A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics

A high-quality chromosome-scale genome assembly of the Cherokee rose (Rosa laevigata)

Rosa laevigata is an excellent rose germplasm, highly resistant to aphid, and immune to both rose black spot and powdery mildew disease. It is also a well-known edible plant with a long history of medicinal use in China, having the effects of improving kidney function, inhibiting arteriosclerosis, and reducing inflammation. In this study, we assembled a high-quality chromosome-scale genome for R. laevigata by combining Illumina, PacBio, and Hi-C data, which has a length of approximately 494.2 Mb with a scaffold N50 of 68.6 Mb. A total of 493.2 Mb (99.8%) of the draft genome sequences were anchored on seven pseudochromosomes and two gapless pseudochromosomes were included in the final genome assembly. A total of 37,117 protein-coding genes were predicted, 34,047 of which were functionally annotated. Repeat annotation revealed 659,558 (285.6 Mb) repeat elements, accounting for 57.8% of the genome. The chromosome-scale genome provides valuable information to facilitate comparative genomic analysis of rose family and will accelerate genome-guided breeding and germplasm improvement of both R. laevigata itself and modern roses.

The Identification of Auxin Response Factors and Expression Analyses of Different Floral Development Stages in Roses

Background/Objectives:Auxin response factors (ARFs) are important in plant growth and development, especially flower development. However, there is limited research on the comprehensive identification and characterization of ARF genes in roses. Methods: We employed bioinformatics tools to identify the ARF genes of roses. These genes were characterized for their phylogenetic relationships, chromosomal positions, conserved motifs, gene structures, and expression patterns. Results: In this study, a total of 17 ARF genes were identified in the genomes of Rosa chinensis 'OB', R. chinensis 'CH', R. rugosa, and R. wichurana. Based on RNA-seq analyses, we found that the ARF genes had diverse transcript patterns in various tissues and cultivars. In 'CH', the expression levels of RcCH_ARFs during different flower-development stages were classified into four clusters. In cluster 3 and cluster 4, RcCH_ARFs were specifically high and low in different stages of floral evocation. Gene expression and phylogenetic analyses showed that RcCH_ARF3, RcCH_ARF4, and RcCH_ARF18 were likely to be the key genes for rose flower development. Conclusions: The identification and characterization of ARF genes in Rosa were investigated. The results presented here provide a theoretical basis for the molecular mechanisms of ARF genes in plant development and flowering for roses, with a broader application for other species in the rose family and for the development of novel cultivars.

Comparative Analysis of Ca2+/Cation Antiporter Gene Family in Rosa roxburghii and Enhanced Calcium Stress Tolerance via Heterologous Expression of RrCAX1a in Tobacco

Rosa roxburghii, a calciphilic species native to the mountainous regions of Southwest China, is renowned for its high vitamin C and bioactive components, making it valuable for culinary and medicinal uses. This species exhibits remarkable tolerance to the high-calcium conditions typical of karst terrains. However, the underlying mechanisms of this calcium resilience remain unclear. The Ca2+/cation antiporter (CaCA) superfamily plays a vital role in the transport of Ca2+ and other cations and is crucial for plant tolerance to metal stress. However, the roles and evolutionary significance of the CaCA superfamily members in R. roxburghii remain poorly understood. This study identified 22 CaCA superfamily genes in R. roxburghii, categorized into four subfamilies. The gene structures of these RrCaCAs show considerable conservation across related species. Selection pressure analysis revealed that all RrCaCAs are subject to purifying selection. The promoter regions of these genes contain numerous hormone-responsive and stress-related elements. qRT-PCR analyses demonstrated that H+/cation exchanger (CAX) RrCAX1a and RrCAX3a were highly responsive to Ca2+ stress, cation/Ca2+ exchanger (CCX) RrCCX4 to Mg2+ stress, and RrCCX11a to Na+ stress. Subcellular localization indicated that RrCAX1a is localized to the plant cell membrane, and its stable transformation in tobacco confirmed its ability to confer enhanced resistance to heavy Ca2+ stresses, highlighting its crucial role in the high-calcium tolerance mechanisms of R. roxburghii. This research establishes a foundation for further molecular-level functional analyses of the adaptation mechanisms of R. roxburghii to high-calcium environments.

C2H2 Zinc Finger Protein Family Analysis of Rosa rugosa Identified a Salt-Tolerance Regulator, RrC2H2-8

Rosa rugosa is a representative aromatic species. Wild roses are known for their strong tolerance to highly salty environments, whereas cultivated varieties of roses exhibit lower salt stress tolerance, limiting their development and industrial expansion. Previous studies have shown that C2H2-type zinc finger proteins play a crucial role in plants' resistance to abiotic stresses. In this study, 102 C2H2-type zinc finger genes (RrC2H2s) were identified in R. rugosa via a comprehensive approach. These genes were categorized into three lineages, and their motif constitutions were grouped into four classes. RrC2H2s were distributed across all seven rose chromosomes, with 15 paralogous gene pairs identified within synteny regions. Additionally, 43 RrC2H2s showed differential expression across various tissues under salt stress, with RrC2H2-8 being the only gene consistently repressed in all tissues. Subcellular localization analysis revealed that the RrC2H2-8 protein was localized in the nucleus. The heterologous expression of RrC2H2-8 in Arabidopsis significantly improved its growth under salt stress compared to the wild-type (WT) plants. Furthermore, the malondialdehyde content in the roots of transgenic Arabidopsis was significantly lower than that in the WT, suggesting that RrC2H2-8 enhanced salt tolerance by reducing cellular damage. This study provides a systematic understanding of the RrC2H2 family and identifies RrC2H2-8 as a regulator of salt tolerance, laying a foundation for future research on the mechanisms of salt stress regulation by RrC2H2.

