Abstract
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.
| Original language | English |
|---|---|
| Article number | evab198 |
| Journal | Genome Biology and Evolution |
| Volume | 13 |
| Issue number | 9 |
| DOIs | |
| State | Published - Sep 1 2021 |
Funding
Notice: This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan ( http://energy.gov/downloads/doe-public-access-plan ). Acknowledgments Author Contributions Data Availability This research was supported by the United States Department of Energy’s Office of Science Early Career Research Program under the Biological and Environmental Research office and, in part, by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, and by the Center for Bioenergy Innovation at Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract Number DE-AC05-00OR22725. Part of this work was performed at the Oak Ridge Leadership Computing Facility (OLCF) including resources of the Compute and Data Environment for Science (CADES) at Oak Ridge National Laboratory. The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. We thank Dr Lawrence Smart and collaborators for prepublication use of the Salix purpurea v1.0 genome and Salix purpurea RNA-Seq data sets. We thank the Department of Energy Joint Genome Institute and colleagues at CBI for prepublication access to RNA-seq data sets and Populus deltoides WV94 v2.1. We thank collaborators at the Oak Ridge National Laboratory, Duke University, and the DOE Joint Genome Institute for access to the prepublication access to the genome and annotation of Sphagnum fallax v0.5. We thank Xiaohan Yang and the Department of Energy Joint Genome Institute for prepublication access to Kalanchoe laxiflora v1.1. We thank the Department of Energy Joint Genome Institute and collaborators for prepublication access to Phaseolus vulgaris v2.1.
Keywords
- de novo gene evolution
- gene regulation
- genome evolution
- orphan genes
- synteny
- whole-genome duplication