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 microsatellite markers for Central American Begonia sect. Gireoudia (Begoniaceae).

ABSTRACT: UNLABELLED: PREMISE OF THE STUDY:Transcriptome sequence data were used to design microsatellite primers for two widespread Central American Begonia species, B. heracleifolia and B. nelumbiifolia, to investigate population structure and hybridization. • METHODS AND RESULTS:The transcriptome from vegetative meristem tissue from the related B. plebeja was mined for microsatellite loci, and 31 primer pairs amplified in the target species. Fifteen primer pairs were combined in two multiplex PCR reactions, which amplified an average of four alleles per locus. • CONCLUSIONS:The markers developed will be a valuable genetic resource for medium-throughput genotyping of Central American species of Begonia sect. Gireoudia. A subset of these markers have perfect sequence matches to Asian B. venusta, and are promising for studies in other Begonia sections.

SUBMITTER: Twyford AD

PROVIDER: S-EPMC4105041 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Development and characterization of microsatellite markers for Central American Begonia sect. Gireoudia (Begoniaceae).

Twyford Alex D AD Ennos Richard A RA Kidner Catherine A CA

Applications in plant sciences 20130430 5

<h4>Unlabelled</h4><h4>Premise of the study</h4>Transcriptome sequence data were used to design microsatellite primers for two widespread Central American Begonia species, B. heracleifolia and B. nelumbiifolia, to investigate population structure and hybridization. •<h4>Methods and results</h4>The transcriptome from vegetative meristem tissue from the related B. plebeja was mined for microsatellite loci, and 31 primer pairs amplified in the target species. Fifteen primer pairs were combined in t ...[more]

PMID: 25202548

Similar Datasets

Development and characterization of EST-SSR markers for Begonia luzhaiensis (Begoniaceae).

Project description:Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.804 with averages of 0.370 and 0.404, respectively. Five loci could be successfully amplified in B. leprosa. The expressed sequence tag-simple sequence repeat markers are the first specifically developed for B. luzhaiensis and the first developed in Begonia sect. Coelocentrum. These markers will be useful for future studies of the genetic structure and phylogeography of B. luzhaiensis.

| S-EPMC5435407 | biostudies-literature

Recircumscription of Begonia sect. Baryandra (Begoniaceae): evidence from molecular data.

Project description:BACKGROUND:Begonia sect. Diploclinium is a 'dust-bin' section for species retaining pleisiomorphic characters and lacking novel synapomorphic characters used to delimit other Asian sections in Begonia. Part of this large and polymorphous section is transferred to Begonia sect. Baryandra in a move towards a more natural classification for the genus. RESULTS:Phylogenetic analysis of nuclear ribosomal ITS DNA sequences show a strongly supported monophyletic group containing Philippine and Bornean species previously in Begonia sect. Diploclinium, and the type of Begonia sect. Baryandra, B. oxysperma. This clade forms the basis for the now much-expanded Begonia sect. Baryandra, which as defined here contains 49 species and has its centre of diversity in the Philippines. CONCLUSIONS:A natural classification for a much expanded Begonia sect. Baryandra has been provided. This paper highlights the feasibility of moving towards a natural classification of Asian Begonia step by step as information comes to light through building upon previous framework phylogenies with denser sampling.

| S-EPMC5432953 | biostudies-literature

<i>Begonia catbensis</i> (sect. Coelocentrum, Begoniaceae), a new species from northern Vietnam.

Project description:Begonia catbensis, a new species in Begonia sect. Coelocentrum is described and illustrated. The new species was discovered in lowland limestone hills at Cat Ba National Park and can be easily distinguished from all its congeners by having dendritic hairs on the petiole, adaxial veins and stipules, fimbriate bracts and bracteoles, dense conical bullae on the upper surface of the leaf blade, two tepals in the pistillate flowers and a glabrescent ovary with verrucose wings. Based on IUCN Criteria, the species is currently assessed as "Endangered" (D).

| S-EPMC8225592 | biostudies-literature

Development of 18 novel microsatellite primers for Begonia fimbristipula (Begoniaceae), an endangered medicinal plant in China.

