Comparative genomics analysis of bHLH genes in cucurbits identifies a novel gene regulating cucurbitacin biosynthesis

CmBr confers fruit bitterness under CPPU treatment in melon

Many biotic or abiotic factors such as CPPU (N-(2-chloro-pyridin-4-yl)-N'-phenylurea), a growth regulator of numerous crops, can induce bitterness in cucurbits. In melon, cucurbitacin B is the major compound leading to bitterness. However, the molecular mechanism underlying CuB biosynthesis in response to different conditions remains unclear. Here, we identified a set of genes involved in CPPU-induced CuB biosynthesis in melon fruit and proposed CmBr gene as the major regulator. Using CRISPR/Cas9 gene editing, we confirmed CmBr's role in regulating CuB biosynthesis under CPPU treatment. We further discovered a CPPU-induced MYB-related transcription factor, CmRSM1, which specifically binds to the Myb motif within the CmBr promoter and activates its expression. Moreover, we developed an introgression line by introducing the mutated Cmbr gene into an elite variety and eliminated CPPU-induced bitterness, demonstrating its potential application in breeding. This study offers a valuable tool for breeding high-quality non-bitter melon varieties and provides new insights into the regulation of secondary metabolites under environmental stresses.

A wild melon reference genome provides novel insights into the domestication of a key gene responsible for melon fruit acidity

KEY MESSAGE

A wild melon reference genome elucidates the genomic basis of fruit acidity domestication. Structural variants (SVs) have been reported to impose major effects on agronomic traits, representing a significant contributor to crop domestication. However, the landscape of SVs between wild and cultivated melons is elusive and how SVs have contributed to melon domestication remains largely unexplored. Here, we report a 379-Mb chromosome-scale genome of a wild progenitor melon accession "P84", with a contig N50 of 14.9 Mb. Genome comparison identifies 10,589 SVs between P84 and four cultivated melons with 6937 not characterized in previously analysis of 25 melon genome sequences. Furthermore, the population-scale genotyping of these SVs was determined in 1175 accessions, and 18 GWAS signals including fruit acidity, fruit length, fruit weight, fruit color and sex determination were detected. Based on these genotyped SVs, we identified 3317 highly diverged SVs between wild and cultivated melons, which could be the potential SVs associated with domestication-related traits. Furthermore, we identify novel SVs affecting fruit acidity and proposed the diverged evolutionary trajectories of CmPH, a key regulator of melon fruit acidity, during domestication and selection of different populations. These results will offer valuable resources for genomic studies and genetic improvement in melon.

Chromosome-scale reference genome of broccoli (Brassica oleracea var. italica Plenck) provides insights into glucosinolate biosynthesis

Broccoli (Brassica oleracea var. italica Plenck) is an important vegetable crop, as it is rich in health-beneficial glucosinolates (GSLs). However, the genetic basis of the GSL diversity in Brassicaceae remains unclear. Here we report a chromosome-level genome assembly of broccoli generated using PacBio HiFi reads and Hi-C technology. The final genome assembly is 613.79 Mb in size, with a contig N50 of 14.70 Mb. The GSL profile and content analysis of different B. oleracea varieties, combined with a phylogenetic tree analysis, sequence alignment, and the construction of a 3D model of the methylthioalkylmalate synthase 1 (MAM1) protein, revealed that the gene copy number and amino acid sequence variation both contributed to the diversity of GSL biosynthesis in B. oleracea. The overexpression of BoMAM1 (BolI0108790) in broccoli resulted in high accumulation and a high ratio of C4-GSLs, demonstrating that BoMAM1 is the key enzyme in C4-GSL biosynthesis. These results provide valuable insights for future genetic studies and nutritive component applications of Brassica crops.

