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

2022 ◽  
Vol 9 ◽  
Author(s):  
Wei-Hua Cui ◽  
Xin-Yu Du ◽  
Mi-Cai Zhong ◽  
Wei Fang ◽  
Zhi-Quan Suo ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Middle Eastern ◽  
Food Additives ◽  
Ornamental Plants ◽  
Phylogenetic Reconstruction ◽  
Internal Transcribed Spacers ◽  
Potential Donor ◽  
Plastid Genomes ◽  
Ribosomal Cistron ◽  
Donor Species

Abstract 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.

scholarly journals Genetic Relationships of Wild Roses, Old Garden Roses, and Modern Roses Based on Internal Transcribed Spacers and matK Sequences

HortScience ◽  
2013 ◽  
Vol 48 (12) ◽  
pp. 1445-1451 ◽  
Author(s):  
Xianqin Qiu ◽  
Hao Zhang ◽  
Hongying Jian ◽  
Qigang Wang ◽  
Ningning Zhou ◽  
...  
Keyword(s):  
Molecular Level ◽  
Genetic Relationships ◽  
Economic Value ◽  
Ornamental Plants ◽  
Germplasm Conservation ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Clustering Data ◽  
Almost All ◽  
Sequence Techniques

Roses are one of the economically most important groups of ornamental plants. The internal transcribed spacers (ITS) of the nuclear ribosomal DNA and the chloroplast gene matK were used to investigate the genetic diversity and genetic relationships among Rosa germplasm including 39 wild species, 21 old garden roses, and 29 modern cultivars. Three dendrograms based on ITS and matK clustering data indicated that 1) 39 wild genotypes were consistent with their classification into botanical sections with only a few exceptions; 2) most of the wild genotypes were separated from rose cultivars. However, three sections, Synstylae, Chinenses, and Rosa, that contributed to the modern roses generally gathered together with almost all old garden and modern roses on the molecular level; and 3) the relationships between cultivated roses as inferred by ITS and matK sequences do not correlate with horticultural groups. Results demonstrated that both sequence techniques can contribute to clarifying the genetic relationships of rose accessions and germplasm conservation to enhance the ornamental and economic value of rose.

scholarly journals Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

2018 ◽  
Vol 19 (12) ◽  
pp. 4039 ◽  
Author(s):  
Mi-Li Liu ◽  
Wei-Bing Fan ◽  
Ning Wang ◽  
Peng-Bin Dong ◽  
Ting-Ting Zhang ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Repeat Sequence ◽  
Biological Research ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Evolutionary Analysis ◽  
Plastid Genomes

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

scholarly journals Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events

2019 ◽  
Vol 125 (1) ◽  
pp. 29-47 ◽  
Author(s):  
Xiao-Chen Huang ◽  
Dmitry A German ◽  
Marcus A Koch
Keyword(s):  
Species Richness ◽  
Driving Forces ◽  
Size Variation ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Published Data ◽  
Glacial Cycles ◽  
Genome Size Variation ◽  
Crown Group ◽  
Plastid Genomes

Abstract Background and Aims Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. Methods We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. Key Results Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. Conclusions The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant ‘pump’ for continuous and high species diversification.

The Carotid Artery as a Coronary Bioprosthesis: Five Potential Donor Species

1985 ◽  
Vol 19 (3) ◽  
pp. 163-173 ◽  
Author(s):  
Hong-De Wu ◽  
Svetlana Kaplan ◽  
Lester R. Sauvage ◽  
Stephen B. Robel ◽  
Knute Berger ◽  
...  
Keyword(s):  
Carotid Artery ◽  
Potential Donor ◽  
Donor Species

Molecular systematics of subtribe Banksiinae (Banksia and Dryandra; Proteaceae) Based on cpDNA and nrDNA sequence data: Implications for taxonomy and biogeography

1998 ◽  
Vol 11 (4) ◽  
pp. 321 ◽  
Author(s):  
Austin R. Mast
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Base Substitution ◽  
Trnl Intron ◽  
Single Root ◽  
Cladistic Analyses ◽  
Molecular Characters