Rosa rugosa R2R3-MYB transcription factors RrMYB12 and RrMYB111 regulate the accumulation of flavonols and anthocyanins

Roses (Rosa rugosa) are a famous flower with high ornamental and economic value. But the petals of roses are usually pink and purple, which restricted its application in garden settings. Flavonols and anthocyanins are crucial secondary metabolites related to flower pigmentation in plants. While MYB transcription factors involved in the biosynthesis pathway of anthocyanins have been identified in roses, the functional characterization of the MYB transcription factor regulating flavonol synthesis in R. rugosa remains unexplored. In this study, we isolated and characterized the R2R3-MYB transcription factors RrMYB12 and RrMYB111 involved in regulation of the flavonol biosynthetic pathway from R. rugosa. The bioinformatics analysis indicated that both the RrMYB12 and RrMYB111 belong to the R2R3-MYB subgroup 7 family. qRT-PCR analysis showed that RrMYB12 and RrMYB111 were expressed at low levels in roots and flowers. And transactivation activity assay indicated that RrMYB12 and RrMYB111 were transcriptional activators. The overexpression of RrMYB12 and RrMYB111 in tobacco resulted in an elevation of flavonol levels and a reduction in anthocyanin levels in flowers due to the upregulation of structural genes involved in flavonol synthesis, while the biosynthesis genes for the anthocyanin pathway were significantly downregulated. The transient reporter assay demonstrated that RrMYB12 exhibited strong activation of the promoters of RrCHS and RrFLS in Nicotiana benthamiana leaves following transient transformation. Furthermore, it was observed that RrMYBs displayed binding specificity to the promoter region of CsFLS.The functional characterization of the flavonol synthesis regulatory factors RrMYB12 and RrMYB111 offers a deeper understanding of the regulatory mechanism governing flavonol biosynthesis in roses, while also presenting an effective tool for genetic manipulation aimed at creating new varieties.

High-quality haplotype-resolved chromosome assembly provides evolutionary insights and targeted steviol glycosides (SGs) biosynthesis in Stevia rebaudiana Bertoni

Stevia rebaudiana Bertoni is popular source of plant-derived low/no-calorie natural sweeteners (LNCSs), collectively known as steviol glycosides (SGs). Nevertheless, genetic predisposition for targeted biosynthesis of SGs is complex due to multi-substrate functionality of key uridine diphosphate glycosyltransferases (UGTs). Here, we created a high-quality monoploid assembly of 1.34 Gb with N50 value of 110 Mb, 55 551 predicted protein-coding genes, and ~80% repetitive regions in Rebaudioside-A (Reb-A) enriched cultivar of S. rebaudiana. Additionally, a haplotype-based chromosome assembly consisting of haplotype A and haplotype B with an overall genome size of 2.33Gb was resolved, harbouring 639 634 variants including single nucleotide polymorphisms (SNPs), indels and structural variants (SVs). Furthermore, a lineage-specific whole genome duplication analysis revealed that gene families encoding UGTs and Cytochrome-P450 (CYPs) were tandemly duplicated. Additionally, expression analysis revealed five tandemly duplicated gene copies of UGT76G1 having significant correlations with Reb-A content, and identified key residue (leu200val) in the glycosylation of Reb-A. Furthermore, missense variations identified in the acceptor region of UGT76G1 in haplotype resolve genome, transcriptional and molecular docking analysis were confirmed with resequencing of 10 diverse stevia genotypes (~25X). Gene regulatory network analysis identified key transcription factors (MYB, bHLH, bZIP and AP2-ERF) as potential regulators of SG biosynthesis. Overall, this study provides haplotype-resolved chromosome-level genome assembly for genome editing and enhancing breeding efforts for targeted biosynthesis of SGs in S. rebaudiana.

Development of a robust SNP marker set for genotyping diverse gene bank collections of polyploid roses

BACKGROUND

Due to genetic depletion in nature, gene banks play a critical role in the long-term conservation of plant genetic resources and the provision of a wide range of plant genetic diversity for research and breeding programs. Genetic information on accessions facilitates gene bank management and can help to conserve limited resources and to identify taxonomic misclassifications or mislabelling. Here, we developed SNP markers for genotyping 4,187 mostly polyploid rose accessions from large rose collections, including the German Genebank for Roses.

RESULTS

We filtered SNP marker information from the RhWag68k Axiom SNP array using call rates, uniformity of the four allelic dosage groups and chromosomal position to improve genotyping efficiency. After conversion to individual PACE® markers and further filtering, we selected markers with high discriminatory power. These markers were used to analyse 4,187 accessions with a mean call rate of 91.4%. By combining two evaluation methods, the mean call rate was increased to 95.2%. Additionally, the robustness against the genotypic groups used for calling was evaluated, resulting in a final set of 18 markers. Analyses of 94 pairs of assumed duplicate accessions included as controls revealed unexpected differences for eight pairs, which were confirmed using SSR markers. After removing the duplicates and filtering for accessions that were robustly called with all 18 markers, 141 out of the 1,957 accessions showed unexpected identical marker profiles with at least one other accession in our PACE® and SSR analysis. Given the attractiveness of NGS technologies, 13 SNPs from the marker set were also analysed using amplicon sequencing, with 76% agreement observed between PACE® and amplicon markers.

CONCLUSIONS

Although sampling error cannot be completely excluded, this is an indication that mislabelling occurs in rose collections and that molecular markers may be able to detect these cases. In future applications, our marker set could be used to develop a core reference set of representative accessions, and thus optimise the selection of gene bank accessions.

The MYC Gene RrbHLH105 Contributes to Salt Stress-Induced Geraniol in Rose by Regulating Trehalose-6-Phosphate Signalling

Rose (Rosa rugosa) is an important perfume plant, but its cultivation is significantly constrained by salt stress. Terpenes represent the most abundant volatile aromatic compounds in roses, yet little is known about how terpene metabolism responds to salt stress. In this study, salt-treated rose petals presented significant accumulation of monoterpenes, including geraniol, due to the disruption of jasmonic acid (JA) biosynthesis and signalling. Overexpression and silencing analyses revealed a MYC transcription factor involved in JA signalling (RrbHLH105) as a repressor of geraniol biosynthesis. RrbHLH105 was shown to activate the trehalose-6-phosphate synthase genes RrTPS5 and RrTPS8 by binding to the E-box (5'-CANNTG-3'). The increased trehalose-6-phosphate content and decreased geraniol content in rose petals overexpressing TPS5 or RrTPS8, along with the high accumulation of geraniol in petals where both RrbHLH105 and TPSs were cosilenced, indicate that trehalose signalling plays a role in the negative regulation of geraniol accumulation via the RrbHLH105-TPS module. In summary, the suppression of RrbHLH105 by salt stress leads to excessive geraniol accumulation through the inhibition of both RrbHLH105-mediated JA signalling and RrTPS-mediated trehalose signalling in rose petals. Additionally, this study highlights the emerging role of RrbHLH105 as a critical integrator of JA and trehalose signalling crosstalk.

