A novel methodology for large-scale phylogeny partition.
Ontology highlight
ABSTRACT:
SUBMITTER: Prosperi MC
PROVIDER: S-EPMC6045912 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundThe subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. However, the phylogenetic relationships based on large-scale chloroplast genomes (CpGenomes) were elusive. Moreover, most of the chloroplast DNA sequencing methods cannot meet the requirements of large-scale CpGenome sequencing, which greatly limits and impedes the in-depth research of plant genetics and evolution.ResultsTo develop a set of bamboo probes, we used 99 high-quality CpGenomes with 6 bamboo CpGenomes as representative species for the probe design, and assembled 15?M unique sequences as the final pan-chloroplast genome. A total of 180,519 probes for chloroplast DNA fragments were designed and synthesized by a novel hybridization-based targeted enrichment approach. Another 468 CpGenomes were selected as test data to verify the quality of the newly synthesized probes and the efficiency of the probes for chloroplast capture. We then successfully applied the probes to synthesize, enrich, and assemble 358 non-redundant CpGenomes of woody bamboo in China. Evaluation analysis showed the probes may be applicable to chloroplasts in Magnoliales, Pinales, Poales et al. Moreover, we reconstructed a phylogenetic tree of 412 bamboos (358 in-house and 54 published), supporting a non-monophyletic lineage of the genus Phyllostachys. Additionally, we shared our data by uploading a dataset of bamboo CpGenome into CNGB ( https://db.cngb.org/search/project/CNP0000502/ ) to enrich resources and promote the development of bamboo phylogenetics.ConclusionsThe development of the CpGenome enrichment pipeline and its performance on bamboos recommended an inexpensive, high-throughput, time-saving and efficient CpGenome sequencing strategy, which can be applied to facilitate the phylogenetics analysis of most green plants.
| S-EPMC7863319 | biostudies-literature
Project description:ImportanceNearly half of children suffering vision impairment reside in China with myopia accounting for the vast majority.BackgroundTo describe the design and methodology of the Shanghai Child and Adolescent Large-scale Eye Study (SCALE).DesignThe SCALE was a city wide, school-based, prospective survey.ParticipantsChildren and adolescents aged 4-14 years from kindergarten (middle and senior), primary schools and junior high schools of all 17 districts and counties of the city of Shanghai, China were examined in 2012-2013.MethodsEach enrolled child underwent vision assessment (distance visual acuity; uncorrected and with corrective device if worn) and their parent/carer completed a questionnaire designed to elicit risk factors associated with myopia. Additionally, non-cycloplegic autorefraction and ocular axial length was measured in a subset of the larger sample.Main outcome measuresPrevalence and the associated factors of vision impairment, myopia and high myopia in Shanghai.ResultsIn 2012-2013, a total of 910 245 of the eligible 1 196 763 children and adolescents identified from census (76%, mean age 9.0 ± 2.7 years [4-14 years]) were enrolled with visual acuity screened in the city of Shanghai. Of these, 610 952 children (67% of the entire sample) underwent non-cycloplegic autorefraction and 219 188 (24% of the entire sample) had both non-cycloplegic autorefraction and axial length measurements.Conclusions and relevanceThe study results will provide insights on the burden of vision impairment, myopia and high myopia in children and adolescents in a metropolitan area of China, and contribute to the policies and strategies to address and limit the burden.
| S-EPMC6032906 | biostudies-literature
Project description:BackgroundFerns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial.ResultsWith the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata.ConclusionsOur result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants.
| S-EPMC5795342 | biostudies-literature
Project description:Oceanic dispersal has emerged as an important factor contributing to biogeographic patterns in numerous taxa. Chameleons are a clear example of this, as they are primarily found in Africa and Madagascar, but the age of the family is post-Gondwanan break-up. A Malagasy origin for the family has been suggested, yet this hypothesis has not been tested using modern biogeographic methods with a dated phylogeny. To examine competing hypotheses of African and Malagasy origins, we generated a dated phylogeny using between six and 13 genetic markers, for up to 174 taxa representing greater than 90 per cent of all named species. Using three different ancestral-state reconstruction methods (Bayesian and likelihood approaches), we show that the family most probably originated in Africa, with two separate oceanic dispersals to Madagascar during the Palaeocene and the Oligocene, when prevailing oceanic currents would have favoured eastward dispersal. Diversification of genus-level clades took place in the Eocene, and species-level diversification occurred primarily in the Oligocene. Plio-Pleistocene speciation is rare, resulting in a phylogeny dominated by palaeo-endemic species. We suggest that contraction and fragmentation of the Pan-African forest coupled to an increase in open habitats (savannah, grassland, heathland), since the Oligocene played a key role in diversification of this group through vicariance.
