Combined genomic, transcriptomic, and metabolomic analyses provide insights into the fruit development of bottle gourd (Lagenaria siceraria)

Abstract

Bottle gourd (Lagenaria siceraria (Molina) Standl) is a widely distributed Cucurbitaceae species, but gaps and low-quality assemblies have limited its genomic study. To address this, we assembled a nearly complete, high-quality genome of the bottle gourd (Pugua) using PacBio HiFi sequencing and Hi-C correction. The genome, being 298.67 Mb long with a ContigN50 of 28.55 Mb, was identified to possess 11 chromosomes, 11 centromeres, 18 telomeres, and 24 439 predicted protein-coding genes; notably, gap-free telomere-to-telomere assembly was accomplished for seven chromosomes. Based on the Pugua genome, the transcriptomic and metabolomic combined analyses revealed that amino acids and lipids accumulate during the expansion stage, while sugars and terpenoids increase during ripening. GA4 and genes of the Aux/IAA family mediate fruit expansion and maturation, while cell wall remodeling is regulated by factors such as XTHs, EXPs, polyphenols, and alkaloids, contributing to environmental adaptation. GGAT2 was positively correlated with glutamate, a source of umami, and SUS5 and SPS4 expression aligned with sucrose accumulation. This study provides a valuable genetic resource for bottle gourd research, enhancing the understanding of Cucurbitaceae evolution and supporting further studies on bottle gourd development, quality, and genetic improvement.

Acknowledgments

This work was supported by the Special Fund for Scientific Innovation Strategy Construction of High Level from the Guangdong Academy of Agriculture Science (R2021YJ-0G001), the Construction of cucurbits Collaboration and Innovation Center (XTCX202301), the 2024 Special Seed Industry Revitalization Project of Rural Revitalization Strategy (2022-440100-4301030107-0013), and the Department of Agriculture and Rural Areas of Guangdong Province of China (2023-NJS-00-003, 2022-NJS-00-005).

Author Contributions

Q.P., J.Z., S.Y., and M.W. conceived and supervised the study. X.H., and Y.Z. performed the data analysis. M.W. and S.Y. collected the Pugua samples. Y.W., Y.L., B.J., D.X., and W.L. contributed to valuable discussions. X.H. wrote the manuscript and drew the figures. Y. Z. and M.W. revised the manuscript and figures. All authors have read and approved the final manuscript.

Data availability

The L. siceraria (Molina) Standl (Pugua) raw genome sequencing, assembly data and TE notes are available from the NCBI under project ID PRJNA1196720.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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