Saline-alkali stress affects the accumulation of proanthocyanidins and sesquiterpenoids via the MYB5-ANR/TPS31 cascades in the rose petals

Rose (Rosa rugosa) petals are rich in diverse secondary metabolites, which have important physiological functions as well as great economic values. Currently, it remains unclear how saline and/or alkaline stress(es) influence the accumulation of secondary metabolites in rose. In this study, we analyzed the transcriptome and metabolite profiles of rose petals under aline-alkali stress and uncovered the induction mechanism underlying major metabolites. Dramatic changes were observed in the expression of 1363 genes and the abundances of 196 metabolites in petals in response to saline-alkali stress. These differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) are mainly associated with flavonoid and terpenoid metabolism and the reconstruction of cell walls. Of them, TERPENE SYNTHASE 31 (TPS31) overexpression in tobacco leaves driven by its own promoter resulted in significant alterations in the levels of diverse terpenoids, which were differentially influenced by saline-alkali stress. An integrated analysis of metabolomic and transcriptomic data revealed a high correlation between the abundances of flavonoids/terpenoids and the expression of the transcription factor MYB5. MYB5 may orchestrate the biosynthesis of sesquiterpenoids and proanthocyanidins through direct regulation of TPS31 and ANR expression under aline-alkali stress. Our finding facilitates improving the bioactive substance accumulation of rose petals by metabolic engineering.

Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose

Modern rose (Rosa hybrida) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid R. hybrida 'Samantha' ('JACmantha') and a genome variation map of 233 Rosa accessions involving various wild species, and old and modern cultivars. Homologous chromosomes of 'Samantha' exhibit frequent homoeologous exchanges. Population genomic and genomic composition analyses reveal the contributions of wild Rosa species to modern roses and highlight that R. odorata and its derived cultivars are important contributors to modern roses, much like R. chinensis 'Old Blush'. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous and recurrent flowering, double flower, flower senescence and disease resistance, are identified. This study provides insights into the genetic basis of modern rose origin and breeding history, and offers unprecedented genomic resources for rose improvement.

Chromosome-scale genome assembly of Docynia delavayi provides new insights into the α-farnesene biosynthesis

Docynia delavayi is an economically significant fruit species with a high market potential due to the special aroma of its fruit. Here, a 653.34 Mb high-quality genome of D. delavayi was first reported, of which 93.8 % of the sequences (612.98 Mb) could be anchored to 17 chromosomes, containing 48,325 protein-coding genes. Ks analysis proved that two whole genome duplication (WGD) events occurred in D. delavayi, resulting in the expansion of genes associated with terpene biosynthesis, which promoted its fruit-specific aroma production. Combined multi-omics analysis, α-farnesene was detected as the most abundant aroma substance emitted by D. delavayi fruit during storage, meanwhile one α-farnesene synthase gene (AFS) and 15 transcription factors (TFs) were identified as the candidate genes potentially involved in α-farnesene biosynthesis. Further studies for the regulation network of α-farnesene biosynthesis revealed that DdebHLH, DdeERF1 and DdeMYB could activate the transcription of DdeAFS. To our knowledge, it is the first report that MYB TF plays a regulatory role in α-farnesene biosynthesis, which will greatly facilitate future breeding programs for D. delavayi.

Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms

Rose is an important ornamental crop cultivated globally for perfume production. However, our understanding of the mechanisms underlying scent production and molecular breeding for fragrance is hindered by the lack of a reference genome for tea roses. We present the first complete telomere-to-telomere (T2T) genome of Rosa gigantea, with high quality (QV > 60), including detailed characterization of the structural features of repetitive regions. The expansion of genes associated with phenylpropanoid biosynthesis may account for the unique tea scent. We uncover the release rhythm of aromatic volatile organic compounds and their gene regulatory networks through comparative genomics and time-ordered gene co-expression networks. Analyzes of eugenol homologs demonstrate how plants attract pollinators using specialized phenylpropanoids in specific tissues. This study highlights the conservation and utilization of genetic diversity from wild endangered species through multi-omics approaches, providing a scientific foundation for enhancing rose fragrance via de novo domestication.

Genome-wide identification of starch phosphorylase gene family in Rosa chinensis and expression in response to abiotic stress

Chinese rose (Rosa chinensis) is an important ornamental plant, with economic, cultural, and symbolic significance. During the application of outdoor greening, adverse environments such as high temperature and drought are often encountered, which affect its application scope and ornamental quality. The starch phosphorylase (Pho) gene family participate in the synthesis and decomposition of starch, not only related to plant energy metabolism, but also plays an important role in plant stress resistance. The role of Pho in combating salinity and high temperature stress in R. chinensis remains unknown. In this work, 4 Phos from R. chinensis were detected with Pfam number of Pho (PF00343.23) and predicted by homolog-based prediction (HBP). The Phos are characterized by sequence lengths of 821 to 997 bp, and the proteins are predicted to subcellularly located in the plastid and cytoplasm. The regulatory regions of the Phos contain abundant stress and phytohormone-responsive cis-acting elements. Based on transcriptome analysis, the Phos were found to respond to abiotic stress factors such as drought, salinity, high temperature, and plant phytohormone of jasmonic acid and salicylic acid. The response of Phos to abiotic stress factors such as salinity and high temperature was confirmed by qRT-PCR analysis. To evaluate the genetic characteristics of Phos, a total of 69 Phos from 17 species were analyzed and then classified into 3 groups in phylogenetic tree. The collinearity analysis of Phos in R. chinensis and other species was conducted for the first time. This work provides a view of evolution for the Pho gene family and indicates that Phos play an important role in abiotic stress response of R. chinensis.

A chromosome-level genome assembly of Chinese quince (Pseudocydonia sinensis)

Introduction

Pseudocydonia sinensis, also known as Chinese quince, is a perennial shrub or small tree highly valued for its edibility and medicinal properties.

Method

This study presents the first chromosome-level genome assembly of P. sinensis, achieved using HiFi sequencing and Hi-C scaffolding technology.

Results

The assembly resulted in a high-quality genome of 576.39 Mb in size. The genome was anchored to 17 pseudo-chromosomes, with a contig N50 of 27.6 Mb and a scaffold N50 of 33.8 Mb. Comprehensive assessment using BUSCO, CEGMA and BWA tools indicates the high completeness and accuracy of the genome assembly. Our analysis identified 116 species-specific genes, 1196 expanded genes and 1109 contracted genes. Additionally, the distribution of 4DTv values suggests that the most recent duplication event occurred before the divergence of P. sinensis from both Chaenomeles pinnatifida and Pyrus pyrifolia.

Discussion

The assembly of this high-quality genome provides a valuable platform for the genetic breeding and cultivation of P. sinensis, as well as for the comparison of the genetic complexity of P. sinensis with other important crops in the Rosaceae family.

