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A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana


De novo genes created in the plant mitochondrial genome have frequently been transferred into the nuclear genome via intergenomic gene transfer events. Therefore, plant mitochondria might be a source of de novo genes in the nuclear genome. However, the functions of de novo genes originating from mitochondria and the evolutionary fate remain unclear. Here, we revealed that an Arabidopsis thaliana specific small coding gene derived from the mitochondrial genome regulates floral transition. We previously identified 49 candidate de novo genes that induce abnormal morphological changes on overexpression. We focused on a candidate gene derived from the mitochondrial genome (sORF2146) that encodes 66 amino acids. Comparative genomic analyses indicated that the mitochondrial sORF2146 emerged in the Brassica lineage as a de novo gene. The nuclear sORF2146 emerged following an intergenomic gene transfer event in the A. thaliana after the divergence between Arabidopsis and Capsella. Although the nuclear and mitochondrial sORF2146 sequences are the same in A. thaliana, only the nuclear sORF2146 is transcribed. The nuclear sORF2146 product is localized in mitochondria, which may be associated with the pseudogenization of the mitochondrial sORF2146. To functionally characterize the nuclear sORF2146, we performed a transcriptomic analysis of transgenic plants overexpressing the nuclear sORF2146. Flowering transition-related genes were highly regulated in the transgenic plants. Subsequent phenotypic analyses demonstrated that the overexpression and knockdown of sORF2146 in transgenic plants resulted in delayed and early flowering, respectively. These findings suggest that a lineage-specific de novo gene derived from mitochondria has an important regulatory effect on floral transition.

Key message

A large-scale intergenomic gene transfer event involving the nuclear and mitochondrial genomes in the Arabidopsis thaliana lineage created a small coding gene that regulates floral timing.

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Data availability

The raw unfiltered microarray results and the normalized data generated during and/or analyzed during the current study are available in the Gene Expression Omnibus (GEO) repository under the subseries entry GSE184689, The sORF2146 full-length transcript sequence generated during and/or analyzed during the current study will be available in the DNA Data Bank of Japan (DDBJ) repository under the subseries entry LC718385 on December 1st 2022,


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This study was supported by Grants-in-Aid for Scientific Research and the Asahi Glass Foundation. We thank the National Institute of Genetics of the Research Organization of Information and Systems for providing excellent supercomputer services. We also thank Edanz ( for editing a draft of this manuscript.


This study was supported by JSPS KAKENHI (JP22H02675 to K.H, JP20H03317 to K.H., JP18H02420 to K.H., JP22K14870 to K.S.), MEXT KAKENHI (JP21H05724 to K.H., JP20H05905 to K.H. JP20H05906 to K.H., JP22H05731 to K.S.), and the Asahi Glass" Foundation (to K.H.).).

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TT, KS, and KH. conceived the project; TT, Y-WK, MH-T, TK, TU, MS, and TM performed the experiments; TT and KS conducted the bioinformatics analysis; TT and KH wrote the article.

Corresponding author

Correspondence to Kousuke Hanada.

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The authors declare no conflicts of interest associated with this manuscript.

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Takeda, T., Shirai, K., Kim, Yw. et al. A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana. Plant Mol Biol 111, 189–203 (2023).

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  • De novo gene
  • Intergenomic Gene Transfer
  • Flowering
  • Arabidopsis