The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements

BMC Genomics

Research Article

E. A. Elisafenko¹  K. V. Gunbin²  V. G. Levitsky²  J. Šafář³  J. Doležel³  A. I. Belousov⁴  A. V. Vershinin⁴  E. V. Evtushenko⁴ 

[1] Institute of Cytology and Genetics, Siberian Branch of the RAS, Novosibirsk, Russia;Institute of Cytology and Genetics, Siberian Branch of the RAS, Novosibirsk, Russia;Novosibirsk State University, Novosibirsk, Russia;Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic;Institute of Molecular and Cellular Biology, Siberian Branch of the RAS, Novosibirsk, Russia;

关键词: Tandem repeats;    Transposable elements;    Subtelomeric heterochromatin;    Rye;    Secale cereale;    1RS BAC library;    454 sequences;    TE–tandem junctions;    DNA motifs;   

DOI  :  10.1186/s12864-016-2667-5

 received in 2015-12-17, accepted in 2016-04-25,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundA prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays. The rapidity with which these regions have formed over the period of speciation remains unexplained.ResultsUsing a BAC library created from the short arm telosome of rye chromosome 1R we uncovered numerous arrays of the pSc200 and pSc250 tandem repeat families which are concentrated in subtelomeric heterochromatin and identified the adjacent DNA sequences. The arrays show significant heterogeneity in monomer organization. 454 reads were used to gain a representation of the expansion of these tandem repeats across the whole rye genome. The presence of multiple, relatively short monomer arrays, coupled with the mainly star-like topology of the monomer phylogenetic trees, was taken as indicative of a rapid expansion of the pSc200 and pSc250 arrays. The evolution of subtelomeric heterochromatin appears to have included a significant contribution of illegitimate recombination. The composition of transposable elements (TEs) within the regions flanking the pSc200 and pSc250 arrays differed markedly from that in the genome a whole. Solo-LTRs were strongly enriched, suggestive of a history of active ectopic exchange. Several DNA motifs were over-represented within the LTR sequences.ConclusionThe large blocks of subtelomeric heterochromatin have arisen from the combined activity of TEs and the expansion of the tandem repeats. The expansion was likely based on a highly complex network of recombination mechanisms.

【 授权许可】

CC BY   
© Evtushenko et al. 2016