The Ancient Salicoid Genome Duplication Event [electronic resource] : A Platform for Reconstruction of De Novo Gene Evolution in <em>Populus trichocarpa</em>
Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper...
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| Format: | Electronic eBook |
| Language: | English |
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Washington, D.C. : Oak Ridge, Tenn. :
United States. Department of Energy. Office of Science ; Distributed by the Office of Scientific and Technical Information, U.S. Department of Energy,
2021.
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MARC
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| 245 | 0 | 4 | |a The Ancient Salicoid Genome Duplication Event |h [electronic resource] : |b A Platform for Reconstruction of De Novo Gene Evolution in <em>Populus trichocarpa</em> |
| 260 | |a Washington, D.C. : |b United States. Department of Energy. Office of Science ; |a Oak Ridge, Tenn. : |b Distributed by the Office of Scientific and Technical Information, U.S. Department of Energy, |c 2021. | ||
| 300 | |a Size: Article No. evab198 : |b digital, PDF file. | ||
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| 500 | |a Published through Scitech Connect. | ||
| 500 | |a 09/01/2021. | ||
| 500 | |a "Journal ID: ISSN 1759-6653." | ||
| 500 | |a Yates, Timothy ; Feng, Kai ; Zhang, Jin ; Singan, Vasanth ; Jawdy, Sara ; Ranjan, Priya ; Abraham, Paul ; Barry, Kerrie ; Lipzen, Anna ; Pan, Chongle ; et al; | ||
| 520 | 3 | |a Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper reconstruction of 13 orphan genes to provide evidence of de novo gene evolution. Populus and its sister genera Salix are particularly well suited for the study of orphan gene evolution because of the Salicoid whole-genome duplication event which resulted in highly syntenic sister chromosomal segments across the Salicaceae. We leveraged this genomic feature to reconstruct de novo gene evolution from intergenera, interspecies, and intragenomic perspectives by comparing the syntenic regions within the P. trichocarpa reference, then P. deltoides, and finally Salix purpurea. Furthermore, we demonstrated that 86.5% of the putative orphan genes had evidence of transcription. Additionally, we also utilized the Populus genome-wide association mapping panel, a collection of 1,084 undomesticated P. trichocarpa genotypes to further determine putative regulatory networks of orphan genes using expression quantitative trait loci (eQTL) mapping. Functional enrichment of these eQTL subnetworks identified common biological themes associated with orphan genes such as response to stress and defense response. We also identify a putative cis-element for a de novo gene and leverage conserved synteny to describe evolution of a putative transcription factor binding site. Overall, 45% of orphan genes were captured in trans-eQTL networks. | |
| 536 | |b AC05-00OR22725. | ||
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| 650 | 7 | |a Orphan genes |2 local. | |
| 650 | 7 | |a De novo gene evolution |2 local. | |
| 650 | 7 | |a Genome evolution |2 local. | |
| 650 | 7 | |a Whole-genome duplication |2 local. | |
| 650 | 7 | |a Gene regulation |2 local. | |
| 650 | 7 | |a Synteny |2 local. | |
| 710 | 2 | |a Oak Ridge National Laboratory. |4 res. | |
| 710 | 2 | |a United States. Department of Energy. Office of Science. |4 spn. | |
| 710 | 1 | |a United States. |b Department of Energy. |b Office of Scientific and Technical Information |4 dst. | |
| 856 | 4 | 0 | |u https://www.osti.gov/servlets/purl/1823342 |z Full Text (via OSTI) |
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