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The pseudogenes of barley

Authors: Verena M. Prade; Heidrun Gundlach; Sven Twardziok; Brett Chapman; Cong Tan; Peter Langridge; Alan H. Schulman; +7 Authors

The pseudogenes of barley

Abstract

SummaryPseudogenes 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.

Countries
Australia, United Kingdom, Finland, Germany
Keywords

570, /dk/atira/pure/subjectarea/asjc/1300/1311, 572, name=Genetics, /dk/atira/pure/subjectarea/asjc/1100/1110, pseudogenes, Genes, Plant, Synteny, 630, Chromosomes, Plant, name=Cell Biology, Gene Duplication, gene fragments, Selection, Genetic, Hordeum vulgare, plants, barley, Chromosome Mapping, Hordeum, ta4111, Pseudogenes ; Barley ; Hordeum Vulgare ; Plants ; Gene Fragments ; Gene Evolution, Multigene Family, gene evolution, name=Plant Science, /dk/atira/pure/subjectarea/asjc/1300/1307, Pseudogenes

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
23
Top 10%
Average
Top 10%
Green
bronze