Gene fusion as an important mechanism to generate new genes in the genus Oryza

Abstract
Background: Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown. Results: We conduct genome-wide interrogations of four Oryza genomes by designing and implementing novel pipelines to detect fusion genes. Based on the phylogeny of ten plant species, we detect 310 fusion genes across four Oryza species. The estimated rate of origination of fusion genes in the Oryza genus is as high as 63 fusion genes per species per million years, which is fixed at 16 fusion genes per species per million years and much higher than that in flies. By RNA sequencing analysis, we find more than 44% of the fusion genes are expressed and 90% of gene pairs show strong signals of purifying selection. Further analysis of CRISPR/Cas9 knockout lines indicates that newly formed fusion genes regulate phenotype traits including seed germination, shoot length and root length, suggesting the functional significance of these genes. Conclusions: We detect new fusion genes that may drive phenotype evolution in Oryza. This study provides novel insights into the genome evolution of Oryza.

Citation
Zhou, Y., Zhang, C., Zhang, L., Ye, Q., Liu, N., Wang, M., Long, G., Fan, W., Long, M., & Wing, R. A. (2022). Gene fusion as an important mechanism to generate new genes in the genus Oryza. Genome Biology, 23(1). https://doi.org/10.1186/s13059-022-02696-w

Acknowledgements
This research was financially funded by National Natural Science Foundation of China (31571311, 32000180), Youth Innovation Promotion Association CAS (2021394), Yunnan Fundamental Research Projects (202001AU070075), Yunnan Young & Elite Talents Project (YNWR-QNBJ-2019-268), and CAS Scholarship. ML was supported by NSF1026200 and NSF1051826; RW by NSF1026200. We are grateful to Yidan Oyang for helpful discussions.

Publisher
Springer Science and Business Media LLC

Journal
Genome biology

DOI
10.1186/s13059-022-02696-w

PubMed ID
35706016

Additional Links
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02696-w

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