Complete chloroplast genome sequence of <i>Rosa roxburghii</i> and its phylogenetic analysis

Wang, Qian; Hu, Huan; An, Jiaxing; Bai, Guohui; Ren, Qunli; Liu, Jianguo

doi:10.1080/23802359.2018.1431074

Cited by 12 publications

(8 citation statements)

References 8 publications

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“…Protein coding genes and ribosomal RNA (rRNA) genes were primarily identified using DOGMA (Dual Organellar GenoMe Annotator) [20], and transfer RNA (tRNA) genes were identified using tRNAscan-SE 2.0 [21]. Further annotations were identified by comparing chloroplast genomes with the well-defined Nicotiana tabacum chloroplast genome (Z00044) [22] and Rosa roxburghii chloroplast genome (NC_032038) [23] from GenBank as references. Finally, all gene annotations were verified and accurately adjusted via BLASTN and BLASTX searches.…”

Section: Methodsmentioning

confidence: 99%

“…The complete chloroplast genomes of R. multiflora , R. luciae , and R. maximowicziana from this study and chloroplast genomes of two other Rosa species from other infrageneric groups in GenBank, Rosa roxburghii (subgenus Platyrhodon ; NC_032038) [23] and Rosa odorata var. gigantea (subgenus Rosa section Chinenses ; KF753637) [25], were compared using mVISTA [26,27] with LAGAN alignment program [28].…”

Section: Methodsmentioning

confidence: 99%

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Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae)

Jeon

Kim

2019

Genes

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Species belonging to Rosa section Synstylae (Rosaceae) are mainly distributed in East Asia, and represent recently diverged lineages within the genus. Over decades, inferring phylogenetic relationships within section Synstylae have been exceptional challenges, due to short branch lengths and low support values. Of approximately 36 species in the section Synstylae, Rosa multiflora, Rosa luciae and Rosa maximowicziana are widely distributed in the Sino-Japanese floristic region. In this study, we assembled chloroplast genomes of these three species to compare the genomic features within section Synstylae, and to compare with other infrageneric groups. We found that three Rosa sect. Synstylae species had lost infA genes with pseudogenization, and they were almost identical to each other. Two protein-coding gene regions (ndhF and ycf1) and five non-coding regions (5’matK-trnK, psbI-trnS-trnG, rps16-trnG, rpoB-trnC, and rps4-trnT) were identified as being highly informative markers. Within three section Synstylae chloroplast genomes, 85 simple sequence repeat (SSR) motifs were detected, of which at least 13 motifs were identified to be effective markers. The phylogenetic relationships of R. multiflora, R. luciae and R. maximowicziana could not be resolved, even with chloroplast genome-wide data. This study reveals the chloroplast genomic data of Rosa sect. Synstylae, and it provides valuable markers for DNA barcoding and phylogenetic analyses for further studies.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae)

Jeon

Kim

2019

Genes

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“…However, to date, only a few cp genomes of Rosa spp. have been published in the GeneBank database [32][33][34][35] , which is a source of data on sequence diversity. Furthermore, few studies have focused on molecular markers from the cp genome of roses.…”

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confidence: 99%

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

Zheng

Huang

2020

Sci Rep

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the rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. the chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. comparative genome analysis showed that the iR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. the phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species. Chloroplasts are vital and unique components of photosynthetic cells in plants and algae. They are responsible for multiple functions, e.g., assimilation of carbon and nitrogen, synthesis of amino acids and fatty acids, etc., and play important roles in plant growth and development 1. Chloroplasts may have originated from cyanobacteria through endosymbiosis 2,3 , and chloroplasts possess their own deoxyribonucleic acid (DNA). In the majority of plant species, the chloroplast genome (cp genome) is inherited maternally, with the exception of certain gymnosperms, in which the cp genome is paternally inherited 4. In recent years, knowledge about the organization and evolution of the cp genome has rapidly improved because of the development of DNA sequencing technology and bioinformatics methods. The cp genome is relatively conserved in angiosperms, and its size ranges from 107 to 218 kb, including 100-200 encoding genes 5. A typical angiosperm cp genome has circular DNA, including two small inverted repeats (IRa and IRb), a large single copy (LSC) region and a small single copy (SSC) region 6. Compared to nuclear DNA, the cp genome is small, single-stranded, relatively conserved and has uniparental inheritance, and its nucleotide m...

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“…In recent years, it was widely applied in food and cosmetics for its nutritional and health benefits ( Yang et al, 2020 ). Its root, leaf, and fruit have been used as traditional medicinal materials in the treatment of several diseases, including strengthening the spleen, dyspepsia, enteritis, and scurvy ( Wang et al, 2018 ). Modern pharmacological studies have demonstrated that some components of R. roxburghii exhibited several biological activities, such as excellent hypoglycemic and hypolipidemic effects, enhancing immunity, antioxidation, and anti-tumor activities ( Wang et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Multigene Phylogeny, Diversity and Antimicrobial Potential of Endophytic Sordariomycetes From Rosa roxburghii

Zhang

Wei

et al. 2021

Front. Microbiol.

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Rosa roxburghii Tratt. is widely applied in food, cosmetics, and traditional medicine, and has been demonstrated to possess diverse bioactivities. Plant endophytic fungi are important microbial resources with great potential for application in many fields. They not only establish mutualistic symbiosis with host plants but also produce a variety of bioactive compounds. Therefore, in the present study, endophytic fungi were isolated from R. roxburghii, the diversity and antimicrobial activities were evaluated. As a result, 242 strains of endophytic Sordariomycetes were successfully isolated. Multigene phylogenetic analyses showed that these isolates included eight orders, 19 families, 33 genera. The dominant genera were Diaporthe (31.4%), Fusarium (14.4%), Chaetomium (7.9%), Dactylonectria (7.0%), Graphium (4.5%), Colletotrichum (4.1%), and Clonostachys (4.1%). For different tissues of R. roxburghii, alpha diversity analysis revealed that the diversity of fungal communities decreased in the order of root, fruit, stem, flower, leaf, and seed, and Clonostachys and Dactylonectria exhibited obvious tissue specificity. Meanwhile, functional annotation of 33 genera indicated that some fungi have multitrophic lifestyles combining endophytic, pathogenic, and saprophytic behavior. Additionally, antimicrobial activities of endophytic Sordariomycetes against Lasiodiplodia theobromae, Botryosphaeria dothidea, Colletotrichum capsici, Pyricularia oryzae, Rhizoctonia solani, Fusarium oxysporum, Pseudomonas syringae, Pantoea agglomerans, Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa were screened. Dual culture test assays showed that there were 40 different endophytic species with strong inhibition of at least one or moderate inhibition of two or more against the 12 tested strains. The results from the filter paper diffusion method suggested that extracellular metabolites may be more advantageous than intracellular metabolites in the development of antimicrobial agents. Eleven isolates with good activities were screened. In particular, Hypomontagnella monticulosa HGUP194009 and Nigrospora sphaerica HGUP191020 have shown promise in both broad-spectrum and intensity. Finally, some fungi that commonly cause disease have been observed to have beneficial biological activities as endophytic fungi. In conclusion, this study showed the species composition, alpha diversity, and lifestyle diversity of endophytic Sordariomycetes from R. roxburghii and demonstrated these isolates are potential sources for exploring antimicrobial agents.

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Complete chloroplast genome sequence of Rosa roxburghii and its phylogenetic analysis

Cited by 12 publications

References 8 publications

Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae)

Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae)

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

Multigene Phylogeny, Diversity and Antimicrobial Potential of Endophytic Sordariomycetes From Rosa roxburghii

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