A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material
16 Pág.
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| Format: | artículo biblioteca |
| Language: | English |
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John Wiley & Sons
2023-03
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| Subjects: | Triticeae‐specific genes, De novo gene evolution, Stress adaptation, Transposable elements, |
| Online Access: | http://hdl.handle.net/10261/310857 http://dx.doi.org/10.13039/501100006447 https://api.elsevier.com/content/abstract/scopus_id/85152383586 |
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dig-inia-es-10261-3108572024-05-16T20:39:44Z A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material Poretti, Manuel Praz, Coraline R. Sotiropoulos, Alexandros G. Wicker, Thomas Swiss National Science Foundation University of Zurich Poretti, Manuel [0000-0001-6915-2238] Praz, Coraline R. [0000-0002-9133-4406] Sotiropoulos, Alexandros G. [0000-0002-3591-0851] Wicker, Thomas [0000-0002-6777-7135] Triticeae‐specific genes De novo gene evolution Stress adaptation Transposable elements 16 Pág. 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. This work was supported by the Swiss National Foundation grant 31003A_163325.University of Zurich Research Priority Program, Grant/Award Number: U-702-21-01; Swiss National Foundation, Grant/Award Number: 31003A_163325 Peer reviewed 2023-06-07T10:14:24Z 2023-06-07T10:14:24Z 2023-03 artículo http://purl.org/coar/resource_type/c_6501 Plant Direct 7(3): (2023) 2475-4455. http://hdl.handle.net/10261/310857 10.1002/pld3.484 http://dx.doi.org/10.13039/501100006447 36937792 2-s2.0-85152383586 https://api.elsevier.com/content/abstract/scopus_id/85152383586 en Centro de Biotecnología y Genómica de Plantas (CBGP) Publisher's version https://doi.org/10.1002/pld3.484 Sí open application/pdf John Wiley & Sons |
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Triticeae‐specific genes De novo gene evolution Stress adaptation Transposable elements Triticeae‐specific genes De novo gene evolution Stress adaptation Transposable elements |
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Triticeae‐specific genes De novo gene evolution Stress adaptation Transposable elements Triticeae‐specific genes De novo gene evolution Stress adaptation Transposable elements Poretti, Manuel Praz, Coraline R. Sotiropoulos, Alexandros G. Wicker, Thomas A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material |
| description |
16 Pág. |
| author2 |
Swiss National Science Foundation |
| author_facet |
Swiss National Science Foundation Poretti, Manuel Praz, Coraline R. Sotiropoulos, Alexandros G. Wicker, Thomas |
| format |
artículo |
| topic_facet |
Triticeae‐specific genes De novo gene evolution Stress adaptation Transposable elements |
| author |
Poretti, Manuel Praz, Coraline R. Sotiropoulos, Alexandros G. Wicker, Thomas |
| author_sort |
Poretti, Manuel |
| title |
A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material |
| title_short |
A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material |
| title_full |
A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material |
| title_fullStr |
A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material |
| title_full_unstemmed |
A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material |
| title_sort |
survey of lineage-specific genes in triticeae reveals de novo gene evolution from genomic raw material |
| publisher |
John Wiley & Sons |
| publishDate |
2023-03 |
| url |
http://hdl.handle.net/10261/310857 http://dx.doi.org/10.13039/501100006447 https://api.elsevier.com/content/abstract/scopus_id/85152383586 |
| work_keys_str_mv |
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1802819740153937920 |