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

Chen, Fei; Su, Liyao; Hu, Shuaiya; Xue, Jia‐Yu; Liu, Hui; Liu, Guanhua; Jiang, Yifan; Du, Jianke; Qiao, Yu; Fan, Yannan; Liu, Huan; Yang, Qi; Lu, Wenjie; Shao, Zhu‐Qing; Zhang, Jian; Zhang, Liangsheng; Chen, Feng; Cheng, Zong‐Ming

doi:10.1038/s41438-021-00594-z

Cited by 42 publications

(53 citation statements)

References 56 publications

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“…Nucleotide sequence of Arabidopsis members of the HDAC and HAT genes were retrieved from Arabidopsis genome database ( , accessed on 1 June 2020) using TBtools [ 25 ] using available gene ID ( Table S1 ) [ 8 ]. Arabidopsis HDACs and HATs amino acid sequences were used to identify HDACs and HATs putative homologues in the genomes of R. chinensis [ 24 ], of R. rugosa [ 26 ], of R. multiflora [ 27 ], and of Fragaria vesca [ 28 ], using blast Wrapper with an E-value ≤ 1 × 10 −5 . Protein sequences of HDACs and HATs from R. chinensis , F. vesca , R. rugosa , R. multiflora were retrieved using NCBI blastp and Swiss-Prot database (BLAST: Basic Local Alignment Search Tool ( , accessed on 2 June 2020)).…”

Section: Methodsmentioning

confidence: 99%

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

Huang

Guan

et al. 2022

Genes

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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.

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Section: Methodsmentioning

confidence: 99%

“…The genome sequence and genes annotation information of R. chinensis [ 24 ], R. Rugosa [ 26 ] and F. vesca [ 28 ] were downloaded. TBtools software [ 25 ] was used to visualize the distribution of the HDAC and HAT genes on the R. chinensis chromosomes.…”

Section: Methodsmentioning

confidence: 99%

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

Huang

Guan

et al. 2022

Genes

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“…The ability of R. rugosa to adapt to many environmental conditions (e.g., salinity and alkaline soils, shade, low temperatures, drought, and high humidity) and to produce a wide spectrum of secondary metabolites that can be industrially exploited makes it an ideal organism for gene mining and molecular breeding to create novel varieties [55]. Indeed, a high-quality genome sequence for R. rugosa both enables comparative genomic studies of Rosa species and reveals the mechanisms underlying its ornamental traits, such as floral biology and its unique ecology and distribution.…”

Section: Genetic Characterisation Of R Rugosamentioning

confidence: 99%

Invasion at the Edge: The Case of Rosa rugosa (Rosaceae) in Italy

et al. 2021

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The Japanese Rose (Rosa rugosa) is a perennial shrub belonging to the family Rosaceae. It was introduced in Europe from East Asia as an ornamental plant in the XIX century and is now considered an invasive species, especially in northern Europe, colonising the Atlantic and Baltic coastal dune habitats and threatening local biodiversity. However, little is known about its presence and invasion patterns in the Mediterranean area. In Italy, R. rugosa has been classified as naturalised and just a few observations have been recorded in dune habitats in the North Adriatic coast. Here, we review the published data on R. rugosa in Europe and present preliminary data on the invasive pattern of R. rugosa on the Italian North Adriatic coast. We surveyed the coastline in two locations (i.e., Brussa and Bibione, Italy) where we characterised the dimension and structure (i.e., number of ramets and stem height) of the R. rugosa populations and listed the associated floristic composition. No occurrence of R. rugosa was recorded in Bibione, probably due to the success of the restoration project carried out on that site. In contrast, several stands of R. rugosa were found in Brussa, where many other alien species were also found (accounting for 15.28% of the sampled species). Given the strong invasiveness of R. rugosa, it is important to keep data on its distribution up-to-date and investigate its ecology and physiology to promote appropriate management strategies to control its spread and anticipate its future potential distribution.

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“…It produces beautiful flowers with a mild fragrance and colorful achenes. Unlike many other cultivated roses, R. rugosa is adapted to a wide range of habitat types and harsh environmental conditions, including salinity, alkalinity, shade, drought, high humidity, and frigid temperatures ( Chen et al, 2021 ). R. rugosa is important in landscaping and because the fruit is rich in secondary metabolites and nutrients, as a raw material in food processing and medicine and cosmetics production ( Chen et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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

Cited by 42 publications

References 56 publications

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

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

Invasion at the Edge: The Case of Rosa rugosa (Rosaceae) in Italy

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

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