The chromosome-level genome and functional database accelerate research about biosynthesis of secondary metabolites in Rosa roxburghii

Rosa roxburghii Tratt, a valuable plant in China with long history, is famous for its fruit. It possesses various secondary metabolites, such as L-ascorbic acid (vitamin C), alkaloids and poly saccharides, which make it a high nutritional and medicinal value. Here we characterized the chromosome-level genome sequence of R. roxburghii, comprising seven pseudo-chromosomes with a total size of 531 Mb and a heterozygosity of 0.25%. We also annotated 45,226 coding gene loci after masking repeat elements. Orthologs for 90.1% of the Complete Single-Copy BUSCOs were found in the R. roxburghii annotation. By aligning with protein sequences from public platform, we annotated 85.89% genes from R. roxburghii. Comparative genomic analysis revealed that R. roxburghii diverged from Rosa chinensis approximately 5.58 to 13.17 million years ago, and no whole-genome duplication event occurred after the divergence from eudicots. To fully utilize this genomic resource, we constructed a genomic database RroFGD with various analysis tools. Otherwise, 69 enzyme genes involved in L-ascorbate biosynthesis were identified and a key enzyme in the biosynthesis of vitamin C, GDH (L-Gal-1-dehydrogenase), is used as an example to introduce the functions of the database. This genome and database will facilitate the future investigations into gene function and molecular breeding in R. roxburghii.

The high-quality genome of Cryptotaenia japonica and comparative genomics analysis reveals anthocyanin biosynthesis in Apiaceae

Cryptotaenia japonica, a traditional medicinal and edible vegetable crops, is well-known for its attractive flavors and health care functions. As a member of the Apiaceae family, the evolutionary trajectory and biological properties of C. japonica are not clearly understood. Here, we first reported a high-quality genome of C. japonica with a total length of 427 Mb and N50 length 50.76 Mb, was anchored into 10 chromosomes, which confirmed by chromosome (cytogenetic) analysis. Comparative genomic analysis revealed C. japonica exhibited low genetic redundancy, contained a higher percentage of single-cope gene families. The homoeologous blocks, Ks, and collinearity were analyzed among Apiaceae species contributed to the evidence that C. japonica lacked recent species-specific WGD. Through comparative genomic and transcriptomic analyses of Apiaceae species, we revealed the genetic basis of the production of anthocyanins. Several structural genes encoding enzymes and transcription factor genes of the anthocyanin biosynthesis pathway in different species were also identified. The CjANSa, CjDFRb, and CjF3H gene might be the target of Cjaponica_2.2062 (bHLH) and Cjaponica_1.3743 (MYB). Our findings provided a high-quality reference genome of C. japonica and offered new insights into Apiaceae evolution and biology.

Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits

Roses are consistently ranked at the forefront in cut flower production. Increasing demands of market and changing climate conditions have resulted in the need to further improve the diversity and quality of traits. However, frequent hybridization leads to highly heterozygous nature, including the allelic variants. Therefore, the absence of comprehensive genomic information leads to them making it challenging to molecular breeding. Here, two haplotype-resolved chromosome genomes for Rosa chinensis 'Chilong Hanzhu' (2n = 14) which is high heterozygous diploid old Chinese rose are generated. An amount of genetic variation (1,605,616 SNPs, 209,575 indels) is identified. 13,971 allelic genes show differential expression patterns between two haplotypes. Importantly, these differences hold valuable insights into regulatory mechanisms of traits. RcMYB114b can influence cyanidin-3-glucoside accumulation and the allelic variation in its promoter leads to differences in promoter activity, which as a factor control petal color. Moreover, gene family expansion may contribute to the abundance of terpenes in floral scents. Additionally, RcANT1, RcDA1, RcAG1 and RcSVP1 genes are involved in regulation of petal number and size under heat stress treatment. This study provides a foundation for molecular breeding to improve important characteristics of roses.

Genome-Wide Analysis of the WRKY Transcription Factor Family in Roses and Their Putative Role in Defence Signalling in the Rose-Blackspot Interaction

WRKY transcription factors are important players in plant regulatory networks, where they control and integrate various physiological processes and responses to biotic and abiotic stresses. Here, we analysed six rose genomes of 5 different species (Rosa chinensis, R. multiflora, R. roxburghii, R. sterilis, and R. rugosa) and extracted a set of 68 putative WRKY genes, extending a previously published set of 58 WRKY sequences based on the R. chinensis genome. Analysis of the promoter regions revealed numerous motifs related to induction by abiotic and, in some cases, biotic stressors. Transcriptomic data from leaves of two rose genotypes inoculated with the hemibiotrophic rose black spot fungus Diplocarpon rosae revealed the upregulation of 18 and downregulation of 9 of these WRKY genes after contact with the fungus. Notably, the resistant genotype exhibited the regulation of 25 of these genes (16 upregulated and 9 downregulated), while the susceptible genotype exhibited the regulation of 20 genes (15 upregulated and 5 downregulated). A detailed RT-qPCR analysis of RcWRKY37, an orthologue of AtWRKY75 and FaWRKY1, revealed induction patterns similar to those of the pathogenesis-related (PR) genes induced in salicylic acid (SA)-dependent defence pathways in black spot inoculation experiments. However, the overexpression of RcWRKY37 in rose petals did not induce the expression of any of the PR genes upon contact with black spot. However, wounding significantly induced the expression of RcWRKY37, while heat, cold, or drought did not have a significant effect. This study provides the first evidence for the role of RcWRKY37 in rose signalling cascades and highlights the differences between RcWRKY37 and AtWRKY75. These results improve our understanding of the regulatory function of WRKY transcription factors in plant responses to stress factors. Additionally, they provide foundational data for further studies.

The scent of roses, a bouquet of fragrance diversity

Roses have been domesticated since antiquity for their therapeutic, cosmetic, and ornamental properties. Their floral fragrance has great economic value, which has influenced the production of rose varieties. The production of rose water and essential oil is one of the most lucrative activities, supplying bioactive molecules to the cosmetic, pharmaceutical, and therapeutic industries. In recent years, major advances in molecular genetics, genomic, and biochemical tools have paved the way for the identification of molecules that make up the specific fragrance of various rose cultivars. The aim of this review is to highlight current knowledge on metabolite profiles, and more specifically on fragrance compounds, as well as the specificities and differences between rose species and cultivars belonging to different rose sections and how they contribute to modern roses fragrance.

