A high-quality chromosome-level genome of wild <i>Rosa rugosa</i>

Zang, Fengqi; Ma, Yan; Tu, Xiaolong; Huang, Ping; Wu, Qingmin; Li, Zhimin; Liu, Tao; Lin, Fu‐Cheng; Pei, Surui; Zang, Dekui; Zhang, Xuemei; Zheng, Yongqi; Yu, Yunyan

doi:10.1093/dnares/dsab017

Cited by 14 publications

(23 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The differences in HDAC and HAT gene numbers ( Table 1 ) could be due to the possibility that these rose species may have evolved independently regarding the process of histone acetylation. This is supported for example by the recent report that proposed that R. rugosa diverged from R. chinensis and over 6 million years ago [ 35 ].…”

Section: Resultsmentioning

confidence: 64%

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

Huang

Guan

et al. 2022

Genes

View full text Add to dashboard Cite

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.

show abstract

Section: Resultsmentioning

confidence: 64%

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

Huang

Guan

et al. 2022

Genes

View full text Add to dashboard Cite

show abstract

“…We performed a genome-wide search for candidate S-RNase genes in the genome databases of Old Blush [ 5 , 6 ], R. multiflora [ 7 ], and R. rugosa [ 16 , 39 ] ( Supplementary data Table D2 ) and identified 16 genes located on four chromosomes ( Fig. 1a ).…”

Section: Resultsmentioning

confidence: 99%

“…1b ) and low genetic divergences between alleles (>94% identity; Table 1 ). One allele of the 6C gene of Old Blush [ 5 ] and that of R. rugosa [ 39 ] are pseudogenes due to frameshift mutations ( Supplementary Data Table D2 ). The 3A gene is homozygous in Old Blush and cannot be identified in two R. rugosa genomes.…”

Section: Resultsmentioning

confidence: 99%

“…All genomic regions with significant hits (E-value <10 –10 ), including the regions without any annotations, were listed and manually annotated to infer the coding regions. The other genome databases of Rosa multiflora [ 7 ] and R. rugosa [ 16 , 39 ] were then searched using the candidate S-RNase genes of Old Blush as queries to identify their orthologous genes. For the phylogenetic reconstruction of S-RNase -like genes in roses, deduced amino acid sequences were aligned using MUSCLE and then converted back to DNA sequences.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

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

Kawamura

Ueda

Matsumoto

et al. 2022

Horticulture Research

View full text Add to dashboard Cite

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 (SC) 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 (SC2) 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 SC2 is allelic to the previously-identified S-RNase (SC1) 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 (SC1–5) were identified from old CF cultivars. The frequency of cultivars with SC 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 SC were found in Rosa multiflora (SC1), Rosa chinensis var. spontanea (SC3), and Rosa gigantea (SC2, SC4), supporting the hypothesis of hybrid origins of CF cultivars and providing a new evidence for the involvement of Rosa multiflora.

show abstract

“…For example, R. × damascena ‘trigintipetala’, a famous oil bearing rose, has been planted in Turkey and Bulgaria since the 16th century and was introduced to Asia (China) in the 1970s [ 9 ]. Meanwhile, the East Asia (China and Japan) origin R. rugosa and its hybrid cultivars R. × rugosa are more popular in the Asian market [ 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

BOX38, a DNA Marker for Selection of Essential Oil Yield of Rosa × rugosa

et al. 2023

View full text Add to dashboard Cite

Rosa rugosa L. was a famous aromatic plant whose cultivars (Rosa × rugosa) have been widely used in the perfume industry in Asia. The perfume market looks for rose cultivars bearing higher essential oil, while the oil yields of most R. × rugosa have not been evaluated due to limiting conditions, such as insufficient cultivation areas. Here, we tested the yield and the aroma components of essential oil of 19 R. × rugosa. The results indicated that the yields of nerol, citronellol, and geraniol could represent an alternative index of the total yield of essential oil. Sequence syntenic analysis indicated that the Rosa genus specific cis-element Box38 was highly polymorphic. The Box38 region isolation of Rosa × rugosa by flanked primers proved that Box38 repeat number was significantly positively correlated with the essential oil yield of the corresponding cultivar. In the breeding of Rosa × rugosa, six-Box38-repeat could be a robust threshold for selection of high-essential-oil roses. Together, we found that Box38 was a DNA marker for essential oil yield and that it would be helpful in the early selection and breeding of essential oil roses.

show abstract

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

Cited by 14 publications

References 45 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

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

BOX38, a DNA Marker for Selection of Essential Oil Yield of Rosa × rugosa

Contact Info

Product

Resources

About