A survey of lineage‐specific genes in Triticeae reveals de novo gene evolution from genomic raw material

Article


Poretti, Manuel, Praz, Coraline R, Sotiropoulos, Alexandros G. and Wicker, Thomas. 2023. "A survey of lineage‐specific genes in Triticeae reveals de novo gene evolution from genomic raw material." Plant Direct. 7 (3), p. e484. https://doi.org/10.1002/pld3.484
Article Title

A survey of lineage‐specific genes in Triticeae reveals de novo gene evolution from genomic raw material

ERA Journal ID213960
Article CategoryArticle
AuthorsPoretti, Manuel, Praz, Coraline R, Sotiropoulos, Alexandros G. and Wicker, Thomas
Journal TitlePlant Direct
Journal Citation7 (3), p. e484
Number of Pages16
Year2023
PublisherJohn Wiley & Sons
Place of PublicationUnited States
ISSN2475-4455
Digital Object Identifier (DOI)https://doi.org/10.1002/pld3.484
Web Address (URL)https://onlinelibrary.wiley.com/doi/10.1002/pld3.484
Abstract

Diploid plant genomes typically contain ~35,000 genes, almost all belonging to highly conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs; however, they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in Triticeae, using newly available genome assemblies of wheat, barley, and rye. Applying a set of stringent criteria, we identified 5942 candidate Triticeae-specific genes (TSGs), of which 2337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in putative secreted proteins. Some were previously described to be involved in Triticeae non-host resistance and cold response. Additionally, we show that 1079 TSGs have sequence homology to transposable elements (TEs), ~68% of them deriving from regulatory non-coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess ~779 lineage-specific genes per haploid genome. TSGs, which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins.

Keywordsde novo gene evolution; Triticeae-specific genes; transposable elements; stress adaptation
ANZSRC Field of Research 2020310499. Evolutionary biology not elsewhere classified
310204. Genomics and transcriptomics
310505. Gene expression (incl. microarray and other genome-wide approaches)
Byline AffiliationsUniversity of Zurich, Switzerland
University of Fribourg, Switzerland
Polytechnic University of Madrid, Spain
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