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The wax gourd (Benincasa hispida) is an important vegetable crop whose fruits contain nutrients and metabolites. Small auxin upregulated RNA (SAUR) genes constitute the largest early auxin-responsive gene family and regulate various biological processes in plants, although this gene family has not been studied in the wax gourd. Here, we performed genome-wide identification of the SAUR gene family in wax gourds and analyzed their syntenic and phylogenetic relationships, gene structures, conserved motifs, cis-acting elements, and expression patterns. A total of 68 SAUR (BhSAUR) genes were identified, which were distributed on nine chromosomes with 41 genes in two clusters. More than half of the BhSAUR genes were derived from tandem duplication events. The BhSAUR proteins were classified into seven subfamilies. BhSAUR gene promoters contained cis-acting elements involved in plant hormone and environmental signal responses. Further expression profiles showed that BhSAUR genes displayed different expression patterns. BhSAUR60 was highly expressed in fruits, and overexpression led to longer fruits in Arabidopsis. In addition, the plants with overexpression displayed longer floral organs and wavy stems. In conclusion, our results provide a systematic analysis of the wax gourd SAUR gene family and facilitate the functional study of BhSAUR60 during wax gourd fruit development. [ABSTRACT FROM AUTHOR]

(1) Background: Wax gourd is an economically important vegetable crop in many tropical and sub-tropical countries in Asia. Fruit color is an important fruit quality trait, but the genetic, biochemical basis and regulatory network of fruit color variation in wax gourd are rarely studied. (2) Methods: In this study, two wax gourd inbred lines with different pericarp colors were used as materials to conduct joint metabolomic and transcriptomic analyses on mature fruit pericarp: B214 with yellow and B227 with dark green color. (3) Results: It was found that the chlorophyll content in the pericarp of B214 was significantly lower than that of B227, consistent with the down-regulation of several genes involved in the chlorophyll biosynthesis pathway, including hemA, hemB, hemC, hemF, chlH, chlI, chlM, POR, and CAO. The 229 metabolites showed differential accumulation levels between B214 and B227, and 4 anthocyanins, 5 flavanones, 25 flavones, 25 flavone C-glycosides, 12 flavonols, and 3 isoflavones were identified. In particular, cyanidin 3-O-glucoside, an anthocyanin contributing to the coloration of dark color, showed higher accumulation in B227 than in B214, probably due to the higher expression of genes of F3′H and glucosyl transferases (GTs) in B227. Transcription factors such as MYBs and bHLHs showed differential expressions between the two lines including bHLH14, a homolog of Arabidopsis AtbHLH14 that had significantly higher expression in B227 than in B214. bHLH14 was located in a region where the pericarp color (pc) locus was mapped, suggesting it may be a candidate gene for the pc locus. (4) Conclusions: This work supports the association of chlorophyll and flavonoid synthesis in wax gourd fruit color variation and also provides a good foundation for understanding the regulatory network for wax gourd coloration. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs of 20–24 nucleotides and play important roles in many plant biological and metabolic processes. Wax gourd is an important vegetable of Cucurbitacea family, with great economic and medicinal value. Although miRNAs have been extensively studied in model plant species, less is known in wax gourd (Benincasa hispida). In this study, in order to identify miRNAs in wax groud, five independent small RNA libraries were constructed using leaf, root, stem, flower, and fruit of B227. Based on high-throughput Illumina deep sequencing. In total, 422 known and 409 novel miRNAs were identified from five libraries. Comparative analysis revealed that many miRNAs were differentially expressed among different tissues, indicating tissue-specific expression of some miRNAs. qRT-PCR verified the reliability of small RNA sequencing results. Furthermore, miRNAs with similar expression patterns among five tissues were clustered into the same profile, among which many miRNAs were found with relatively high expression in the fruit of wax gourd. MiR164-x had the highest expression in fruit than in other tissues and many NAC transcription factors were predicted as its target genes. We propose that miR164 might regulate fruit development by forming miR164-NAC module in wax gourd. Taken together, this study provides the first global miRNAs profiling of wax gourd, and lays the foundation for understanding the regulatory roles of miRNAs in the growth and development processes of wax gourd. [ABSTRACT FROM AUTHOR]

Wax gourd (2n = 2 x = 24) is an important vegetable species in Cucurbitaceae . Because it can be stored for a very long period of time, it plays an important role in ensuring the annual supply and regulating off-season supply of the vegetables. However, the availability of genetic information about wax gourd is limited. This study aimed to identify the useful genetic information for wax gourd. The conserved domains of reverse transcriptase (RT) genes of Ty1- copia retrotransposons were isolated from the genome of wax gourd using degenerate oligonucleotide primers. A total of twenty eight RT sequences were obtained, which showed high heterogeneity with the similarity ranging from 47.5% to 94.3%. Sixteen (57.1%) of them were found to be defective, being disrupted by stop codons and/or frameshift mutations. These 28 sequences were divided into five subfamilies. The comparative phylogenetic analysis with other Cucurbitaceae species from GenBank database showed that most retrotransposons derived from the same genus tended to cluster together, although there were a few exceptions. These results indicate that both vertical transmission and horizontal transmission are the sources of Ty1- copia retrotransposons in wax gourd. Fluorescent in situ hybridization (FISH) with Ty1- copia retrotransposon sequences as probes revealed that this kind of retrotransposons had a dispersed genomic organization, physically distributed among all the chromosomes of wax gourd, with clusters in the heterochromatin regions. This is the first report of Ty1- copia retrotransposons in wax gourd, which would be helpful for our understanding about the organization and evolutions of wax gourd genome and also provide valuable information for our utilization of wax gourd retrotransposons. [ABSTRACT FROM AUTHOR]

• Time-course transcriptome analysis of bilateral and unilateral seeds in wax gourd. • Comparative analysis discovered transcriptomic differences between two types of seeds. • Secondary metabolite biosynthesis-related genes were highly differentially expressed between bilateral and unilateral seeds. • Lignin might play a crucial role in the formation of seed ribs and final seed shape. Wax gourd is an important vegetable crop in Cucurbitaceae. There are two shapes of wax gourd seeds, bilateral and unilateral. Bilateral seeds are more popular than unilateral seeds because they germinate faster along with a higher germination rate. Previously, we identified the seed shape determination gene YABBY4 through genetic mapping and genome-wide association study. However, the molecular mechanisms underlying seed shape differentiation remain elusive. In this study, the B214 variety containing bilateral seeds and the B227 variety containing unilateral seeds were subjected to time-course transcriptome analysis. Our results showed that genes related to secondary metabolite biosynthesis were differentially expressed between B214 and B227 seeds at all stages, and some lignin biosynthesis-related genes were highly expressed in B214 seeds at the later stages. At the early stages, genes associated with cell periphery, plasma membrane, plant hormone signal transduction, and MAPK signaling pathway were more active. Catalytic activity, biosynthetic, and metabolic process-related genes were differentially expressed at the later stages. Together, our findings dissect the transcriptomic differences between the two types of seeds and gain insights into the regulatory networks of seed shape differentiation in wax gourd. [Display omitted] [ABSTRACT FROM AUTHOR]