Chromosomal-scale genomes of two Rosa species provide insights into genome evolution and ascorbate accumulation

Rosa roxburghii and Rosa sterilis, two species belonging to the Rosaceae family, are widespread in the southwest of China. These species have gained recognition for their remarkable abundance of ascorbate in their fresh fruits, making them an ideal vitamin C resource. In this study, we generated two high-quality chromosome-scale genome assemblies for R. roxburghii and R. sterilis, with genome sizes of 504 and 981.2 Mb, respectively. Notably, we present a haplotype-resolved, chromosome-scale assembly for diploid R. sterilis. Our results indicated that R. sterilis originated from the hybridization of R. roxburghii and R. longicuspis. Genome analysis revealed the absence of recent whole-genome duplications in both species and identified a series of duplicated genes that possibly contributing to the accumulation of flavonoids. We identified two genes in the ascorbate synthesis pathway, GGP and GalLDH, that show signs of positive selection, along with high expression levels of GDP-d-mannose 3', 5'-epimerase (GME) and GDP-l-galactose phosphorylase (GGP) during fruit development. Furthermore, through co-expression network analysis, we identified key hub genes (MYB5 and bZIP) that likely regulate genes in the ascorbate synthesis pathway, promoting ascorbate biosynthesis. Additionally, we observed the expansion of terpene synthase genes in these two species and tissue expression patterns, suggesting their involvement in terpenoid biosynthesis. Our research provides valuable insights into genome evolution and the molecular basis of the high concentration of ascorbate in these two Rosa species.

Characterization and mechanism of seed dormancy in Symplocos paniculata

Symplocos paniculata is a highly desirable oil species for biodiesel and premium edible oil feedstock. While germplasm preservation and breeding are crucial, the severity of seed dormancy poses a challenge to successful germination. We employed S. paniculata seeds as experimental materials and conducted an investigation into the types and causes of seed dormancy by analyzing the morphology and developmental characteristics of its embryo, exploring the water permeability property of the endocarp, and examining the presence of endogenous inhibitors, aiming to establish a theoretical foundation for overcoming seed dormancy and maximizing germplasm resource utilization. The findings revealed that the seed embryo had matured into a fully developed embryo, and no dormancy in terms of embryo morphology was observed. Upon reaching maturity, the endocarp of seeds undergoes significant lignification, resulting in notable differences in water absorption between cracked and intact seeds. The impermeability of the endocarp is one of the factors contributing to mechanical restriction. The different phases of endosperm extraction exerted varying effects on the germination of Chinese cabbage seeds, with the methanol phase exhibiting the most potent inhibitory effect. The presence of endogenous inhibitors emerged as the primary factor contributing to physiological dormancy in seeds. GC-MS analysis and validation trials revealed that fatty acids and phenolics, including hexadecanoic acid, oxadecanoic acid, and m-cresol, constituted the main types of endogenous inhibitory compounds found within the endosperm. These findings suggest that the seed dormancy in S. paniculata seeds has endocarp mechanical restriction, and the presence of endogenous inhibitors causes physiological dormancy.

GWAS of adventitious root formation in roses identifies a putative phosphoinositide phosphatase (SAC9) for marker-assisted selection

Rose propagation by cuttings is limited by substantial genotypic differences in adventitious root formation. To identify possible genetic factors causing these differences and to develop a marker for marker-assisted selection for high rooting ability, we phenotyped 95 cut and 95 garden rose genotypes in a hydroponic rooting system over 6 weeks. Data on rooting percentage after 3 to 6 weeks, root number, and root fresh mass were highly variable among genotypes and used in association mappings performed on genotypic information from the WagRhSNP 68 K Axiom SNP array for roses. GWAS analyses revealed only one significantly associated SNP for rooting percentage after 3 weeks. Nevertheless, prominent genomic regions/peaks were observed and further analysed for rooting percentage after 6 weeks, root number and root fresh mass. Some of the SNPs in these peak regions were associated with large effects on adventitious root formation traits. Very prominent were ten SNPs, which were all located in a putative phosphoinositide phosphatase SAC9 on chromosome 2 and showed very high effects on rooting percentage after 6 weeks of more than 40% difference between nulliplex and quadruplex genotypes. SAC9 was reported to be involved in the regulation of endocytosis and in combination with other members of the SAC gene family to regulate the translocation of auxin-efflux PIN proteins via the dephosphorylation of phosphoinositides. For one SNP within SAC9, a KASP marker was successfully derived and used to select genotypes with a homozygous allele configuration. Phenotyping these homozygous genotypes for adventitious root formation verified the SNP allele dosage effect on rooting. Hence, the presented KASP derived from a SNP located in SAC9 can be used for marker-assisted selection in breeding programs for high rooting ability in the future.

RoseAP: an analytical platform for gene function of Rosa rugosa

Rosa rugosa, a perennial shrub belonging to family Rosaceae, is a well-known ornamental plant. Its petals contain an abundance of essential oils and anthocyanins with enormous economic and health benefits when used as edible or cosmetic ingredients. The whole genome of R. rugosa was sequenced in 2021, which provided opportunities and challenges for gene regulation. However, many gene functions remain unknown. Therefore, an analytical platform named RoseAP (http://www.gzybioinformatics.cn/RoseAP/index.php) for the functional analysis of R. rugosa genes was constructed. It improved the gene annotation rate by integrating and analyzing genomic and transcriptomic datasets. First, 38,815 genes, covering 97.76% of the coding genes, were annotated functionally and structurally using a variety of algorithms and rules. Second, a total of 33 transcriptome samples were integrated, including 23 samples from our lab and 10 samples from the SRA database. A co-expression network containing approximately 29,657 positive or negative gene pairs, covering 74.7% of the coding genes, was constructed based on PCC and MR algorithms. Network analysis revealed that the DFR function was closely related to anthocyanin metabolism. It demonstrated the reliability of the network. Several SAUR genes of R. rugosa shared similar expression patterns. RoseAP was used to determine the sequence, structure, functional annotation, expression profile, regulatory network, and functional modules at the transcriptional and protein levels by inputting gene IDs. In addition, auxiliary analytical tools, including BLAST, gene set enrichment, orthologue conversion, gene sequence extraction, gene expression value extraction, and JBrowse, were utilized. Regular updates to RoseAP are expected to facilitate mining of gene function and promote genetic improvement in R. rugosa.

