Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection

Yuan Huang, Jiahui Chen, Chuan Dong, Dylan Sosa, Shengqian Xia, Yidan Ouyang, Chuanzhu Fan, Dezhu Li, Emily Mortola, Manyuan Long, Joy Bergelson

Research output: Contribution to journalArticlepeer-review

Abstract

Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, how new duplicate genes contribute to phenotypic evolution remains largely unknown, especially in plants. Here, we identified the new gene EXOV, derived from a partial gene duplication of its parental gene EXOVL in Arabidopsis thaliana. EXOV is a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNA-sequencing analyses revealed that, despite its young age, EXOV has acquired many novel direct and indirect interactions in which the parental gene does not engage. This observation is consistent with the high, selection-driven substitution rate of its encoded protein, in contrast to the slowly evolving EXOVL, suggesting an important role for EXOV in phenotypic evolution. We observed significant differentiation of morphological changes for all phenotypes assessed in genome-edited and T-DNA insertional single mutants and in double T-DNA insertion mutants in EXOV and EXOVL. We discovered a substantial divergence of phenotypic effects by principal component analyses, suggesting neofunctionalization of the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological evolution in A. thaliana.

Original languageEnglish (US)
Pages (from-to)802-817
Number of pages16
JournalPlant Cell
Volume34
Issue number2
DOIs
StatePublished - Feb 2022

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology

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