Genome-Wide Identification of MYC Transcription Factors and Their Potential Functions in the Growth and Development Regulation of Tree Peony (Paeonia suffruticosa)

Tree peony (Paeonia suffruticosa Andr.) is a traditional Chinese flower with significant ornamental and medicinal value. Its growth and development process is regulated by some internal and external factors, and the related regulatory mechanism is largely unknown. Myelocytomatosis transcription factors (MYCs) play significant roles in various processes such as plant growth and development, the phytohormone response, and the stress response. As the identification and understanding of the MYC family in tree peony remains limited, this study aimed to address this gap by identifying a total of 15 PsMYCs in tree peony and categorizing them into six subgroups based on bioinformatics methods. Furthermore, the gene structure, conservative domains, cis-elements, and expression patterns of the PsMYCs were thoroughly analyzed to provide a comprehensive overview of their characteristics. An analysis in terms of gene structure and conserved motif composition suggested that each subtribe had similarities in function. An analysis of the promoter sequence revealed the presence of numerous cis-elements associated with plant growth and development, the hormone response, and the stress response. qRT-PCR results and the protein interaction network further demonstrated the potential functions of PsMYCs in the growth and development process. While in comparison to the control, only PsMYC2 exhibited a statistically significant variation in expression levels in response to exogenous hormone treatments and abiotic stress. A promoter activity analysis of PsMYC2 revealed its sensitivity to Flu and high temperatures, but exhibited no discernible difference under exogenous GA treatment. These findings help establish a basis for comprehending the molecular mechanism by which PsMYCs regulate the growth and development of tree peony.

Cucurbitacins B, E and I Concentrations and Relationship with Drought Tolerance in Bottle Gourd [Lagenaria siceraria (Molina) Standl.]

Bottle gourd [Lagenaria siceraria (Molina) Standl.]) is a relatively drought-tolerant cucurbit due to the high composition of unique biochemical compositions, including cucurbitacin. The objective of this study was to determine the concentrations of cucurbitacins in bottle gourd and their relationship to drought tolerance. The study assessed 12 bottle gourd accessions grown under two moisture levels (i.e., non-stressed (NS) and drought-stressed (DS)) and three drought stress intensities (i.e., mild, moderate, and severe) using a 12 × 2 × 3 factorial experiment designed in a randomized complete block design with three replications. Control studies were undertaken under glasshouse conditions. The content of cucurbitacins B, E, and I were quantified in leaves and roots using high-performance liquid Cchromatography-mass spectrometry (HPLC-MS). The free radical scavenging activities of pure cucurbitacins B, E, and I were quantified using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and a ferrulic acid power assay (FRAP). Results revealed that cucurbitacins B and I were present in accessions BG-48, BG-58, BG-70, BG-78, BG-79, BG-81, BG-52, and GC in leaves and roots under DS condition. The contents of cucurbitacins B and I were enhanced under increased drought intensity for accessions BG-48, BG-81, and GC. In all the leaf and root samples, cucurbitacin E was not detectable. Based on the DPPH test, pure cucurbitacins I, B, and E reduced free radicals at maximum values of 78, 60, and 66%, respectively. Based on the FRAP assay, pure cucurbitacins I, B, and E had maximum ferric-reducing powers of 67, 62, and 48%. Additionally, cucurbitacin I recorded the highest antioxidant activity compared to cucurbitacins B and E. Increased cucurbitacin accumulation and antioxidant properties indicate their role in minimising cell damage caused by oxidative stress under drought-stressed environments. The present study revealed that cucurbitacins B and I serve as novel biochemical markers for screening drought tolerance in bottle gourd or related cucurbits.

Comparative genomics analysis of WAK/WAKL family in Rosaceae identify candidate WAKs involved in the resistance to Botrytis cinerea

BACKGROUND

Wall associated kinase (WAK) and WAK-like (WAKL) are typical pattern recognition receptors act as the first sentry of plant defense. But little of WAK/WAKL family is known in Rosaceae.

