Journal article
The repetitive landscape of the 5100 Mbp barley genome
Mobile DNA, Vol.8(1)
2017
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.
Details
- Title
- The repetitive landscape of the 5100 Mbp barley genome
- Authors/Creators
- T. Wicker (Author/Creator) - University of ZurichA.H. Schulman (Author/Creator) - University of HelsinkiJ. Tanskanen (Author/Creator) - University of HelsinkiM. Spannagl (Author/Creator) - Helmholtz Zentrum MünchenS. Twardziok (Author/Creator) - Helmholtz Zentrum MünchenM. Mascher (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)N.M. Springer (Author/Creator) - University of MinnesotaQ. Li (Author/Creator) - University of MinnesotaR. Waugh (Author/Creator) - University of DundeeC. Li (Author/Creator) - Government of Western AustraliaG. Zhang (Author/Creator) - Wuhan CollegeN. Stein (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)K.F. X. Mayer (Author/Creator) - Technical University of MunichH. Gundlach (Author/Creator) - Helmholtz Zentrum München
- Publication Details
- Mobile DNA, Vol.8(1)
- Publisher
- BioMed Central
- Identifiers
- 991005541215107891
- Copyright
- © 2017 The Author(s).
- Murdoch Affiliation
- Western Barley Genetics Alliance
- Language
- English
- Resource Type
- Journal article
UN Sustainable Development Goals (SDGs)
This output has contributed to the advancement of the following goals:
Source: InCites
Metrics
137 File views/ downloads
56 Record Views
InCites Highlights
These are selected metrics from InCites Benchmarking & Analytics tool, related to this output
- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 1 Clinical & Life Sciences
- 1.54 Molecular & Cell Biology - Genetics
- 1.54.1122 Transposable Elements
- Web Of Science research areas
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics