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Plant J. 2018 Feb;93(3):502-514. doi: 10.1111/tpj.13794. Epub 2018 Jan 7.

The pseudogenes of barley.

Author information

1
Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
2
Centre for Comparative Genomics, Murdoch University, 90 South Street, WA6150, Murdoch, Australia.
3
School of Veterinary and Life Sciences, Murdoch University, 90 South Street, WA6150, Murdoch, Australia.
4
School of Agriculture, University of Adelaide, Waite Campus, SA5064, Urrbrae, Australia.
5
Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland.
6
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
7
School of Plant Biology, University of Western Australia, Crawley, WA6009, Australia.
8
The James Hutton Institute, Dundee, DD2 5DA, UK.
9
School of Life Sciences, University of Dundee, Dundee, DD2 5DA, UK.
10
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
11
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany.
12
Department of Agriculture and Food, Government of Western Australia, South Perth, WA, 6151, Australia.
13
TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354, Freising, Germany.

Abstract

Pseudogenes have a reputation of being 'evolutionary relics' or 'junk DNA'. While they are well characterized in mammals, studies in more complex plant genomes have so far been hampered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.1 Gb. With the first high-quality genome reference assembly available for a Triticeae crop, we conducted a whole-genome assessment of pseudogenes on the barley genome. We identified, characterized and classified 89 440 gene fragments and pseudogenes scattered along the chromosomes, with occasional hotspots and higher densities at the chromosome ends. Full-length pseudogenes (11 015) have preferentially retained their exon-intron structure. Retrotransposition of processed mRNAs only plays a marginal role in their creation. However, the distribution of retroposed pseudogenes reflects the Rabl configuration of barley chromosomes and thus hints at founding mechanisms. While parent genes related to the defense-response were found to be under-represented in cultivated barley, we detected several defense-related pseudogenes in wild barley accessions. The percentage of transcriptionally active pseudogenes is 7.2%, and these may potentially adopt new regulatory roles.The barley genome is rich in pseudogenes and small gene fragments mainly located towards chromosome tips or as tandemly repeated units. Our results indicate non-random duplication and pseudogenization preferences and improve our understanding of the dynamics of gene birth and death in large plant genomes and the mechanisms that lead to evolutionary innovations.

KEYWORDS:

Hordeum vulgare ; barley; gene evolution; gene fragments; plants; pseudogenes

PMID:
29205595
DOI:
10.1111/tpj.13794
[Indexed for MEDLINE]
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