Despite considerable research interest in the subtribe Banksiinae (Banksia L.f. and Dryandra R.Br.), no strongly supported phylogenetic hypothesis for the relationship between the genera exists, nor have molecular characters been sampled for phylogenetic reconstruction at any level. In this study, DNA sequence characters were sampled from chloroplast DNA (cpDNA; the trnL intron, the trnL 3′ exon, and the spacer between the trnL 3′ exon and trnF) and nuclear ribosomal DNA (nrDNA; both internal transcribed spacers) of 18 species of Banksia and five of Dryandra, with six outgroup taxa from the subfamily Grevilleoideae. The molecular characters provided the opportunity to code taxa outside of Banksia for cladistic comparison with the genus—an opportunity not previously provided by morphological characters. Cladistic analyses, using parsimony, explored the effects of various weightings of transition to transversion events and base substitution to insertion and deletion events to determine which relationships in the cladograms were robust. The trnL/trnF and ITS characters strongly supported a paraphyletic Banksia with respect to a monophyletic Dryandra. The molecular results supported a single root for Thiele and Ladiges’(1996) unrooted morphological cladogram along the branch between the Isotylis to B. fuscolutea clade and the Grandes to B. tricuspis clade. George’s (1981) subgenus Banksia and section Banksia appeared dramatically non-monophyletic. The distribution of eastern taxa at derived positions on the molecular cladograms suggested considerable cladogenesis in the the genus prior to the formation of the Nullarbor Plain during the Tertiary.

Characterization ofDicrocoelium dendriticumisolates from small ruminants in Shaanxi Province, north-western China, using internal transcribed spacers of nuclear ribosomal DNA

2013 ◽  
Vol 89 (1) ◽  
pp. 124-129 ◽  
Author(s):  
Q.Q. Bian ◽  
G.H. Zhao ◽  
Y.Q. Jia ◽  
Y.Q. Fang ◽  
W.Y. Cheng ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Small Ruminants ◽  
Internal Transcribed Spacers ◽  
Shaanxi Province ◽  
Western China ◽  
Nuclear Ribosomal Dna ◽  
Specific Sequence ◽  
Sheep And Goats ◽  
Rdna Sequences ◽  
Geographical Regions

AbstractThe genetic variations in internal transcribed spacers (ITS) spanning ITS-1, 5.8S and ITS-2 rDNA ofDicrocoelium dendriticum, isolated from sheep and goats in four geographical regions in Shaanxi province, were examined. The lengths of ITS-1, 5.8S and ITS-2 rDNA sequences forD. dendriticumwere 749 bp, 161 bp and 234 bp, respectively. Intra-specific sequence variations ofD. dendriticumwere 0–0.5% for ITS-1 and 0–1.3% for ITS-2 rDNA, while the inter-specific variations among species in genusDicrocoeliumin ITS-2 rDNA were 3.4–12.3%. Phylogenetic analysis based on sequences of ITS-2 rDNA showed that allD. dendriticumisolates in the present study were grouped with referenceD. dendriticumisolates from sheep and goats, andD. dendriticumisolates from cattle and Japanese serow were clustered in a sister clade. However, the phylogenetic tree could not reveal geographically genetic relationships ofD. dendriticumisolates in different origins and hosts. These findings provided basic information for further study of molecular epidemiology and control ofD. dendriticuminfection in Shaanxi province as well as in the world.

scholarly journals Pathogenicity and Molecular Characterization of Colletotrichum gloeosporioides Causing Anthracnose Disease in Anthurium

2019 ◽  
pp. 1-8
Author(s):  
B. Rex ◽  
J. Sheela ◽  
M. Theradimani ◽  
E. G. Ebenezar ◽  
C. Vanniarajan ◽  
...  
Keyword(s):  
Tamil Nadu ◽  
Colletotrichum Gloeosporioides ◽  
Sequence Data ◽  
Genetic Relationships ◽  
Molecular Study ◽  
Internal Transcribed Spacers ◽  
Pathogenicity Test ◽  
Species Determination ◽  
Anthracnose Disease ◽  
Cent Disease