Project description:Begonia fimbristipula (Begoniaceae) is a medicinal herb distributed in the Chinese provinces of Fujian, Guangdong, Guangxi, Hainan, Hunan, Jiangxi, and Zhejiang, and it is on the verge of extinction due to habitat destruction and deterioration of its ecosystem. Here we developed a set of highly polymorphic microsatellite markers for population genetic and conservation studies of this endangered medicinal plant. Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, 18 polymorphic microsatellite markers were identified within 48 individuals from two geographic locations. The observed and expected heterozygosities ranged from 0.208 to 1.000 and from 0.291 to 0.812, respectively. These microsatellite markers were cross-amplified in five related Begonia species, and six loci were successfully amplified in all species. These 18 markers will be useful for better conservation and utilization of wild resources of B. fimbristipula and other Begonia species in the future.

| S-EPMC4948904 | biostudies-literature

Characterization of the complete chloroplast genome of <i>Begonia fimbristipula</i> (Begoniaceae).

Project description:Begonia fimbristipula is a plant of perennial flowering plants in the family Begoniaceae. In this article, the complete chloroplast genome of B. fimbristipula was studied and illustrated to add more genetic information. The chloroplast genome is 169,436 bp in length as the circular, which exhibits a large single-copy region (LSC) of 77,058 bp, a small single-copy region (SSC) of 18,128 bp, and a pair of inverted repeat regions (IRs) of 37,123 bp in each. The overall nucleotide composition of chloroplast genome is: 31.8% A, 32.6% T, 18.0% C, 17.5% G, and the total GC content 35.5%. A total of 142 genes were annotated that included 91 protein-coding genes (PCGs), 43 transfer RNA (tRNAs), and 8 ribosome RNA (rRNAs). Phylogenetic relationship shows that Begonia fimbristipula is more closely related to Begonia pulchrifolia on genetic relationships using the Maximum-Likelihood (ML) method.

| S-EPMC7748561 | biostudies-literature

Chloroplast and nuclear DNA exchanges among Begonia sect. Baryandra species (Begoniaceae) from Palawan Island, Philippines, and descriptions of five new species.

Project description:The Philippine island of Palawan is highly biodiverse. During fieldwork there in 2011 & 2014 we found five unknown species in the large genus Begonia. The species are similar in their rhizomatous stems, four-tepaled flowers, inferior two- or three-locular ovaries with bilamellate placentas, and are assignable to Begonia sect. Baryandra. Our observations support the recognition of these as five new species endemic to Palawan: B. elnidoensis, B. gironellae, B. quinquealata, B. tabonensis and B. tenuibracteata which are described here. The five new species were added to phylogenies based Bayesian analysis of nrDNA (ITS) and chloroplast DNA (ndhA, ndhF-rpl32, rpl32-trnL, trnC-trnD), along with 45 other allied ingroup species. A majority of the species show incongruent positions in the two phylogenies, with evidence of prevalent chloroplast capture. Models show chloroplast capture is more likely in plant populations with high levels of inbreeding following a reduction in selfing rate after hybridisation; we suggest that this is a possible explanation for the massive amount of chloroplast exchange seen in our phylogeny, as Begonia species often exist as small isolated populations and may be prone to inbreeding depression. Our data also indicate a level of nuclear genetic exchange between species. The high prevalence of hybrid events in Begonia is potentially an important factor in driving genomic change and species evolution in this mega-diverse genus.

| S-EPMC5931476 | biostudies-literature

Three new species of Begonia (Begoniaceae) from Bahia, Brazil.