RESULTS

In this study, 131 WAK/WAKL genes from apple, peach and strawberry were identified using a bioinformatics approach. Together with 68 RcWAK/RcWAKL in rose, we performed a comparative analysis of 199 WAK/WAKL in four Rosaceae crops. The phylogenetic analysis divided all the WAK/WAKL into five clades. Among them, the cis-elements of Clade II and Clade V promoters were enriched in jasmonic acid (JA) signaling and abiotic stress, respectively. And this can also be verified by the rose transcriptome responding to different hormone treatments. WAK/WAKL families have experienced a considerable proportion of purifying selection during evolution, but still 26 amino acid sites evolved under positive selection, which focused on extracellular conserved domains. WAK/WAKL genes presented collinearity relationship within and between crops, throughout four crops we mined four orthologous groups (OGs). The WAK/WAKL genes in OG1 and OG4 were speculated to involve in plant-Botrytis cinerea interaction, which were validated in rose via VIGS as well as strawberry by qRT-PCR.

CONCLUSIONS

These results not only provide genetic resources and valuable information for the evolutionary relationship of WAK/WAKL gene family, but also offer a reference for future in-depth studies of Rosaceae WAK/WAKL genes.

Gibberellin biosynthesis is required for CPPU-induced parthenocarpy in melon

Spraying N-(2-chloro-4-pyridyl)-N'-phenylurea (CPPU), an exogenous cytokinin (CK) growth regulator, is the conventional method for inducing fruit set during melon (Cucumis melo L.) production; however, the mechanism by which CPPU induces fruit set is unclear. Through histological and morphological observations, fruit size was comparable between CPPU-induced fruits and normal pollinated fruits because CPPU-induced fruits had higher cell density but smaller cell size compared with normal pollinated fruits. CPPU promotes the accumulation of gibberellin (GA) and auxin and decreases the level of abscisic acid (ABA) during fruit set. Moreover, application of the GA inhibitor paclobutrazol (PAC) partially inhibits CPPU-induced fruit set. Transcriptome analysis revealed that CPPU-induced fruit set specifically induced the GA-related pathway, in which the key synthase encoding gibberellin 20-oxidase 1 (CmGA20ox1) was specifically upregulated. Further study indicated that the two-component response regulator 2 (CmRR2) of the cytokinin signaling pathway, which is highly expressed at fruit setting, positively regulates the expression of CmGA20ox1. Collectively, our study determined that CPPU-induced melon fruit set is dependent on GA biosynthesis, providing a theoretical basis for the creation of parthenocarpic melon germplasm.

Watermelon domestication was shaped by stepwise selection and regulation of the metabolome

Although crop domestication has greatly aided human civilization, the sequential domestication and regulation of most quality traits remain poorly understood. Here, we report the stepwise selection and regulation of major fruit quality traits that occurred during watermelon evolution. The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation, whereas sugar and carotenoid contents were positively selected during domestication. Interestingly, fruit malic acid and citric acid showed the opposite selection trends during the improvement. We identified a novel gene cluster (CGC1, cucurbitacin gene cluster on chromosome 1) containing both regulatory and structural genes involved in cucurbitacin biosynthesis, which revealed a cascade of transcriptional regulation operating mechanisms. In the CGC1, an allele caused a single nucleotide change in ClERF1 binding sites (GCC-box) in the promoter of ClBh1, which resulted in reduced expression of ClBh1 and inhibition of cucurbitacin synthesis in cultivated watermelon. Functional analysis revealed that a rare insertion of 244 amino acids, which arose in C. amarus and became fixed in sweet watermelon, in ClOSC (oxidosqualene cyclase) was critical for the negative selection of cucurbitacins during watermelon evolution. This research provides an important resource for metabolomics-assisted breeding in watermelon and for exploring metabolic pathway regulation mechanisms.

