A chromosome-level reference genome of the wax gourd cv. pf3 (Benincasa hispida)
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PROVIDER: PRJEB58675 | ENA |
REPOSITORIES: ENA
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Project description:A chromosome-level reference genome of the wax gourd (Benincasa hispida)
| PRJNA898819 | ENA
Project description:Wax gourd (Benincasa hispida) fruit RNA-seq raw sequence reads
| PRJNA576156 | ENA
Project description: Not available
| S-EPMC10570438 | biostudies-literature
Project description:Peel color is an important factor affecting commodity quality in vegetables; however, the genes controlling this trait remain unclear in wax gourd. Here, we used two F2 genetic segregation populations to explore the inheritance patterns and to clone the genes associated with green and white skin in wax gourd. The F2 and BC1 trait segregation ratios were 3:1 and 1:1, respectively, and the trait was controlled by nuclear genes. Bulked segregant analysis of both F2 plants revealed peaks on Chr5 exceeding the confidence interval. Additionally, 6,244 F2 plants were used to compress the candidate interval into a region of 179 Kb; one candidate gene, Bch05G003950 (BhAPRR2), encoding two-component response regulator-like protein Arabidopsis pseudo-response regulator2 (APRR2), which is involved in the regulation of peel color, was present in this interval. Two bases (GA) present in the coding sequence of BhAPRR2 in green-skinned wax gourd were absent from white-skinned wax gourd. The latter contained a frameshift mutation, a premature stop codon, and lacked 335 residues required for the protein functional region. The chlorophyll content and BhAPRR2 expression were significantly higher in green-skinned than in white-skinned wax gourd. Thus, BhAPRR2 may regulate the peel color of wax gourd. This study provides a theoretical foundation for further studies of the mechanism of gene regulation for the fruit peel color of wax gourd.
| S-EPMC8517133 | biostudies-literature
Project description:cucumber (Cucumis sativus), melon (C. melo), watermelon (Citrullus lanatus), bottle gourd (Lagenaria siceraria), wax gourd (Benincasa hispida) and squash (Cucurbita maxima). Epigenomics
| PRJNA934853 | ENA
Project description:Soluble solids content (SSC) is an important quality trait of wax gourd, but reports about its regulatory genes are scarce. In this study, the SSC regulatory gene BhSSC2.1 in wax gourd was mined via quantitative trait locus (QTL) mapping based on high-density genetic mapping containing 12 linkage groups (LG) and bulked segregant analysis (BSA)-seq. QTL mapping and BSA-seq revealed for the first time that the SSC QTL (107.658-108.176 cM) of wax gourd was on Chr2 (LG2). The interpretable phenotypic variation rate and maximum LOD were 16.033% and 6.454, respectively. The QTL interval contained 13 genes. Real-time fluorescence quantitative expression analysis, functional annotation, and sequence analysis suggested that Bch02G016960, named BhSSC2.1, was a candidate regulatory gene of the SSC in wax gourd. Functional annotation of this gene showed that it codes for a NADP-dependent malic enzyme. According to BhSSC2.1 sequence variation, an InDel marker was developed for molecular marker-assisted breeding of wax gourd. This study will lay the foundation for future studies regarding breeding and understanding genetic mechanisms of wax gourd.
| S-EPMC9266771 | biostudies-literature
Project description:Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among B. hispida and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as trnR-UCU-atpA and atpH-atpI, were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between B. hispida with the Citrullus, Lagenaria, and Cucumis. Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of B. hispida provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae.
