Incidence and evolutionary relevance of autotriploid cytotypes in a relict member of the genus Daphne (Thymelaeaceae)
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PROVIDER: S-EPMC10601019 | biostudies-literature | 2023 Aug
REPOSITORIES: biostudies-literature
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Project description:The complete plastome sequence for the type species of Daphne, Daphne laureola, was assembled and annotated in this study. The total length of the D. laureola plastome is 171,613 bp and comprises the large single copy (LSC) spanning 85,316 bp, the small single copy (SSC) spanning 2855 bp, and two inverted repeat (IR) regions each of 41,721 bp length. The SSC contains only two genes: ndhF and rpl32. This sequence extends the list of Thymelaeaceae plastomes to be used in future systematic studies of the family and is the first European species to be sampled.
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Project description:Ten microsatellite markers were developed and characterized in a gynodioecious summer-deciduous shrub, Daphne jezoensis, to facilitate studies of the evolution of gynodioecy in the species. • We used a next-generation sequencing approach with the Ion Personal Genome Machine (PGM) system to identify and develop microsatellite markers with perfect di- and trinucleotide repeats. These markers were tested with 47 samples from two natural populations. The mean observed and expected heterozygosities per population ranged from 0.40 to 0.46 and 0.60 to 0.66, respectively. • The developed markers will be useful to study the mating system, gene flow, and population genetic structure of D. jezoensis.
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Project description:Daphne pseudomezereum A. Gray var. koreana (Nakai) Hamaya is a shrub distributed in high mountains in Japan and Korea and is used as a medicinal plant. The complete chloroplast genome of D. pseudomezereum var. koreana is 171,152 bp long with four subregions consisting of a large single-copy region (84,963 bp), a small single-copy region (41,725 bp), and a pair of inverted repeats (2739 bp). The genome includes 139 genes (93 protein-coding genes, eight rRNAs, and 38 tRNAs). Phylogenetic analyses show that D. pseudomezereum var. koreana is nested within the Daphne clade in the narrow sense and that it forms a distinct lineage.
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Project description:Daphne mucronata Royle and Thymelaea hirsuta (L.) Endl both belong to the Thymelaeaceae family. Both species are used traditionally to treat several diseases along with various daily applications by Jordanian Bedouins. Traditionally, those species are identified through personal proficiency, which could be misleading due to human errors or lack of expertise. This study aims to investigate an effective DNA barcoding method to identify and characterize Daphne mucronata Royle and Thymelaea hirsuta plant species at the molecular level. Daphne mucronata Royle and Thymelaea hirsuta were collected from the ancient city of Petra in the Southern part of Jordan. Sequences of candidate DNA barcodes were amplified (rbcL, matK, and rpoC1), sequenced, and aligned to the blastn database. Moreover, the obtained sequences were compared with available sequences of related species at the GenBank database. Our results showed that DNA barcoding successfully identifies the two plant species using any of chloroplast genes (rbcL, matK, or rpoC1). The results emphasize the ability of DNA barcoding for identifying and characterizing different plant species through the recruitment of different barcode loci in molecular identification.
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Project description:PremiseThe endangered shrub Daphne rodriguezii (Thymelaeaceae) is endemic to the Balearic island of Menorca, where fragmentation and severe population decline are ongoing threats to this taxon. We developed a set of microsatellite markers to analyze the fine-scale genetics of its few extant populations.Methods and resultsFifteen microsatellite markers were obtained through Illumina high-throughput sequencing and tested in two populations. Twelve of these loci showed no evidence of null alleles and were highly polymorphic, with a mean number of 8.3 alleles per locus. Levels of observed and expected heterozygosity ranged from 0.100 to 0.952 and from 0.095 to 0.854, respectively. Seven to nine of these loci were successfully amplified in five other Daphne species.ConclusionsThis set of markers provides a useful tool for investigating the factors driving fine-scale population structure in this threatened species, and it represents a novel genetic resource for other European Daphne species.
