The repetitive landscape of the 5100 Mbp barley genome

Thomas Wicker, Alan H. Schulman, Jaakko Tanskanen, Manuel Spannagl, Sven Twardziok, Martin Mascher, Nathan M. Springer, Qing Li, Robbie Waugh, Chengdao Li, Guoping Zhang, Nils Stein, Klaus F.X. Mayer, Heidrun Gundlach

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

Background: While transposable elements (TEs) comprise the bulk of plant genomic DNA, how they contribute to genome structure and organization is still poorly understood. Especially in large genomes where TEs make the majority of genomic DNA, it is still unclear whether TEs target specific chromosomal regions or whether they simply accumulate where they are best tolerated. Results: Here, we present an analysis of the repetitive fraction of the 5100 Mb barley genome, the largest angiosperm genome to have a near-complete sequence assembly. Genes make only about 2% of the genome, while over 80% is derived from TEs. The TE fraction is composed of at least 350 different families. However, 50% of the genome is comprised of only 15 high-copy TE families, while all other TE families are present in moderate or low copy numbers. We found that the barley genome is highly compartmentalized with different types of TEs occupying different chromosomal "niches", such as distal, interstitial, or proximal regions of chromosome arms. Furthermore, gene space represents its own distinct genomic compartment that is enriched in small non-autonomous DNA transposons, suggesting that these TEs specifically target promoters and downstream regions. Furthermore, their presence in gene promoters is associated with decreased methylation levels. Conclusions: Our data show that TEs are major determinants of overall chromosome structure. We hypothesize that many of the the various chromosomal distribution patterns are the result of TE families targeting specific niches, rather than them accumulating where they have the least deleterious effects.

Original languageEnglish (US)
Article number22
JournalMobile DNA
Volume8
Issue number1
DOIs
StatePublished - Dec 20 2017

Bibliographical note

Funding Information:
TW was funded by the University of Zurich; AHS and JT were supported by Green Technology, Natural Resources Institute Finland (Luke), by the Institute of Biotechnology, University of Helsinki, and by Academy of Finland Project 266,430; CL was funded by Grain Research and Development Corporation(GRDC) grant DAW00233 and Department of Agriculturel and Food, Government of Western Australia grant 681; CL and GZ were supported by National Natural Science Foundation of China (NSFC) grant 31,129,005; GZ was funded by NSFC grant 31,330,055; RW was supported by Scottish Government/UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/100663X/1 and Scottish Government RESAS Work Program 2.1.1; KFXM acknowledges support from the German Ministry of Education and Research (BMBF) grant 0314000 “BARLEX”, 0315954 “TRITEX”, and 031A536 “de.NBI”, and the European Commission 7th Framework Infrastructure Programme 283,496; NS acknowledges support from the German Ministry of Education and Research (BMBF) grant 0314000 “BARLEX”, 0315954 “TRITEX” and the Leibniz Association grant (‘Pakt f. Forschung und Innovation’) “sequencing barley chromosome 3H”; NMS acknowledges support from National Science Foundation Grants DBI-1237931. The authors declare that they have no competing interests.

Funding Information:
TW was funded by the University of Zurich; AHS and JT were supported by Green Technology, Natural Resources Institute Finland (Luke), by the Institute of Biotechnology, University of Helsinki, and by Academy of Finland Project 266,430; CL was funded by Grain Research and Development Corporation(GRDC) grant DAW00233 and Department of Agriculturel and Food, Government of Western Australia grant 681; CL and GZ were supported by National Natural Science Foundation of China (NSFC) grant 31,129,005; GZ was funded by NSFC grant 31,330,055; RW was supported by Scottish Government/UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/100663X/1 and Scottish Government RESAS Work Program 2.1.1; KFXM acknowledges support from the German Ministry of Education and Research (BMBF) grant 0314000 BARLEX, 0315954 TRITEX, and 031A536 de.NBI, and the European Commission 7th Framework Infrastructure Programme 283,496; NS acknowledges support from the German Ministry of Education and Research (BMBF) grant 0314000 BARLEX, 0315954 TRITEX and the Leibniz Association grant (Pakt f. Forschung und Innovation) sequencing barley chromosome 3H; NMS acknowledges support from National Science Foundation Grants DBI-1237931

Publisher Copyright:
© 2017 The Author(s).

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