| S-EPMC8954987 | biostudies-literature
Project description:Wax gourd is an important vegetable crop of the Cucurbitaceae family. According to the shape and structure of the seed coat, the seeds of the wax gourd can be divided into bilateral and unilateral. Bilateral seeds usually germinate quickly and have a high germination rate than unilateral seeds. Thereby, wax gourd varieties with bilateral seeds are more welcomed by seed companies and growers. However, the genetic basis and molecular mechanism regulating seed shape remain unclear in the wax gourd. In this study, the genetic analysis demonstrated that the seed shape of wax gourd was controlled by a single gene, with bilateral dominant to unilateral. Combined with genetic mapping and genome-wide association study, Bhi04G000544 (BhYAB4), encoding a YABBY transcription factor, was identified as the candidate gene for seed shape determination in the wax gourd. A G/A single nucleotide polymorphism variation of BhYAB4 was detected among different germplasm resources, with BhYAB4G specifically enriched in bilateral seeds and BhYAB4A in unilateral seeds. The G to A mutation caused intron retention and premature stop codon of BhYAB4. Expression analysis showed that both BhYAB4G and BhYAB4A were highly expressed in seeds, while the nuclear localization of BhYAB4A protein was disturbed compared with that of BhYAB4G protein. Finally, a derived cleaved amplified polymorphic sequence marker that could efficiently distinguish between bilateral and unilateral seeds was developed, thereby facilitating the molecular marker-assisted breeding of wax gourd cultivars.
| S-EPMC9493316 | biostudies-literature
Project description:IntroductionWilt is a soil-borne disease caused by Fusarium that has become a serious threat to wax gourd production. Disease-resistant graft wax gourds are an effective treatment for Fusarium wilt. However, there are few reports on the defense mechanism of graft wax gourd against wilt diseases.MethodsIn the present study, disease and growth indices were compared between grafted and original wax gourds after infection with Fusarium. High level of disease resistance was observed in the grafted wax gourd, with a lower disease index and low impacts on growth after infection. RNA-seq was performed to identify the differentially expressed genes (DEGs) between the adjacent treatment time points in the grafted and original wax gourds, respectively. Then a comparative temporal analysis was performed and a total of 1,190 genes were identified to show different gene expression patterns between the two wax gourd groups during Fusarium infection.Result and discussionHere, high level of disease resistance was observed in the grafted wax gourd, with a lower disease index and low impacts on growth after infection. The DEG number was higher in grafted group than original group, and the enriched functional categories and pathways of DEGs were largely inconsistent between the two groups. These genes were enriched in multiple pathways, of which the mitogen-activated protein kinase (MAPK) signaling pathway enhanced the early defense response, and cutin, suberin, and wax biosynthesis signaling pathways enhanced surface resistance in grafted wax gourd in comparison to original group. Our study provides insights into the gene regulatory mechanisms underlying the resistance of grafted wax gourds to Fusarium wilt infection, which will facilitate the breeding and production of wilt-resistant rootstocks.
| S-EPMC10641703 | biostudies-literature
Project description:Wax gourd (Benincasa hispida), a popular fruit of the Cucurbitaceae (cucurbits) family, contains many nutrients with health benefits and is widely grown in China and other tropical areas. In this study, a wax gourd mutant hfc12 with light-color pericarp was obtained through ethane methylsulfonate (EMS) mutagenesis. Integrative analysis of the metabolome and transcriptome identified 31 differentially accumulated flavonoids (DAFs; flavonoids or flavonoid glycosides) and 828 differentially expressed genes (DEGs) between the hfc12 mutant and wild-type 'BWT'. Furthermore, BSA-seq and kompetitive allele specific PCR (KASP) analysis suggested that the light-color pericarp and higher flavonoid content was controlled by a single gene BhiPRR6 (Bhi12M000742), a typical two-component system (TCS) pseudo-response regulator (PRR). Genetic analysis detected only one nonsynonymous mutation (C-T) in the second exon region of the BhiPRR6. Weighted correlation network analysis (WGCNA) identified the downstream target genes of BhiPRR6, probably regulated by light and were intermediated in the regulatory enzyme reaction of flavonoid biosynthetic pathway. Thus, these results speculated that the transcription factor BhiPRR6, interacting with multiple genes, regulates the absorption of light signals and thereby changes the pericarp color and synthesis of flavonoids in wax gourd.
| S-EPMC9549291 | biostudies-literature