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Combined genomic, transcriptomic, and metabolomic analyses provide insights into the fruit development of bottle gourd (Lagenaria siceraria)
Horticulture Research ( IF 7.6 ) Pub Date : 2024-11-27 , DOI: 10.1093/hr/uhae335
Xuelian He, Yanyan Zheng, Songguang Yang, Ying Wang, Yu’e Lin, Biao Jiang, Dasen Xie, Wenrui Liu, Qingwu Peng, Jinhua Zuo, Min Wang

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.

中文翻译:


基因组、转录组学和代谢组学相结合的分析为葫芦 (Lagenaria siceraria) 的果实发育提供了见解



葫芦 (Lagenaria siceraria (Molina) Standl) 是一种分布广泛的葫芦科物种,但差距和低质量组装限制了其基因组研究。为了解决这个问题,我们使用 PacBio HiFi 测序和 Hi-C 校正组装了一个近乎完整、高质量的葫芦 (Pugua) 基因组。基因组长 298.67 Mb,ContigN50 为 28.55 Mb,经鉴定具有 11 条染色体、11 个着丝粒、18 个端粒和 24,439 个预测的蛋白质编码基因;值得注意的是,七条染色体完成了无间隙端粒到端粒组装。基于普瓜基因组,转录组学和代谢组学联合分析表明,氨基酸和脂质在扩增阶段积累,而糖类和萜类化合物在成熟过程中增加。GA4 和 Aux/IAA 家族的基因介导果实的膨胀和成熟,而细胞壁重塑受 XTH、EXP、多酚和生物碱等因素的调节,有助于环境适应。GGAT2 与鲜味来源谷氨酸呈正相关,SUS5 和 SPS4 表达与蔗糖积累一致。本研究为葫芦研究提供了宝贵的遗传资源,增强了对葫芦科进化的理解,并支持了对葫芦发育、品质和遗传改良的进一步研究。
更新日期:2024-11-27
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