Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Dec 21;9(1):15.
doi: 10.3390/plants9010015.

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

Mikhail G Divashuk  1   2 , Gennady I Karlov  1   2 , Pavel Yu Kroupin  1   2
Affiliations

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

Mikhail G Divashuk et al. Plants (Basel). .

Abstract

Diploid and polyploid wild species of Triticeae have complex relationships, and the understanding of their evolution and speciation could help to increase the usability of them in wheat breeding as a source of genetic diversity. The diploid species Pseudoroegneria spicata (St), Thinopyrum bessarabicum (Jb), Dasypyrum villosum (V) derived from a hypothetical common ancestor are considered to be possible subgenome donors in hexaploid species Th. intermedium (JrJvsSt, where indices r, v, and s stand for the partial relation to the genomes of Secale, Dasypyrum, and Pseudoroegneria, respectively). We quantified 10 families of transposable elements (TEs) in P. spicata, Th. bessarabicum, D. villosum (per one genome), and Th. intermedium (per one average subgenome) using the quantitative real time PCR assay and compared their abundance within the studied genomes as well as between them. Sabrina was the most abundant among all studied elements in P. spicata, D. villosum, and Th. intermedium, and among Ty3/Gypsy elements in all studied species. Among Ty1/Copia elements, Angela-A and WIS-A showed the highest and close abundance with the exception of D. villosum, and comprised the majority of all studied elements in Th. bessarabicum. Sabrina, BAGY2, and Angela-A showed similar abundance among diploids and in Th. intermedium hexaploid; Latidu and Barbara demonstrated sharp differences between diploid genomes. The relationships between genomes of Triticeae species based on the studied TE abundance and the role of TEs in speciation and polyploidization in the light of the current phylogenetic models is discussed.

Keywords: Dasypyrum; Pseudoroegneria; Thinopyrum; copy number variation; genome evolution; polyploidization; transposable elements.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The decimal logarithm of relative quantity of TEs per one genome in P. spicata (St), Th. bessarabicum (Jb), D. villosum (V), Th. intermedium (JrJvsSt, the plot is for one average subgenome).
Figure 2
Figure 2
Relative quantification (compared to Ae. tauschii, which is taken as 1, see text) of Gypsy LTR retrotransposon Latidu in the following species: Ae. tauschii, P. spicata, Th. bessarabicum, D. villosum, one average subgenome (OAS) of Th. intermedium, and Th. intermedium. The numbers above chart bars are decimal logarithm of relative quantity of TEs; error bars show standard deviation.
Figure 3
Figure 3
Relative quantification (compared to Ae. tauschii, set as 1, see text) of Gypsy LTR retrotransposon Geneva in the following species: Ae. tauschii, P. spicata, Th. bessarabicum, D. villosum, one average subgenome (OAS) of Th. intermedium, and Th. intermedium. The numbers above chart bars are decimal logarithm of relative quantity of TEs; error bars show standard deviation.
Figure 4
Figure 4
Relative quantification (compared to Ae. tauschii, set as 1, see text) of Copia LTR retrotransposon Barbara in the following species: Ae. tauschii, P. spicata, Th. bessarabicum, D. villosum, one average subgenome of Th. intermedium, and Th. intermedium. The numbers above chart bars are decimal logarithm of relative quantity of TEs; error bars show standard deviation.
Figure 5
Figure 5
Relative quantification (compared to Ae. tauschii, set as 1, see text) of CACTA TIR transposon Balduin in the following species: Ae. tauschii, P. spicata, Th. bessarabicum, D. villosum, one average subgenome of Th. intermedium, and Th. intermedium. The numbers above chart bars are decimal logarithm of relative quantity of TEs; error bars show standard deviation.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408:796–815. doi: 10.1038/35048692. - DOI - PubMed
    1. Meyers B. Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res. 2001;11:1660–1676. doi: 10.1101/gr.188201. - DOI - PMC - PubMed
    1. Li W., Zhang P., Fellers J., Friebe B., Gill B. Sequence composition, organization, and evolution of the core Triticeae genome. Plant J. 2004;40:500–511. doi: 10.1111/j.1365-313X.2004.02228.x. - DOI - PubMed
    1. Paux E., Roger D., Badaeva E., Gay G., Bernard M., Sourdille P., Feuillet C. Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J. 2006;48:463–474. doi: 10.1111/j.1365-313X.2006.02891.x. - DOI - PubMed
    1. Charles M., Belcram H., Just J., Huneau C., Viollet A., Couloux A., Segurens B., Carter M., Huteau V., Coriton O., et al. Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. Genetics. 2008;180:1071–1086. doi: 10.1534/genetics.108.092304. - DOI - PMC - PubMed

LinkOut - more resources