Nanopore long-read RNAseq reveals transcriptional variations in citrus species

The number of studies on plant transcriptomes using ONT RNAseq technology is rapidly increasing in recent. It is a powerful method to decipher transcriptomic complexity, particularly alternative splicing (AS) event detection. Citrus plants are the most important widely grown fruit crops. Exploring different AS events in citrus contributes to transcriptome improvement and functional genome study. Here, we performed ONT RNAseq in 9 species (Atalantia buxifolia, Citrus clementina, C. grandis, C. ichangensis, C. reticulata, C. sinensis, Clausena lansium, Fortunella hindsii, and Poncirus trifoliata), accompanied with Illumina sequencing. Non-redundant full-length isoforms were identified between 41,957 and 76,974 per species. Systematic analysis including different types of isoforms, number of isoforms per gene locus, isoform distribution, ORFs and lncRNA prediction and functional annotation were performed mainly focused on novel isoforms, unraveling the capability of novel isoforms detection and characterization. For AS events prediction, A3, RI, and AF were overwhelming types across 9 species. We analyzed isoform similarity and evolutionary relationships in all species. We identified that multiple isoforms derived from orthologous single copy genes among different species were annotated as enzymes, nuclear-related proteins or receptors. Isoforms with extending sequences on 5', 3', or both compared with reference genome were filtered out to provide information for transcriptome improvement. Our results provide novel insight into comprehending complex transcriptomes in citrus and valuable information for further investigation on the function of genes with diverse isoforms.

Genome-Wide Identification of the SAUR Gene Family in Wax Gourd (Benincasa hispida) and Functional Characterization of BhSAUR60 during Fruit Development

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.

AtGCS promoter-driven clustered regularly interspaced short palindromic repeats/Cas9 highly efficiently generates homozygous/biallelic mutations in the transformed roots by Agrobacterium rhizogenes-mediated transformation

Agrobacterium rhizogenes-mediated (ARM) transformation is an efficient and powerful tool to generate transgenic roots to study root-related biology. For loss-of-function studies, transgenic-root-induced indel mutations by CRISPR/Cas9 only with homozygous/biallelic mutagenesis can exhibit mutant phenotype(s) (excluding recessive traits). However, a low frequency of homozygous mutants was produced by a constitutive promoter to drive Cas9 expression. Here, we identified a highly efficient Arabidopsis thaliana gamma-glutamylcysteine synthetase promoter, termed AtGCSpro, with strong activity in the region where the root meristem will initiate and in the whole roots in broad eudicots species. AtGCSpro achieved higher homozygous/biallelic mutation efficiency than the most widely used CaMV 35S promoter in driving Cas9 expression in soybean, Lotus japonicus, and tomato roots. Using the pAtGCSpro-Cas9 system, the average homozygous/biallelic mutation frequency is 1.7-fold and 8.3-fold higher than the p2 × 35Spro-Cas9 system for single and two target site(s) in the genome, respectively. Our results demonstrate the advantage of the pAtGCSpro-Cas9 system used in ARM transformation, especially its great potential in diploids with multiple-copy genes targeted mutations and polyploid plants with multiplex genome editing. AtGCSpro is conservatively active in various eudicots species, suggesting that AtGCSpro might be applied in a wide range of dicots species.

Comparison of rockwool and coir for greenhouse cucumber production: chemical element, plant growth, and fruit quality

Replacing rockwool with more sustainable materials, such as coir, is an effective measure to improve the sustainability of soilless cultivation in the greenhouse. To comprehensively assess the feasibility of coir before using it widely, coir was compared to rockwool as a cucumber cultivation substrate to evaluate its performance on mineral elements in the substrates, drainage, and in the plants. Plant growth, amino acids, and flavor substances of cucumber fruits were also compared between the two substrates. Compared to rockwool, coir significantly increased the LAI and yield of cucumber crops as well as contents of Ca, Mg, S, Cl and Zn in leaves and fruits. Contents of P, K, Ca, Mg, Cl, Zn, and B in the substrate were higher for coir while those of Fe, Cu, and Mn in the drainage lower. Moreover, coir also significantly increased contents of amino acids (His, Leu, Ile, Phe, Lys, Asp, Glu and Pro) and flavor substance (TC, PS, TP, CLL, CuB, and LA) in cucumber fruits. Our results demonstrated the potential of coir as a replacement of rockwool to improve sustainability of soilless cultivation in the greenhouse.

