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Organelle genome assembly uncovers the dynamic genome reorganization and cytoplasmic male sterility associated genes in tomato

Kosuke Kuwabara, Issei Harada, Yuma Matsuzawa, View ORCID ProfileTohru Ariizumi, View ORCID ProfileKenta Shirasawa
doi: https://doi.org/10.1101/2021.03.03.433741
Kosuke Kuwabara
1Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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Issei Harada
1Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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Yuma Matsuzawa
2TOKITA Seed Co. LTD., Kazo, Saitama 349-1144, Japan
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Tohru Ariizumi
1Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
3Tsukuba Plant Innovation Research Center, Tsukuba, Ibaraki 305-8577, Japan
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  • ORCID record for Tohru Ariizumi
  • For correspondence: ariizumi.toru.ge@u.tsukuba.ac.jp shirasaw@kazusa.or.jp
Kenta Shirasawa
4Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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  • ORCID record for Kenta Shirasawa
  • For correspondence: ariizumi.toru.ge@u.tsukuba.ac.jp shirasaw@kazusa.or.jp
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Abstract

To identify cytoplasmic male sterility (CMS)-associated genes in tomato, we determined the genome sequences of mitochondria and chloroplasts in three CMS tomato lines derived from independent asymmetric cell fusions, their nuclear and cytoplasmic donors, and male fertile weedy cultivated tomato and wild relatives. The structures of the CMS mitochondrial genomes were highly divergent from those of the nuclear and cytoplasmic donors, and genes of the donors were mixed up in these genomes. On the other hand, the structures of CMS chloroplast genomes were moderately conserved across the donors, but CMS chloroplast genes were unexpectedly likely derived from the nuclear donors. Comparative analysis of the structures and contents of organelle genes and transcriptome analysis identified three genes that were uniquely present in the CMS lines, but not in the donor or fertile lines. RNA sequencing analysis indicated that these three genes transcriptionally expressed in anther, two of which were also expressed in pollen. They could be potential candidates for CMS-associated genes. This study suggests that organelle reorganization mechanisms after cell fusion events differ between mitochondria and chloroplasts, and provides insight into the development of new F1 hybrid breeding programs employing the CMS system in tomato.

Competing Interest Statement

YM is an employee of TOKITA Seed Co. LTD. All other authors declare no competing interests.

Footnotes

  • E-mail addresses of all authors KK: s1921107{at}s.tsukuba.ac.jp, IH: s2021044{at}s.tsukuba.ac.jp, YM: ymatsuzawa{at}tokitaseed.co.jp, TA: ariizumi.toru.ge{at}u.tsukuba.ac.jp, KS: shirasaw{at}kazusa.or.jp

  • http://www.kazusa.or.jp/tomato

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 04, 2021.
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Organelle genome assembly uncovers the dynamic genome reorganization and cytoplasmic male sterility associated genes in tomato
Kosuke Kuwabara, Issei Harada, Yuma Matsuzawa, Tohru Ariizumi, Kenta Shirasawa
bioRxiv 2021.03.03.433741; doi: https://doi.org/10.1101/2021.03.03.433741
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Organelle genome assembly uncovers the dynamic genome reorganization and cytoplasmic male sterility associated genes in tomato
Kosuke Kuwabara, Issei Harada, Yuma Matsuzawa, Tohru Ariizumi, Kenta Shirasawa
bioRxiv 2021.03.03.433741; doi: https://doi.org/10.1101/2021.03.03.433741

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