Characterization of volatiles in flowers from four Rosa chinensis cultivars by HS-SPME-GC × GC-QTOFMS

Rosa chinensis cultivars with volatile aromas are important resources in the perfume industry. The four rose cultivars introduced to Guizhou province are rich in volatile substances. In this study, volatiles from four Rosa chinensis cultivars were extracted using headspace-solid phase microextraction (HS-SPME), and analyzed with two-dimensional gas chromatography quadrupole time of flight mass spectrometry (GC × GC-QTOFMS). A total of 122 volatiles were identified; the main compounds in these samples were benzyl alcohol, phenylethyl alcohol, citronellol, beta-myrcene and limonene. A total of 68, 78, 71, and 56 volatile compounds were identified in Rosa 'Blue River' (RBR), Rosa 'Crimson Glory' (RCG), Rosa 'Pink Panther' (RPP), and Rosa 'Funkuhr' (RF) samples, respectively. The total volatile contents were in the following order: RBR > RCG > RPP > RF. Four cultivars exhibited similar volatility profiles, with alcohols, alkanes, and esters as the major chemical groups, followed by aldehydes, aromatic hydrocarbons, ketones, benzene, and other compounds. Alcohols and aldehydes were quantitatively the two most abundant chemical groups that included the highest number and highest content of compounds. Different cultivars have different aromas, and RCG had high contents of phenyl acetate, rose oxide, trans-rose oxide, phenylethyl alcohol and 1,3,5-trimethoxybenzene, characterized by floral and rose descriptors. RBR contained a high content of phenylethyl alcohol, and RF contained a high content of 3,5-dimethoxytoluene. Hierarchical cluster analysis (HCA) of all volatiles showed that the three cultivars (RCG, RPP, and RF) had similar volatile characteristics and were significantly different from RBR. Differential metabolites among cultivars were screened based on the OPLS-DA model, and there were six main enriched pathways of differential metabolites: biosynthesis of secondary metabolites, monoterpenoid biosynthesis, metabolic pathways, limonene and pinene degradation, sesquiterpenoid and triterpenoid biosynthesis, and alpha-linolenic acid metabolism. The biosynthesis of secondary metabolites is the most differential metabolic pathway.

Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways

BACKGROUND

Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions.

RESULTS

A total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth.

CONCLUSIONS

The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.

E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus

BACKGROUND

Eucalyptus urophylla × Eucalyptus grandis, an economically important forest tree, provides important raw material for energy and reduces damage to native forests. However, the absence of a high-quality E. urophylla × E. grandis reference genome has significantly hindered its evolution and genetic analysis.

RESULTS

We successfully presented a high-quality reference genome of E. urophylla × E. grandis (545.75 Mb; scaffold N50, 51.62 Mb) using a combination of the Illumina, PacBio HiFi, and Hi-C sequencing platforms. A total of 34,502 genes and 58.56% of the repetitive sequences in this genome were annotated. Using genome evolution analyses, we identified a recent whole-genome duplication (WGD) event in E. urophylla × E. grandis. We further found that gene families associated with starch and sucrose metabolism, flavonoid biosynthesis, and plant-pathogen interaction were significantly expanded in E. urophylla × E. grandis. Moreover, comparative genomic and evolutionary analyses showed large structural variations among the different chromosomes of the 34 Eucalyptus accessions, which were divided into six clades.

CONCLUSIONS

Overall, our findings provide a valuable resource for expanding our understanding of the E. urophylla × E. grandis genome evolution, genetic improvement, and its comparative biology.

The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry

Fragaria vesca, commonly known as wild or woodland strawberry, is the most widely distributed diploid Fragaria species and is native to Europe and Asia. Because of its small plant size, low heterozygosity, and relative ease of genetic transformation, F. vesca has been a model plant for fruit research since the publication of its Illumina-based genome in 2011. However, its genomic contribution to octoploid cultivated strawberry remains a long-standing question. Here, we de novo assembled and annotated a telomere-to-telomere, gap-free genome of F. vesca 'Hawaii 4', with all seven chromosomes assembled into single contigs, providing the highest completeness and assembly quality to date. The gap-free genome is 220 785 082 bp in length and encodes 36 173 protein-coding gene models, including 1153 newly annotated genes. All 14 telomeres and seven centromeres were annotated within the seven chromosomes. Among the three previously recognized wild diploid strawberry ancestors, F. vesca, F. iinumae, and F. viridis, phylogenomic analysis showed that F. vesca and F. viridis are the ancestors of the cultivated octoploid strawberry F. × ananassa, and F. vesca is its closest relative. Three subgenomes of F. × ananassa belong to the F. vesca group, and one is sister to F. viridis. We anticipate that this high-quality, telomere-to-telomere, gap-free F. vesca genome, combined with our phylogenomic inference of the origin of cultivated strawberry, will provide insight into the genomic evolution of Fragaria and facilitate strawberry genetics and molecular breeding.

The Identification of SQS/SQE/OSC Gene Families in Regulating the Biosynthesis of Triterpenes in Potentilla anserina

The tuberous roots of Potentilla anserina (Pan) are an edible and medicinal resource in Qinghai-Tibetan Plateau, China. The triterpenoids from tuberous roots have shown promising anti-cancer, hepatoprotective, and anti-inflammatory properties. In this study, we carried out phylogenetic analysis of squalene synthases (SQSs), squalene epoxidases (SQEs), and oxidosqualene cyclases (OSCs) in the pathway of triterpenes. In total, 6, 26, and 20 genes of SQSs, SQEs, and OSCs were retrieved from the genome of Pan, respectively. Moreover, 6 SQSs and 25 SQEs genes expressed in two sub-genomes (A and B) of Pan. SQSs were not expanded after whole-genome duplication (WGD), and the duplicated genes were detected in SQEs. Twenty OSCs were divided into two clades of cycloartenol synthases (CASs) and β-amyrin synthases (β-ASs) by a phylogenetic tree, characterized with gene duplication and evolutionary divergence. We speculated that β-ASs and CASs may participate in triterpenes synthesis. The data presented act as valuable references for future studies on the triterpene synthetic pathway of Pan.

Creating novel ornamentals via new strategies in the era of genome editing

Ornamental breeding has traditionally focused on improving novelty, yield, quality, and resistance to biotic or abiotic stress. However, achieving these goals has often required laborious crossbreeding, while precise breeding techniques have been underutilized. Fortunately, recent advancements in plant genome sequencing and editing technology have opened up exciting new frontiers for revolutionizing ornamental breeding. In this review, we provide an overview of the current state of ornamental transgenic breeding and propose four promising breeding strategies that have already proven successful in crop breeding and could be adapted for ornamental breeding with the help of genome editing. These strategies include recombination manipulation, haploid inducer creation, clonal seed production, and reverse breeding. We also discuss in detail the research progress, application status, and feasibility of each of these tactics.