Comparative transcriptome analysis and identification of candidate genes involved in cucurbitacin IIa biosynthesis in Hemsleya macrosperma

Hemsleya macrosperma (H. macrosperma) is widely used in southwestern China as folk medicine with various bioactivities. Cucurbitacin IIa is the main active component in H. macrosperma and draws increased attention for its potential pharmacological activities. In order to reveal the mechanism of cucurbitacin IIa biosynthesis and regulation in H. macrosperma, transcriptome analysis was performed to compare differentially expressed genes in three tissues (root tuber, stem and leaf). A total of 47 946 unigenes were generated from these tissues and 55 unigenes were identified as candidate genes involved in triterpenoid backbone biosynthesis. Three homologous genes encoding squalene epoxidase (HmSE) were discovered and successfully expressed in a prokaryotic system. HmSE1 was found to be responsible for oxidization of squalene. In addition, several cytochrome P450s and transcription factors were predicted as candidates associated to cucurbitacin IIa biosynthesis. Notably, the expression profiles of those putative genes showed a positive correlation with elevated curcurbitacin IIa production in methyl jasmonate-elicited suspension cells of H. macrosperma., suggesting probable functions of the candidates on curcurbitacin IIa biosynthesis. These findings provide insights on cucurbitacin IIa biosynthesis and regulation in H. macrosperma.

Genome-wide characterization and expression analysis of bHLH gene family in physic nut (Jatropha curcas L.)

The basic helix loop helix (bHLH) transcription factor perform essential roles in plant development and abiotic stress. Here, a total of 122 bHLH family members were identified from the physic nut (Jatropha curcas L.) genomic database. Chromosomal localization results showed that 120 members were located on 11 chromosomes. The phylogenetic tree manifested that the JcbHLHs could be grouped into 28 subfamilies. Syntenic analysis showed that there were 10 bHLH collinear genes among the physic nut, Arabidopsis thaliana and Oryza sativa. These genes, except JcbHLH84, were highly expressed in various tissues of the physic nut, implying a key role in plant development. Gene expression profiles showed that ten genes (especially JcbHLH33, JcbHLH45 and JcbHLH55) correspond to both salinity and drought stresses; while eight genes only respond to salinity and another eight genes only respond to drought stress. Moreover, the protein interaction network revealed that the JcbHLHs are involved in growth, development and stress signal transduction pathways. These discoveries will help to excavate several key genes may involve in salt or drought stresses and seed development, elucidate the complex transcriptional regulation mechanism of JcbHLH genes and provide the theoretical basis for stress response and genetic improvement of physic nut.

Metabolome and Transcriptome Analyses of Cucurbitacin Biosynthesis in Luffa (Luffa acutangula)

Cucurbitacins are extremely bitter compounds mainly present in Cucurbitaceae, where Luffa belongs. However, there is no comprehensive analysis of cucurbitacin biosynthesis in Luffa fruit. Therefore, this study analyzed bitter (WM709) and non-bitter (S1174) genotypes of Luffa to reveal the underlying mechanism of cucurbitacin biosynthesis by integrating metabolome and transcriptome analyses. A total of 422 metabolites were detected, including vitamins, essential amino acids, antioxidants, and antitumor substances. Of these, 131 metabolites showed significant differences between bitter (WM709) and non-bitter (S1174) Luffa fruits. The levels of isocucurbitacin B, cucurbitacin D, 23,24-dihydro cucurbitacin E, cucurbitacin F were significantly higher in bitter than in non-bitter Luffa. Transcriptome analysis showed that Bi, cytochromes P450s (CYP450s), and acyltransferase (ACT) of the cucurbitacin biosynthesis pathway, were significantly up-regulated. Moreover, drought stress and abscisic acid (ABA) activated genes of the cucurbitacin biosynthesis pathway. Furthermore, dual-luciferase reporter and yeast one-hybrid assays demonstrated that ABA-response element binding factor 1 (AREB1) binds to the Bi promoter to activate Bi expression. Comparative analysis of the Luffa and cucumber genomes showed that Bi, CYP450s, and ACT are located in the conserved syntenic loci, and formed a cucurbitacin biosynthesis cluster. This study provides important insights into major genes and metabolites of the cucurbitacin biosynthetic pathway, deepening the understanding of regulatory mechanisms of cucurbitacin biosynthesis in Luffa.