Anthurium is an excellent cut flower crop commercially cultivated throughout the world. Anthracnose or spadix rot disease leads to massive flower loss to anthurium growing farmers. Survey was conducted for anthurium anthracnose disease during the year 2017-2018 in anthurium growing areas of Tamil Nadu, India. Colletotrichum gloeosporioides cultures (10 isolates) were isolated and pathogenicity test was proved by several artificial inoculation methods. Among this, pin prick plus spraying spore suspension method has recorded the highest per cent disease index of 64.38 on anthurium plants. Molecular analysis based on obtained sequences (MH479426) of the rDNA internal transcribed spacers (ITS1 and ITS4) resulted more than 92 per cent identical to ITS sequence of C. gloeosporioides published in GenBank database. The molecular study confirmed that anthracnose disease of anthurium is caused by C. gloeosporioides. The molecular-based clustering demonstrated the genetic relationships of the isolates and species of Colletotrichum and indicated that ITS rDNA sequence data were potentially useful in taxonomic species determination.

scholarly journals Evolution of Australasian Plantago (Plantaginaceae)

2021 ◽  
Author(s):  
◽  
Mei Lin Tay
Keyword(s):  
New Zealand ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Molecular Dating ◽  
Evolutionary Patterns ◽  
Its Phylogeny ◽  
Suitable Habitats

<p>Phylogenetic analyses using molecular data were used to investigate biogeographic and evolutionary patterns of Australasian Plantago. The Internal Transcribed Spacers (ITS) from nuclear DNA, ndhF-rpl32 from chloroplast DNA and cox1 from mitochondrial DNA were selected from a primer assay of 24 primer pairs for further phylogenetic analyses. Phylogenetic reconstruction and molecular dating of a dataset concatenated from these regions comprising 20 Australasian Plantago species rejected a hypothesis of Gondwanan vicariance for the Australasian group. The phylogeny revealed three independent dispersal events from Australia to New Zealand that match expected direction because of West Wind Drift and ocean currents. Following this study, a dataset with 150 new ITS sequences from Australasian Plantago, combined with 89 Plantago sequences from previous studies, revealed that the New Zealand species appear to have a recent origin from Australia, not long after the formation of suitable habitats formed by the uplift of the Southern Alps (about 5 mya), followed by radiation. The ITS phylogeny also suggests that a single migration event of alpine species to lowland habitats has occurred and that recurrent polyploidy appears to be an important speciation mechanism in the genus. Species boundaries between New Zealand Plantago were unclear using both morphological and molecular data, which was a result of low genetic divergences and plastic morphology. The taxonomy of several New Zealand Plantago species need revision based on the ITS phylogeny.</p>

scholarly journals A Design of Experiment (DoE) Approach to Model the Yield and Chemical Composition of Ajowan (Trachyspermum ammi L.) Essential Oil Obtained by Microwave-Assisted Extraction

2021 ◽  
Vol 14 (8) ◽  
pp. 816
Author(s):  
Eugenia Mazzara ◽  
Serena Scortichini ◽  
Dennis Fiorini ◽  
Filippo Maggi ◽  
Riccardo Petrelli ◽  
...  
Keyword(s):  
Essential Oil ◽  
Design Of Experiment ◽  
High Efficiency ◽  
Middle Eastern ◽  
Food Additives ◽  
Microwave Assisted Extraction ◽  
Experimental Conditions ◽  
Microwave Assisted ◽  
Assisted Extraction ◽  
Trachyspermum Ammi

Ajowan (Trachyspermum ammi L.) is a spice traditionally used in Middle Eastern medicine and contains a valuable essential oil (EO) exploited in different fields, such as pharmaceutics, agrochemicals and food additives. This EO is mostly characterized by the thymol to which most of its biological properties are related. Given the economic value of ajowan and its increasing demand across the globe, the extraction method used for its EO is of paramount importance in terms of quality and quantity of the final product. In the present study, we used the design of experiment (DoE) approach to study and optimize the extraction of the ajowan EO using the microwave-assisted extraction (MAE), a novel extraction technique with high efficiency, low energy consumption, short process length and low environmental impact. A two-step DoE (screening followed by surface response methodology) was used to reduce the number of experiments and to improve the cost/benefit ratio. Reliable mathematical models, relating the more relevant EO features with the extraction conditions, were obtained and used to identify the best experimental conditions able to maximize the yield and thymol concentration. The optimized MAE procedure assures an EO with a higher yield and thymol amount compared with the standard hydrodistillation procedure.

Sign in / Sign up

Export Citation Format

Share Document