Transcriptome and chemical analyses revealed the mechanism of flower color formation in Rosa rugosa

Rosa rugosa is a famous Chinese traditional flower with high ornamental value and well environmental adapt ability. The cultivation of new colorful germplasms to improve monotonous flower color could promote its landscape application. However, the mechanism of flower color formation in R. rugosa remains unclear. In this study, combined analyses of the chemical and transcriptome were performed in the R. rugosa germplasms with representative flower colors. Among the identified anthocyanins, cyanidin 3,5-O-diglucoside (Cy3G5G) and peonidin 3,5-O-diglucoside (Pn3G5G) were the two dominant anthocyanins in the petals of R. rugosa. The sum content of Cy3G5G and Pn3G5G was responsible for the petal color intensity, such as pink or purple, light- or dark- red. The ratio of Cy3G5G to Pn3G5G was contributed to the petal color hue, that is, red or pink/purple. Maintaining both high relative and high absolute content of Cy3G5G may be the precondition for forming red-colored petals in R. rugosa. Cyanidin biosynthesis shunt was the dominant pathway for anthocyanin accumulation in R. rugosa, which may be the key reason for the presence of monotonous petal color in R. rugosa, mainly pink/purple. In the upstream pathway of cyanidin biosynthesis, 35 differentially expressed structural genes encoding 12 enzymes co-expressed to regulate the sum contents of Cy3G5G and Pn3G5G, and then determined the color intensity of petals. RrAOMT, involved in the downstream pathway of cyanidin biosynthesis, regulated the ratio of Cy3G5G to Pn3G5G via methylation and then determined the color hue of petals. It was worth mentioning that significantly higher delphinidin-3,5-O-diglucoside content and RrF3'5'H expression were detected from deep purple-red-flowered 8-16 germplasm with somewhat unique and visible blue hue. Three candidate key transcription factors identified by correlation analysis, RrMYB108, RrC1, and RrMYB114, might play critical roles in the control of petal color by regulating the expression of both RrAOMT and other multiple structural genes. These results provided novel insights into anthocyanin accumulation and flower coloration mechanism in R. rugosa, and the candidate key genes involved in anthocyanin biosynthesis could be valuable resources for the breeding of ornamental plants in future.

The chromosome-level genome of Gypsophila paniculata reveals the molecular mechanism of floral development and ethylene insensitivity

Gypsophila paniculata, belonging to the Caryophyllaceae of the Caryophyllales, is one of the most famous worldwide cut flowers. It is commonly used as dried flowers, whereas the underlying mechanism of flower senescence has not yet been addressed. Here, we present a chromosome-scale genome assembly for G. paniculata with a total size of 749.58 Mb. Whole-genome duplication signatures unveil two major duplication events in its evolutionary history: an ancient one occurring before the divergence of Caryophyllaceae and a more recent one shared with Dianthus caryophyllus. The integrative analyses combining genomic and transcriptomic data reveal the mechanisms regulating floral development and ethylene response of G. paniculata. The reduction of AGAMOUS expression probably caused by sequence polymorphism and the mutation in miR172 binding site of PETALOSA are associated with the double flower formation in G. paniculata. The low expression of ETHYLENE RESPONSE SENSOR (ERS) and the reduction of downstream ETHYLENE RESPONSE FACTOR (ERF) gene copy number collectively lead to the ethylene insensitivity of G. paniculata, affecting flower senescence and making it capable of making dried flowers. This study provides a cornerstone for understanding the underlying principles governing floral development and flower senescence, which could accelerate the molecular breeding of the Caryophyllaceae species.

Effect of Developmental Stages on Genes Involved in Middle and Downstream Pathway of Volatile Terpene Biosynthesis in Rose Petals

Terpenoids are economically and ecologically important compounds, and they are vital constituents in rose flower fragrance and rose essential oil. The terpene synthase genes (TPSs), trans-prenyltransferases genes (TPTs), NUDX1 are involved in middle and downstream pathway of volatile terpene biosynthesis in rose flowers. We identified 7 complete RcTPTs, 49 complete RcTPSs, and 9 RcNUDX1 genes in the genome of Rosachinensis. During the flower opening process of butterfly rose (Rosachinensis ‘Mutabilis’, MU), nine RcTPSs expressed in the petals of opening MU flowers exhibited two main expression trends, namely high and low, in old and fresh petals. Five short-chain petal-expressed RcTPTs showed expression patterns corresponding to RcTPSs. Analysis of differential volatile terpenes and differential expressed genes indicated that higher emission of geraniol from old MU petals might be related to the RcGPPS expression. Comprehensive analysis of volatile emission, sequence structure, micro-synteny and gene expression suggested that RcTPS18 may encode (E,E)-α-farnesene synthase. These findings may be useful for elucidating the molecular mechanism of terpenoid metabolism in rose and are vital for future studies on terpene regulation.

Comprehensive Genome-Wide Analysis of Histone Acetylation Genes in Roses and Expression Analyses in Response to Heat Stress

Roses have high economic values as garden plants and for cut-flower and cosmetics industries. The growth and development of rose plants is affected by exposure to high temperature. Histone acetylation plays an important role in plant development and responses to various stresses. It is a dynamic and reversible process mediated by histone deacetylases (HDAC) and histone acetyltransferases (HAT). However, information on HDAC and HAT genes of roses is scarce. Here, 23 HDAC genes and 10 HAT genes were identified in the Rosa chinensis ‘Old Blush’ genome. Their gene structures, conserved motifs, physicochemical properties, phylogeny, and synteny were assessed. Analyses of the expression of HDAC and HAT genes using available RNAseq data showed that these genes exhibit different expression patterns in different organs of the three analyzed rose cultivars. After heat stress, while the expression of most HDAC genes tend to be down-regulated, that of HAT genes was up-regulated when rose plants were grown at high-temperature conditions. These data suggest that rose likely respond to high-temperature exposure via modification in histone acetylation, and, thus, paves the way to more studies in order to elucidate in roses the molecular mechanisms underlying rose plants development and flowering.

The identification of the Rosa S-locus provides new insights into the breeding and wild origins of continuous-flowering roses

This study aims to: (i) identify the Rosa S-locus controlling self-incompatibility (SI); (ii) test the genetic linkage of the S-locus with other loci controlling important ornamental traits, such as the continuous-flowering (CF) characteristic; (iii) identify the S-alleles (S_C ) of old Chinese CF cultivars (e.g, Old Blush, Slater's Crimson China) and examine the changes in the frequency of cultivars with Sc through the history of breeding; (iv) identify wild species carrying the Sc-alleles to infer wild origins of CF cultivars. We identified a new S-RNase (S_C2 ) of Rosa chinensis in a contig from a genome database that has not been integrated into one of the seven chromosomes yet. Genetic mapping indicated that S_C2 is allelic to the previously-identified S-RNase (S_C1 ) in chromosome 3. Pollination experiments with half-compatible pairs of roses confirmed that they are the pistil-determinant of SI. The segregation analysis of an F₁ -population indicated genetic linkage between the S-locus and the floral repressor gene KSN. The non-functional allele ksn is responsible for the CF characteristic. A total of five S-alleles (S_C1-5 ) were identified from old CF cultivars. The frequency of cultivars with S_C dramatically increased after the introgression of ksn from Chinese to European cultivars and remains high (80%) in modern cultivars, suggesting that S-genotyping is helpful for effective breeding. Wild individuals carrying S_C were found in Rosa multiflora (S_C1 ), Rosa chinensis var. spontanea (S_C3 ), and Rosa gigantea (S_C2 , S_C4 ), supporting the hypothesis of hybrid origins of CF cultivars and providing a new evidence for the involvement of Rosa multiflora.

