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Prade, V.M. ; Gundlach, H. ; Twardziok, S.O. ; Chapman, B.* ; Tan, C.S.* ; Langridge, P.* ; Schulman, A.H.* ; Stein, N.* ; Waugh, R.* ; Zhang, G.* ; Platzer, M.* ; Li, C.* ; Spannagl, M. ; Mayer, K.F.X.

The pseudogenes of barley.

Plant J. 93, 502-514 (2017)
Verlagsversion Postprint Forschungsdaten DOI PMC
Open Access Green
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.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Pseudogenes ; Barley ; Hordeum Vulgare ; Plants ; Gene Fragments ; Gene Evolution; Processed Pseudogenes; Signal-transduction; Human Genome; Plant-cells; Cd-hit; Gene; Dna; Identification; Evolutionary; Calcium
ISSN (print) / ISBN 0960-7412
e-ISSN 1365-313X
Zeitschrift Plant Journal, The
Quellenangaben Band: 93, Heft: 3, Seiten: 502-514 Artikelnummer: , Supplement: ,
Verlag Wiley
Verlagsort Hoboken
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Research Unit Plant Genome and Systems Biology (PGSB)
Research Unit Analytical Pathology (AAP)