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Project description:Daphne giraldii Nitsche. (Thymelaeaceae) is a slow-growing shrub which has been used in Chinese folk medicine and commonly called 'Zu Shima'. In this study, we assembled the complete chloroplast (cp) genome of D. giraldii using data from high-throughput Illumina sequencing. The D. giraldii cp genome is 171,643 bp in size and includes two inverted repeat regions of 41,798 bp each, which is separated by a large single copy region of 85,171 bp and a small single copy region of 2876 bp. A total of 137 genes were predicted, including 38 tRNA, 8 rRNA, and 90 protein-coding genes. In addition, 10 PCG genes possess a single intron, 92 PCG genes no intron, 1 gene harbor two introns. Six tRNA genes harbor a single intron. Phylogenetic analysis indicated that D. giraldii is closer to Daphne kiusiana and Daphne tangutica than other taxa.
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Project description:There are abundant natural diterpenoids in the plants of the genus Daphne from the Thymelaeaceae family, featuring a 5/7/6-tricyclic ring system and usually with an orthoester group. So far, a total of 135 diterpenoids has been isolated from the species of the genus Daphne, which could be further classified into three main types according to the substitution pattern of ring A and oxygen-containing functions at ring B. A variety of studies have demonstrated that these compounds exert a wide range of bioactivities both in vitro and in vivo including anticancer, anti-inflammatory, anti-HIV, antifertility, neurotrophic, and cholesterol-lowering effects, which is reviewed herein. Meanwhile, the fascinating structure-activity relationship is also concluded in this review in the hope of providing an easy access to available information for the synthesis and optimization of efficient drugs.
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Project description:Daphne retusa Hemsl. (Thymelaeaceae) is an evergreen shrub plant. First, we characterized the complete nucleotide sequence of chloroplast (cp) genome of D. retusa. The total length of cp genome was found to be 170,553 bp, including a large single copy (LSC) region of 84,886 bp, a small single copy (SSC) region of 2,437 bp, and a pair of inverted repeats (IRs) of 41,617 bp. The cp genome of Daphne retusa Hemsl. contains 134 genes, including 90 protein-coding genes (75 PCG species), 37 transfer RNA genes (29 tRNA species), and 6 rRNA genes (3 RNA species). A total of 13 genes (trnK-UUU, trnS-CGA, atpF, rpoC1, trnL-UAA, trnC-ACA, petD, rpl16, rpl2, ndhB, trnE-UUC, ndhA, and trnA-UGC) contain a single intron, and one gene (ycf3) contains two introns. The GC content in whole cp genome, LSC region, SSC region, and IR region was 36.75%, 34.83%, 28.19%, and 38.96% respectively, like other Thymelaeaceae plants. Phylogenetic analysis suggested that D. retusa has a close relationship with congeneric Daphne tangutica.
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Project description:Daphnane-type diterpenenoids are the major biologically active constituents in the genus Daphne. We find that there are about 101 Daphnane-type diterpenes in this genus, most of those compounds show different degrees of inhibitory effect on various cancer cell. Some of them have been studied in depth and the potent molecular mechanisms might be associated with modulation of different cell-signaling pathways. In addition, some compounds of this type also can inhibit the synthesis of protein and DNA. Absolutely, the anti-tumor activity of Daphnane-type diterpenes is worthy of attention. Unfortunately, most of the current research on the activity of these compounds is focused on simple drug efficacy, and its in-depth mechanism research is far from enough. On the other point of view, there still exists wide growing space on the depth of these compounds.
| S-EPMC9476389 | biostudies-literature
Project description:The diverse members of the genus Daphne are prized for their fragrant flowers. Despite being promising ornamental plants in many countries, genetic information of Daphne is scarce. In this study, the plastomes of four species and one variety of Daphne were sequenced and analyzed. The plastomes were typical and contained a pair of inverted repeat (IR) regions that separated the large single-copy (LSC) region from the small single-copy (SSC) region. With a length ranging from 132,869 bp (D. genkwa) to 174,773 bp (D. championii), 106 to 141 genes were predicted. Comparative plastome analysis of the newly sequenced plastomes with four publicly available Daphne plastomes identified an expansion of the IRs, sequence variations, and mutational hotspots. Phylogenetic analyses indicated that the genus Daphne in its current circumscription is polyphyletic. Daphne genkwa was nested within the genus Wikstroemia, while D. championii was well resolved as sister to Edgeworthia. These findings concurred with results from our study that used nuclear ribosomal internal transcribed spacer sequence data. The conflicts on the molecular placement of D. championii and D. genkwa and the present taxonomic classification in Daphne suggest that a new intergeneric classification system of Daphneae warrants consideration.
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