138(3):849-54. PMC: 1206232. DOI: 10.1093/genetics/138.3.849. View

Muotri A, Chu V, Marchetto M, Deng W, Moran J, Gage F . Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature. 2005; 435(7044):903-10. DOI: 10.1038/nature03663. View

Raskina O, Belyayev A, Nevo E . Activity of the En/Spm-like transposons in meiosis as a base for chromosome repatterning in a small, isolated, peripheral population of Aegilops speltoides Tausch. Chromosome Res. 2004; 12(2):153-61. DOI: 10.1023/b:chro.0000013168.61359.43. View

10.

Wicker T, Buchmann J, Keller B . Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Res. 2010; 20(9):1229-37. PMC: 2928501. DOI: 10.1101/gr.107284.110. View

11.

ONeill R, ONeill M, Graves J . Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature. 1998; 393(6680):68-72. DOI: 10.1038/29985. View

12.

Hubner M, Eckersley-Maslin M, Spector D . Chromatin organization and transcriptional regulation. Curr Opin Genet Dev. 2012; 23(2):89-95. PMC: 3612554. DOI: 10.1016/j.gde.2012.11.006. View

13.

Badaeva E, Friebe B, Gill B . Genome differentiation in Aegilops. 1. Distribution of highly repetitive DNA sequences on chromosomes of diploid species. Genome. 1996; 39(2):293-306. DOI: 10.1139/g96-040. View

14.

Wicker T, Sabot F, Hua-Van A, Bennetzen J, Capy P, Chalhoub B . A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007; 8(12):973-82. DOI: 10.1038/nrg2165. View

15.

Salina E, Sergeeva E, Adonina I, Shcherban A, Afonnikov D, Belcram H . Isolation and sequence analysis of the wheat B genome subtelomeric DNA. BMC Genomics. 2009; 10:414. PMC: 2756281. DOI: 10.1186/1471-2164-10-414. View

16.

Heslop-Harrison J, Schwarzacher T . Organisation of the plant genome in chromosomes. Plant J. 2011; 66(1):18-33. DOI: 10.1111/j.1365-313X.2011.04544.x. View

17.

Kohany O, Gentles A, Hankus L, Jurka J . Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics. 2006; 7:474. PMC: 1634758. DOI: 10.1186/1471-2105-7-474. View

18.

Feschotte C, Jiang N, Wessler S . Plant transposable elements: where genetics meets genomics. Nat Rev Genet. 2002; 3(5):329-41. DOI: 10.1038/nrg793. View

19.

Hosid E, Brodsky L, Kalendar R, Raskina O, Belyayev A . Diversity of long terminal repeat retrotransposon genome distribution in natural populations of the wild diploid wheat Aegilops speltoides. Genetics. 2011; 190(1):263-74. PMC: 3249373. DOI: 10.1534/genetics.111.134643. View

20.

Kubis S, Heslop-Harrison J, Desel C, Schmidt T . The genomic organization of non-LTR retrotransposons (LINEs) from three Beta species and five other angiosperms. Plant Mol Biol. 1998; 36(6):821-31. DOI: 10.1023/a:1005973932556. View