Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development and characterization of 15 microsatellite markers for Cephalotaxus fortunei (Cephalotaxaceae).

ABSTRACT: To survey population variation and the adaptive evolution of Cephalotaxus fortunei (Cephalotaxaceae), an endemic and endangered conifer in China, microsatellite markers were developed and characterized for this species. Based on the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, 15 microsatellite markers were developed for C. fortunei, 13 of which were polymorphic within a sample of 75 individuals representing five natural populations. The number of alleles per locus ranged from one to seven. The expected and observed heterozygosities were 0.108-0.738 and 0.000-1.000, respectively. Ten polymorphic loci were also successfully amplified in C. oliveri. These polymorphic loci provide a valuable tool for population genetic analysis of C. fortunei, which will contribute to its management and conservation.

SUBMITTER: Wang C

PROVIDER: S-EPMC4873268 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Development and characterization of 15 microsatellite markers for Cephalotaxus fortunei (Cephalotaxaceae).

Wang Chunbo C Guo Zhiyou Z Huang Xilian X Huang Lu L

Applications in plant sciences 20160516 5

<h4>Premise of the study</h4>To survey population variation and the adaptive evolution of Cephalotaxus fortunei (Cephalotaxaceae), an endemic and endangered conifer in China, microsatellite markers were developed and characterized for this species.<h4>Methods and results</h4>Based on the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, 15 microsatellite markers were developed for C. fortunei, 13 of which were polymorphic within a sample of 75 individuals representing fiv ...[more]

PMID: 27213121

Similar Datasets

Characterization of 15 polymorphic microsatellite loci for Cephalotaxus oliveri (Cephalotaxaceae), a conifer of medicinal importance.

Project description:Cephalotaxus oliveri is a scarce medicinal conifer endemic to the south central region of China and Vietnam. A small fragmented population presently exists due to anthropogenic disturbance. C. oliveri has been used for its alkaloids harringtonine and homoharringtonine, which are effective against leucocythemia and lymphadenosarcoma. Monoecious plants have been detected in nature, although they were understood to be dioecious. In order to study the mating system, population genetics and the genetic effects of habitat fragmentation on C. oliveri, 15 polymorphic and 12 monomorphic microsatellite loci were developed for C. oliveri by using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol. The polymorphisms were assessed in 96 individuals from three natural populations (32 individuals per population). The number of alleles per locus ranged from two to 33, the observed and expected heterozygosity per locus ranged from 0.000 to 1.000 and from 0.000 to 0.923, respectively. These loci would facilitate a comprehensive understanding of the genetic dynamics on C. oliveri, which will be useful for establishing effective conservation strategies for this species.

| S-EPMC3472736 | biostudies-literature

Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera.

Project description:Background and aimsCephalotaxus is a paleo-endemic genus in East Asia that consists of about 7-9 conifer species. Despite its great economic and ecological importance, the relationships between Cephalotaxus and related genera, as well as the interspecific relationships within Cephalotaxus, have long been controversial, resulting in contrasting taxonomic proposals in delimitation of Cephalotaxaceae and Taxaceae. Based on plastome data, this study aims to reconstruct a robust phylogeny to infer the systematic placement and the evolutionary history of Cephalotaxus.MethodsA total of 11 plastomes, representing all species currently recognized in Cephalotaxus and two Torreya species, were sequenced and assembled. Combining these with previously published plastomes, we reconstructed a phylogeny of Cephalotaxaceae and Taxaceae with nearly full taxonomic sampling. Under a phylogenetic framework and molecular dating, the diversification history of Cephalotaxus and allied genera was explored.Key resultsPhylogenetic analyses of 81 plastid protein-coding genes recovered robust relationships between Cephalotaxus and related genera, as well as providing a well-supported resolution of interspecific relationships within Cephalotaxus, Taxus, Torreya and Amentotaxus. Divergence time estimation indicated that most extant species of these genera are relatively young, although fossil and other molecular evidence consistently show that these genera are ancient plant lineages.ConclusionsOur results justify the taxonomic proposal that recognizes Cephalotaxaceae as a monotypic family, and contribute to a clear-cut delineation between Cephalotaxaceae and Taxaceae. Given that extant species of Cephalotaxus are derived from recent divergence events associated with the establishment of monsoonal climates in East Asia and Pleistocene climatic fluctuations, they are not evolutionary relics.

| S-EPMC8052924 | biostudies-literature

Development of 15 polymorphic microsatellite markers for Ficus virens (Moraceae).

Project description:Ficus virens (Moraceae) is distributed widely in South and Southeast Asia, Melanesia, and northern Australia, and it is also cultivated outside its original northern range limit in southwestern China. Therefore, the species is well suited to explore the mechanism of range limits of Ficus species. However, little is known about its genetic background. Fifteen polymorphic microsatellite markers were developed using the biotin-streptavidin capture method. Polymorphism was tested in 85 F. virens individuals sampled from three populations. The number of alleles ranged from three to 17. The observed and expected heterozygosity of each population varied from 0.0667 to 0.9286 and 0.0650 to 0.8890, respectively. Cross-species amplification was also carried out in eight other Ficus species. These 15 markers will be valuable for studying the genetic variation and population structure of F. virens and related Ficus species.

| S-EPMC5231912 | biostudies-literature

The complete chloroplast genome of the endangered species <i>Cephalotaxus hainanensis</i> (Cephalotaxaceae).

