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Transcriptomic variation of the flower–fruit transition in Physalis and Solanum

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Abstract

Main conclusion

Gene expression variations in response to fertilization between Physalis and Solanum might play essential roles in species divergence and fruit evolution.

Abstract

Fertilization triggers variation in fruit development and morphology. The Chinese lantern, a morphological novelty derived from the calyx, is formed upon fertilization in Physalis but is not observed in Solanum. The underlying genetic variations are largely unknown. Here, we documented the developmental and morphological differences in the flower and fruit between Physalis floridana and Solanum pimpinellifolium and then evaluated both the transcript sequence variation and gene expression at the transcriptomic level at fertilization between the two species. In Physalis transcriptomic analysis, 468 unigenes were identified as differentially expressed genes (DEGs) that were strongly regulated by fertilization across 3 years. In comparison with tomato, 14,536 strict single-copy orthologous gene pairs were identified between P. floridana and S. pimpinellifolium in the flower–fruit transcriptome. Nine types of gene variations with specific GO-enriched patterns were identified, covering 58.82% orthologous gene pairs that were DEGs in either trend or dosage at the flower–fruit transition between the two species, which could adequately distinguish Solanum and Physalis, implying that differential gene expression at fertilization might play essential roles during the divergence and fruit evolution of Solanum–Physalis. Virus-induced gene silencing analyses revealed the developmental roles of some transcription factor genes in fertility, Chinese lantern development, and fruit weight control in Physalis. This study presents the first floral transcriptomic resource of Physalis, and reveals some candidate genetic variations accounting for the early fruit developmental evolution in Physalis in comparison to Solanum.

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Data availability

All relevant supporting data can be found within the additional files accompanying this article. The RNA-Seq reads described in the article were deposited at the Sequence Read Archive (SRA) database under the accession number PRJNA552437.

Abbreviations

DEG:

Differentially expressed gene

GO:

Gene ontology

ICS:

Inflated calyx syndrome

PCA:

Principal component analysis

TF:

Transcription factor

VIGS:

Virus-induced gene silencing

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Acknowledgements

We appreciate Drs PC Gong and J Zhao for their assistances respectively in photograph under microscope, pollen staining and VIGS analyses.

Funding

This work was supported by grants from the National Natural Science Foundation of China (31525003 and 91331103) and by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB27010106).

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Author notes

  1. Huihui Gao and Jing Li contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China

    Huihui Gao, Jing Li, Li Wang, Jisi Zhang & Chaoying He

  2. University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China

    Huihui Gao, Jing Li, Jisi Zhang & Chaoying He

  3. School of Agronomy, Anhui Agricultural University, Hefei, 230036, China

    Huihui Gao

  4. The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China

    Chaoying He

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  1. Huihui Gao
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Gao, H., Li, J., Wang, L. et al. Transcriptomic variation of the flower–fruit transition in Physalis and Solanum. Planta 252, 28 (2020). https://doi.org/10.1007/s00425-020-03434-x

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