Cool-Warm Temperature Stratification and Simulated Bird Digestion Optimize Removal of Dormancy in Rosa rugosa Seeds

Rosa rugosa Thunb. has been explored multi-function in medicinal, edible, cosmetic, ornamental and ecological etc. However, R. rugosa natural populations have recently declined substantially in China, besides of global climate change, this species also has the defect of limiting the reproduction of itself such as the hard-to-release seed dormancy. In this study, only 30% of R. rugosa seeds were viable, and the others were incompletely developed or diseased seeds. Without stratification, morphologically complete viable seeds imbibed water but those seeds could not germinate even after seed husk removal under suitable condition to exhibit a physiological dormancy. After cold (4°C) and warm (18 ± 2°C) stratification, macromolecular substances containing carbon or nitrogen accumulated, and respiration, antioxidant enzyme activity, and gibberellin (GA₃) /abscisic acid (ABA) and auxin (IAA)/ABA ratios increased significantly in seeds. Water absorption also increased as endocarps softened. Thus, physiological dormancy of seed was broken. Although warm and cold stratification increased separation between endocarp and embryo, the endocarp binding force was removed insufficiently, because only 10.20% of seeds germinated. Therefore, stratified seeds were treated with simulated bird digestion. Then, folds and cracks in loosened endocarps increased permeability, and water absorption rate increased to 64.43% compare to 21.14% in cold and warm stratification treatment. With simulated digestion, 24.20% of radicles broke through the endocarp with plumules and cambiums to develop into seedlings. Thus, the seed dormancy type of R. rugosa is physiological as seeds imbibed water and possessed fully developed embryos with a low growth potential in combination with a mechanical constraint from the endocarp. Cold stratification helped remove physiological dormancy, and additional warm stratification accelerated the process. The optimal stratification treatment was 4°C for 45 days followed by 18 ± 2°C for 15 days. After warm and cold stratification, simulated bird digestion broke the mechanical constraint from the seed covering layers. Based on this research, production of R. rugosa seedlings can be greatly increased to help protect the species from further declines.

Complex and reticulate origin of edible roses (Rosa, Rosaceae) in China

While roses are today among the most popular ornamental plants, the petals and fruits of some cultivars have flavored foods for millennia. The genetic origins of these edible cultivars remain poorly investigated. We collected the major varieties of edible roses available in China, assembled their plastome sequences, and phased the haplotypes for internal transcribed spacers (ITS1/ITS2) of the 18S-5.8S-26S nuclear ribosomal cistron. Our phylogenetic reconstruction using 88 plastid genomes, of primarily maternal origin, uncovered well-supported genetic relationships within Rosa, including all sections and all subgenera. We phased the ITS sequences to identify potential donor species ancestral to the development of known edible cultivars. The tri-parental Middle-Eastern origin of R. × damascena, the species most widely used in perfume products and food additives, was confirmed as a descendent of past hybridizations among R. moschata, R. gallica, and R. majalis/R. fedtschenkoana/R. davurica. In contrast, R. chinensis, R. rugosa, and R. gallica, in association with six other wild species, were the main donors for fifteen varieties of edible roses. The domesticated R. rugosa 'Plena' was shown to be a hybrid between R. rugosa and R. davurica, sharing a common origin with R. 'Fenghua'. Only R. 'Jinbian' and R. 'Crimson Glory' featured continuous flowering. All remaining cultivars of edible roses bloomed only once a year. Our study provides important resources for clarifying the origin of edible roses and suggests a future for breeding new cultivars with unique traits, such as continuous flowering.

Genome-Wide Identification of LATERAL ORGAN BOUNDARIES DOMAIN (LBD) Transcription Factors and Screening of Salt Stress Candidates of Rosa rugosa Thunb

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are regulators of lateral organ morphogenesis, boundary establishment, and secondary metabolism in plants. The responsive role of LBD gene family in plant abiotic stress is emerging, whereas its salt stress responsive mechanism in Rosa spp. is still unclear. The wild plant of Rosa rugosa Thunb., which exhibits strong salt tolerance to stress, is an ideal material to explore the salt-responsive LBD genes. In our study, we identified 41 RrLBD genes based on the R. rugosa genome. According to phylogenetic analysis, all RrLBD genes were categorized into Classes I and II with conserved domains and motifs. The cis-acting element prediction revealed that the promoter regions of most RrLBD genes contain defense and stress responsiveness and plant hormone response elements. Gene expression patterns under salt stress indicated that RrLBD12c, RrLBD25, RrLBD39, and RrLBD40 may be potential regulators of salt stress signaling. Our analysis provides useful information on the evolution and development of RrLBD gene family and indicates that the candidate RrLBD genes are involved in salt stress signaling, laying a foundation for the exploration of the mechanism of LBD genes in regulating abiotic stress.

A high-quality chromosome-level genome of wild Rosa rugosa

Rosa rugosa is an important shrub with economic, ecological, and pharmaceutical value. A high-quality chromosome-scale genome for R. rugosa sequences was assembled using PacBio and Hi-C technologies. The final assembly genome sequences size was about 407.1 Mb, the contig N50 size was 2.85 Mb, and the scaffold N50 size was 56.6 Mb. More than 98% of the assembled genome sequences were anchored to seven pseudochromosomes (402.9 Mb). The genome contained 37,512 protein-coding genes, with 37,016 genes (98.68%) that were functionally annotated, and 206.67 Mb (50.76%) of the assembled sequences are repetitive sequences. Phylogenetic analyses indicated that R. rugosa diverged from Rosa chinensis ∼6.6 million years ago, and no lineage-specific whole-genome duplication event occurred after divergence from R. chinensis. Chromosome synteny analysis demonstrated highly conserved synteny between R. rugosa and R. chinensis, between R. rugosa and Prunus persica as well. Comparative genome and transcriptome analysis revealed genes related to colour, scent, and environment adaptation. The chromosome-level reference genome provides important genomic resources for molecular-assisted breeding and horticultural comparative genomics research.