Project description:Cephalotaxus hainanensis is an endangered tree endemic to China with high medicinal values. In this study, the complete chloroplast genome of C. hainanensis was de novo assembled using Illumina high-throughput sequencing technology. The whole chloroplast genome was 136,877 bp long with an asymmetric base composition (32.6% A, 17.6% C, 17.4% G and 32.4% T). The genome annotation predicted a total of 114 genes, including 82 protein-coding genes, 28 tRNA genes, and four rRNA genes. The neighbour-joining phylogenetic analysis based on 41 complete chloroplast genome sequences showed that C. hainanensis was more closely related to the congeneric C. sinensis. The assembled chloroplast genome of C. hainanensis will provide useful genomic data both for the phylogenetic research of Cephalotaxus and the conservation of this endangered species.

| S-EPMC7800532 | biostudies-literature

Cephalotaxus fortunei

Project description:Cephalotaxus fortunei overview

| PRJNA747609 | ENA

Five New Alkaloids from Cephalotaxus lanceolata and C. fortunei var. alpina.

Project description:Five new alkaloids (1-5) were isolated from the leaves and twigs of Cephalotaxus lanceolata and C. fortunei var. alpina along with 24 known alkaloids. The new structures were elucidated based on spectroscopic data including 1D and 2D NMR, FTIR, UV and MS. These new alkaloids showed no cytotoxicity to HeLa, SGC-7901 gastric cancer, and A-549 lung cancer cell lines.

| S-EPMC5385657 | biostudies-literature

Cytochalasins from Xylaria sp. CFL5, an Endophytic Fungus of Cephalotaxus fortunei.

Project description:Three previously undescribed cytochalasins, named xylariasins A‒C (1‒3), together with six known ones (4‒9) were isolated from Xylaria sp. CFL5, an endophytic fungus of Cephalotaxus fortunei. The chemical structures of all new compounds were elucidated on the basis of extensive spectroscopic data analyses and electronic circular dichroism calculation, as well as optical rotation calculation. Biological activities of compounds 1, 4‒9 were evaluated, including cytotoxic, LAG3/MHC II binding inhibition and LAG3/FGL1 binding inhibition activities. Compounds 6 and 9 possessed cytotoxicity against AGS cells at 5 μM, with inhibition rates of 94% and 64%, respectively. In addition, all tested isolates, except compound 6, exhibited obvious inhibitory activity against the interaction of both LAG3/MHC II and LAG3/FGL1. Compounds 1, 5, 7, and 8 inhibited LAG3/MHC II with IC50 values ranging from 2.37 to 4.74 μM. Meanwhile, the IC50 values of compounds 1, 7, and 8 against LAG3/FGL1 were 11.78, 4.39, and 7.45 μM, respectively.

| S-EPMC7933320 | biostudies-literature

Development and characterization of microsatellite markers for Melastoma dodecandrum (Melastomataceae).

Project description:Microsatellite markers were developed for Melastoma dodecandrum to investigate the genetic diversity of this species and to detect hybridization and introgression in Melastoma. • Fourteen microsatellite loci were characterized by screening primers developed using two simple sequence repeat (SSR)-enriched libraries. Based on the genotyping of two natural populations, 13 loci were polymorphic and the number of alleles per locus ranged from two to 15. The observed and expected heterozygosities for the 13 loci ranged from 0.235 to 0.941 and 0.219 to 0.922, respectively. Cross-species amplification was successful for all 14 loci in each of two congeneric species, M. candidum and M. sanguineum. • These polymorphic SSR markers could be used as multilocus molecular makers to study the population genetics of M. dodecandrum, as well as hybridization and introgression among Melastoma species.

| S-EPMC4105283 | biostudies-literature

Development and characterization of microsatellite markers for Veratrum maackii (Melanthiaceae).

Project description:Microsatellite markers were developed in Veratrum maackii (Melanthiaceae) to assess the pattern of population genetic structures across the species' distribution. Ten polymorphic loci were isolated from V. maackii using 454 shotgun pyrosequencing and the biotin capture method. The number of alleles per locus ranged from three to 19. The observed heterozygosity and expected heterozygosity ranged from 0.143 to 0.929 and 0.269 to 0.904, respectively. These newly developed microsatellite markers are useful for assessing the genetic diversity, population structure, and demographic history of V. maackii across its distribution range.

| S-EPMC4467762 | biostudies-literature

Development and characterization of microsatellite markers for Piptadenia gonoacantha (Fabaceae).

Project description:• Microsatellite primers were designed for Piptadenia gonoacantha (Fabaceae) and characterized to estimate genetic diversity parameters. The species is a native tree from the Atlantic Forest biome commonly used in forest restoration; it has medicinal potential and the wood is economically useful. • Twenty-eight microsatellite loci were identified from an enriched genomic library. Fifteen loci resulted in successful amplifications and were characterized in a natural population of 94 individuals. Twelve loci were polymorphic, with allele numbers ranging from three to 15 per locus, and expected and observed heterozygosities ranging from 0.2142 to 0.8325 and 0.190 to 0.769, respectively. • The developed markers will be used in further studies of population genetics of P. gonoacantha, aimed at conservation and management of the species in natural populations and in forest restoration projects.

| S-EPMC4332145 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data