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

Yanli Zhou, Chengjun Zhang, Li Zhang, Qiannan Ye, Ningyawen Liu, Muhua Wang, Guangqiang Long, Wei Fan, Manyuan Long, Rod A. Wing

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

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.

Original languageEnglish (US)
Article number130
JournalGenome biology
Volume23
Issue number1
DOIs
StatePublished - Dec 2022

Keywords

  • Evolutionary patterns
  • Fusion gene
  • Oryza
  • Phenotype

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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