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

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.

Chromosome-level genome assembly of Gynostemma pentaphyllum provides insights into gypenoside biosynthesis

“…The total length of the final chromosome-level genome was 582 Mb, ∼91.65% of the estimated genome size, which is similar to that of Sechium edule (i.e. 606 Mb) 39 but larger than those of other members of the Cucurbitaceae family, such as C. sativus , 40 C. melo , 41 and S. grosvenorii. 42 The genome assembly comprised 1,232 contigs and had a scaffold N50 of 50.78 Mb.…”

Origin, Evolution, Breeding, and Omics of Chayote, an Important Cucurbitaceae Vegetable Crop

“…Transcriptomics and metabolomics are used to investigate the sequence information and metabolite changes in different tissues/organs or the same tissues/organs at the different developmental stages. In 2021, the transcriptome and metabolome of the fruits at different developmental stages of S. edule were established, and the results revealed that the genes involved in fruit texture, pigment, flavor, flavonoids, antioxidants, and plant hormones are expressed at different levels during chayote fruit development (Fu et al, 2021). To our knowledge, this transcriptome and metabolome are the first ones reported for the S. edule plant.…”

“…With the advent of functional genomic research, the genome sequencing of the plants has been substantially accelerated, and a large amount of data has been generated (Morozova and Marra, 2008;Ondov et al, 2008). As an important squash vegetable, genomic, transcriptomic, and metabolomic analyses of the S. edule plant have been generated (Fu et al, 2021). A high-quality wholegenome sequence of S. edule with a size of 606.42 Mb has been completed.…”

Exploring the genic resources underlying metabolites through mGWAS and mQTL in wheat: From large-scale gene identification and pathway elucidation to crop improvement

“…Meanwhile, the low coverage (hundreds detected versus thousands predicted) of targeted metabolomics over the metabolome of given plant organisms has lessened the efficacy relative to uncovering the metabolic pathways and underlying genes. Given this, we have developed a widely targeted metabolomics method that combines merits from both targeted and untargeted metabolomics ( Chen et al., 2013 ), which has been successfully utilized in numerous species ( Chen et al., 2014 ; Wen et al., 2014 ; Song et al., 2015 ; Geng et al., 2016 ; Li et al., 2017 , 2021a ; Wang et al., 2017 ; Ghareeb et al., 2018 ; Cao et al., 2019 ; Lee et al., 2020 ; Liu et al., 2020 ; Zeng et al., 2020 ; Fu et al., 2021 ; Nie et al., 2021 ). By applying this protocol, we are now able to detect some 5000 metabolites from bread wheat samples within a single run that typically takes 20 min (data not published).…”