Project description:The taxonomic treatment of Begoniaceae for the state of Bahia, Brazil, led to the recognition of three new species of Begonia with narrow distributions, which are described and illustrated here: Begoniadelicata Gregório & J.A.S. Costa, sp. nov. is a herb restricted to the region of the Recôncavo; Begoniaelianeae Gregório & J.A.S. Costa, sp. nov. is a shrub endemic to the Atlantic forest of the southern part of the state; and Begoniapaganuccii Gregório & J.A.S. Costa, sp. nov. is a subshrub known only from the type material, collected in the Piedmont of Paraguaçu. Notes on morphology, comparisons with morphologically similar species, etymology, geographic distribution, habitat and phenological data for each species are also presented. Furthermore, keys are provided as an aid to separating the new species from congeneric species that occur in their surroundings. Due to the sparse knowledge of the new species, there is as yet insufficient data to accurately assess their conservation status.

| S-EPMC4329388 | biostudies-literature

<i>Begonia guangdongensis</i>, a new species of <i>Begonia</i> (Begoniaceae) from Guangdong, China.

Project description:A new species of Begonia section Coelocentrum, B. guangdongensis W.H. Tu, B.M. Wang & Y.L. Li from Guangdong Province, China, is described and illustrated here. Morphologically, the new species is most similar to B. biflora T. C. Ku and B. longistyla Y. M. Shui & W. H. Chen, but differs from B. biflora by its rugose leaves and glabrous capsules and from B. longistyla by its glabrous stipules without ciliate margin, densely hirsute-pilose leaves and obtuse apex of bracts. Additionally, it is also somewhat similar to B. chongzuoensis Yan Liu, S. M. Ku & C.-I Peng, but there are significant distinctions in their stipules, leaves and bracts. The conservation status of B. guangdongensis is assessed as Critically Endangered (CR), according to the IUCN Red List Categories and Criteria.

| S-EPMC7560510 | biostudies-literature

Microsatellite markers for hoop-petticoat daffodils (Narcissus sect. Bulbocodii; Amaryllidaceae).

Project description:Microsatellite markers were developed using hoop-petticoat daffodils (Narcissus sect. Bulbocodii; Amaryllidaceae) to aid in the taxonomic revision of the section, and to further evaluate their broad applicability for daffodil cultivar identification. Three hundred fifty-one primer pairs were developed using a commercial service. Nineteen polymorphic and repeatable markers were developed by screening 67 of these primer pairs. Of these, 11 chosen markers were used to screen 317 samples; the number of alleles per locus ranged from four to 21, and the observed heterozygosity ranged from 0.101 to 0.297. There were null genotypes in some samples for six of the markers. All the microsatellites were transferable to other Narcissus sections. The results indicate that these new markers have sufficient potential variation to be used for taxonomic revision of the genus and to distinguish many commercial daffodil cultivars.

| S-EPMC4850056 | biostudies-literature

The complete chloroplast genome sequence of <i>begonia</i> (Begoniaceae).

Project description:Begonia L. (Begoniaceae) is the sixth largest genus in the world which consists of more than 2,039 species. Many species of Begonia have highly ornamental leaves and flowers, so they are mainly used for ornamental purposes, and some species can also be used as medicines or vegetables. Begonia gulongshanensis is a newly discovered species in 2018 which occurs exclusively in Jingxi county in Southern China, however, there are few studies on the molecular biology and phylogeny of this species currently. Therefore, we report its complete chloroplast genome sequence for the first time, hoping to provide a foundation for its future phylogenetic analysis. The chloroplast genome of B. gulongshanensis was 169,153 bp in size, which contained a large single-copy region of 75,998 bp, a small single-copy region of 18,063 bp, and two inverted repeat regions of the same 37,546 bp. The total GC content was 35.51%. The genome encodes 42 transfer RNA genes, 8 ribosomal RNA genes and 90 protein-coding genes. The phylogenetic analysis indicated that the genetic relationship between B. gulongshanensis and the other three begonias was very close, but there was still certain distance.

| S-EPMC8757601 | 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