| S-EPMC3619509 | biostudies-literature
Project description:Despite the steadily decreasing costs of genome sequencing, prioritizing organisms for sequencing remains important in large-scale projects. Phylogeny-based selection is of interest to identify those organisms whose genomes can be expected to differ most from those that have already been sequenced. Here, we describe a method that infers a phylogenetic scoring independent of which set of organisms has previously been targeted, which is computationally simple and easy to apply in practice. The scoring itself, as well as pre- and post-processing of the data, is illustrated using two real-world examples in which the method has already been applied for selecting targets for genome sequencing. These projects are the JGI CSP Genomic Encyclopedia of Bacteria and Archaea phase I, targeting 1,000 type strains, and, on a smaller-scale, the phylogenomics of the Roseobacter clade. Potential artifacts of the method are discussed and compared to a selection approach based on the taxonomic classification.
| S-EPMC3746418 | biostudies-literature
Project description:Analyses of 15,314 electron velocity distribution functions (VDFs) within ±2 hr of 52 interplanetary (IP) shocks observed by the Wind spacecraft near 1 au are introduced. The electron VDFs are fit to the sum of three model functions for the cold dense core, hot tenuous halo, and field-aligned beam/strahl component. The best results were found by modeling the core as either a bi-kappa or a symmetric (or asymmetric) bi-self-similar VDF, while both the halo and beam/strahl components were best fit to bi-kappa VDF. This is the first statistical study to show that the core electron distribution is better fit to a self-similar VDF than a bi-Maxwellian under all conditions. The self-similar distribution deviation from a Maxwellian is a measure of inelasticity in particle scattering from waves and/or turbulence. The ranges of values defined by the lower and upper quartiles for the kappa exponents are κec ~ 5.40-10.2 for the core, κeh ~ 3.58-5.34 for the halo, and κeb ~ 3.40-5.16 for the beam/strahl. The lower-to-upper quartile range of symmetric bi-self-similar core exponents is sec ~ 2.00-2.04, and those of asymmetric bi-self-similar core exponents are pec ~ 2.20-4.00 for the parallel exponent and qec ~ 2.00-2.46 for the perpendicular exponent. The nuanced details of the fit procedure and description of resulting data product are also presented. The statistics and detailed analysis of the results are presented in Paper II and Paper III of this three-part study.
| S-EPMC6894189 | biostudies-literature
Project description:Large-scale analysis of novel cellular microbes
| PRJEB50943 | ENA
Project description:Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology.
| S-EPMC6987248 | biostudies-literature
Project description:Statistical methods for phylogeny estimation, especially maximum likelihood (ML), offer high accuracy with excellent theoretical properties. However, RAxML, the current leading method for large-scale ML estimation, can require weeks or longer when used on datasets with thousands of molecular sequences. Faster methods for ML estimation, among them FastTree, have also been developed, but their relative performance to RAxML is not yet fully understood. In this study, we explore the performance with respect to ML score, running time, and topological accuracy, of FastTree and RAxML on thousands of alignments (based on both simulated and biological nucleotide datasets) with up to 27,634 sequences. We find that when RAxML and FastTree are constrained to the same running time, FastTree produces topologically much more accurate trees in almost all cases. We also find that when RAxML is allowed to run to completion, it provides an advantage over FastTree in terms of the ML score, but does not produce substantially more accurate tree topologies. Interestingly, the relative accuracy of trees computed using FastTree and RAxML depends in part on the accuracy of the sequence alignment and dataset size, so that FastTree can be more accurate than RAxML on large datasets with relatively inaccurate alignments. Finally, the running times of RAxML and FastTree are dramatically different, so that when run to completion, RAxML can take several orders of magnitude longer than FastTree to complete. Thus, our study shows that very large phylogenies can be estimated very quickly using FastTree, with little (and in some cases no) degradation in tree accuracy, as compared to RAxML.
| S-EPMC3221724 | biostudies-literature
Project description:Recently, a different class of collagen-like molecules has been identified in numerous bacteria. Initial studies have shown that these collagens are readily produced in Escherichia coli and they have been isolated and purified by various small-scale chromatography approaches. These collagens are non-cytotoxic, are non-immunogenic, and can be produced in much higher yields than mammalian collagens, making them potential new collagens for biomedical materials. One of the major drawbacks with large-scale fermentation of collagens has been appropriate scalable down-stream processing technologies. Like other collagens, the triple helical domains of bacterial collagens are particularly resistant to proteolysis. The present study describes the development and optimization of a simple, scalable procedure using a combination of acid precipitation of the E. coli host proteins, followed by proteolysis of residual host proteins to produce purified collagens in large scale without the use of chromatographic methods.
| S-EPMC3968793 | biostudies-literature