Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development

Anzhen Fu,Fengling Wang,Yunxiang Wang,Qing Wang,Xuewen Zhang,Xiaoyan Zhao,Lili Ma,Kai Shi,Jinhua Zuo,Lipu Gao,Jian Li,Changlong Wen,Xuechuan Zhang,Jianlou Mu,Donald Grierson

doi:10.1038/s41438-021-00487-1

Abstract

Chayote (Sechium edule) is an agricultural crop in the Cucurbitaceae family that is rich in bioactive components. To enhance genetic research on chayote, we used Nanopore third-generation sequencing combined with Hi–C data to assemble a draft chayote genome. A chromosome-level assembly anchored on 14 chromosomes (N50 contig and scaffold sizes of 8.40 and 46.56 Mb, respectively) estimated the genome size as 606.42 Mb, which is large for the Cucurbitaceae, with 65.94% (401.08 Mb) of the genome comprising repetitive sequences; 28,237 protein-coding genes were predicted. Comparative genome analysis indicated that chayote and snake gourd diverged from sponge gourd and that a whole-genome duplication (WGD) event occurred in chayote at 25 ± 4 Mya. Transcriptional and metabolic analysis revealed genes involved in fruit texture, pigment, flavor, flavonoids, antioxidants, and plant hormones during chayote fruit development. The analysis of the genome, transcriptome, and metabolome provides insights into chayote evolution and lays the groundwork for future research on fruit and tuber development and genetic improvements in chayote.

Highlights

Chayote (Sechium edule) is a diploid perennial herbaceous climbing plant with 28 chromosomes (2n = 2x = 28)[1] that belongs to the Cucurbitaceae family[2]
Two libraries were built for the Illumina sequencing platform, and 39.01 Gb of high-quality data were obtained after filtration, with a total sequencing depth of approximately 55 with Q20 and Q30 percentages of 97.09 and 92.02, respectively
This study reports the first high-quality genome assembly of 14 chayote chromosomes

Summary

Introduction

Chayote is believed to have originated in Mexico, where it was first cultivated approximately 500 years ago[5,6]. It is commonly cultivated in tropical and subtropical areas, such as Brazil, India, Costa Rica, China, and Mexico, and is a significant commercial crop worldwide[7,8]. Chayote contains abundant bioactive compounds, such as phenolics, flavonoids, carotenoids, and bioactive polysaccharides[9,10,11] in the fruit, leaves, tubers, and stems[4,12], and has potential for the treatment of hypertension, diabetes, and inflammation, as well as other pharmacological applications[2,13,14].

Methods

Results

Conclusion