The Repetitive Landscape of the Barley Genome

Thomas Wicker, Heidrun Gundlach, Alan Howard Schulman

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Abstract

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. The barley genome with its vast repetitive fraction is an ideal system to study chromosomal organization and evolution of TEs. 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. 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. Some TE families also show a strong preference to insert in specific sequence motifs which may, in part, explain their distribution. The family-specific distribution patterns result in distinct TE compositions of different chromosomal compartments.
Original languageEnglish
Title of host publicationThe Barley Genome
EditorsNils Stein, Gary J. Muehlbauer
Number of pages16
PublisherSpringer Nature
Publication date19 Aug 2018
Pages123-138
ISBN (Print)978-3-319-92527-1
ISBN (Electronic)978-3-319-92528-8
DOIs
Publication statusPublished - 19 Aug 2018
MoE publication typeA3 Book chapter

Publication series

NameCompendium of Plant Genomes
ISSN (Print)2199-4781
ISSN (Electronic)2199-479X

Fields of Science

  • 1183 Plant biology, microbiology, virology

Cite this

Wicker, T., Gundlach, H., & Schulman, A. H. (2018). The Repetitive Landscape of the Barley Genome. In N. Stein, & G. J. Muehlbauer (Eds.), The Barley Genome (pp. 123-138). (Compendium of Plant Genomes). Springer Nature. https://doi.org/10.1007/978-3-319-92528-8_9
Wicker, Thomas ; Gundlach, Heidrun ; Schulman, Alan Howard. / The Repetitive Landscape of the Barley Genome. The Barley Genome. editor / Nils Stein ; Gary J. Muehlbauer. Springer Nature, 2018. pp. 123-138 (Compendium of Plant Genomes).
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Wicker, T, Gundlach, H & Schulman, AH 2018, The Repetitive Landscape of the Barley Genome. in N Stein & GJ Muehlbauer (eds), The Barley Genome. Compendium of Plant Genomes, Springer Nature, pp. 123-138. https://doi.org/10.1007/978-3-319-92528-8_9

The Repetitive Landscape of the Barley Genome. / Wicker, Thomas; Gundlach, Heidrun; Schulman, Alan Howard.

The Barley Genome. ed. / Nils Stein; Gary J. Muehlbauer. Springer Nature, 2018. p. 123-138 (Compendium of Plant Genomes).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

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N2 - 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. The barley genome with its vast repetitive fraction is an ideal system to study chromosomal organization and evolution of TEs. 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. 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. Some TE families also show a strong preference to insert in specific sequence motifs which may, in part, explain their distribution. The family-specific distribution patterns result in distinct TE compositions of different chromosomal compartments.

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Wicker T, Gundlach H, Schulman AH. The Repetitive Landscape of the Barley Genome. In Stein N, Muehlbauer GJ, editors, The Barley Genome. Springer Nature. 2018. p. 123-138. (Compendium of Plant Genomes). https://doi.org/10.1007/978-3-319-92528-8_9