A Playground for Innovations: Pseudogenes and Gene Fragments in Barley

Pseudogenes are gene-like sequences featuring serious mutations which destroy their original function. Although originally dismissed as “junk DNA”, they are now increasingly studied in mammals, due to mounting reports of pseudogene functionality. Studies in more complex plant genomes such as the Triticeae were hampered by the absence of reference genome sequences. The barley genome (5 Gb) is the first average sized plant genome assembled to an unprecedented completeness, and was also among the first to be included in our detailed plant pseudogene survey.

Using a homology-based approach and a query set of 38,157 high confidence barley genes, we identified 11,015 full length pseudogenes and 78,425 smaller pseudogene fragments. Interestingly, and unlike in mammals, the common intron-based classification of pseudogenes into ‘duplicated’ and ‘retroposed’ demonstrates a surprisingly small contribution of retrotransposon mediated sources. In fact, a major proportion of pseudogenes originates from tandem cluster situations or is located in close vicinity to their homologous parent gene. The overall chromosomal distribution of pseudogenes follows that of genes with high densities towards the telomeres. Further results on gene family relationships, functional biases in the parent gene set and transcriptional evidences were investigated. For example, we found transcriptional evidence for 7,018 pseudogenes - including 1,340 full length pseudogenes. They hold the potential to take part in regulatory processes.

In conclusion, our results indicate non-random duplication and pseudogenization preferences and finally provide a basis for in-depth studies of the potential impact of pseudogenes on gene functions and chromosomal organization.