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opencc-by-4.0Jun 2021View details →

Data release: Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration

Source data used in the publication: Berger et al. (2021) - Provisional title: 'Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration'. These data were used to generate all figures used in the publication and all files are organised and labelled specifically to run with the custom code that uses these data can be found at: http://doi.org/10.5281/zenodo.4975908.  File descriptions: SOURCE DATA.zip - All source data for all figures.  Figure 1b: <ul> <li>supplementary_data_9.txt - Metadata</li> </ul> Figure 2a&b: <ul> <li>207_PCA.eigenvec - PCA eigenvectors</li> <li>207_PCA.eigenval - PCA eigenvalues</li> </ul> Figure 2c: <ul> <li>autosomes.mdist - PLINK distance matrix used to build the neighbour joining phylogeny</li> </ul> Figure 2d: <ul> <li>all.pi.pixy.schools.txt - Nucleotide diversity results for each school subpopulation.</li> </ul> Figure 2e: <ul> <li>autosomes.dxy.5kb.schools.txt - Autosomal DXY results between school subpopulations. </li> <li>autosomes.fst.5kb.schools.txt - Autosomal FST results between school subpopulations.</li> </ul> Figure 2f: <ul> <li>admixture_all.txt - ADMIXTURE results for each sample and population sizes, column 1 represents number of populations (K), columns 3-8 represent admixture values for each population. </li> </ul> Figure 3a, Supplementary figure 10a: <ul> <li>sfs.csv - Site frequency spectra (allelic proportions at each frequency bin) for each school. </li> </ul> Figure 3b: <ul> <li>TD.all.txt - Tajima's D values calculated in 5 kb windows for each school subpopulation. </li> </ul> Figure 4a, Supplementary figures 13-18:  <ul> <li>ALL.MAYUGE.IHS.ihs.out.100bins.norm.txt.zip  - Normalised iHS scores for the Mayuge district parasite populations (Selscan output).</li> </ul> Figure 4b, Supplementary figures 13-18:  <ul> <li>ALL.TORORO.IHS.ihs.out.100bins.norm.txt.zip - - Normalised iHS scores for the Tororo district parasite populations (Selscan output).</li> </ul> Figure 4c, Supplementary figures 13-18:  <ul> <li>ALL.MAYUGEvsTORORO.xpehh.xpehh.out.norm.txt.zip - - Normalised XP-EHH scores between Mayuge and Tororo parasite populations.</li> </ul> Figure 4d, Supplementary figures 13-18: <ul> <li>MAYUGE_TORORO_2000.windowed.weir.txt.zip - FST values calculated between Mayuge and Tororo populations in 2kb windows.  </li> </ul> Figure 4e, Supplementary figures 12a&c: <ul> <li>MAYUGE_PI.windowed.pi.zip - Nucleotide diversity values calculated in 2 kb windows for Mayuge populations. </li> <li>TORORO_PI.windowed.pi.zip - Nucleotide diversity values calculated in 2 kb windows for Kocoge populations (Tororo district).</li> </ul> Figure 5a: <ul> <li>all.pi.treat.fix.txt.zip - Nucleotide diversity results for each treatment subpopulation</li> </ul> Figure 5b <ul> <li>autosomes.dxy.5kb.treatment.txt -  - Autosomal DXY results between clearance phenotype subpopulations. </li> <li>autosomes.fst.5kb.treatment.txt - Autosomal FST results between clearance phenotype subpopulations. </li> </ul> Figure 5c: <ul> <li>fst.windows.2kb.treatment.txt.zip - FST values for comparisons between different treatment groups (Pre-treatment, post-treatment (good clearers), post-treatment (poor clearers))</li> </ul> Figure 5d:  <ul> <li>assoc_err_binary.txt.zip - Results of binary trait association between miracidia sampled from hosts with good clearance phenotypes (where treatment appeared to be highly effective) and miracidia isolated post-treatment from hosts with poor clearance phenotypes (where miracidia are potentially derived from parasites that survived treatment.</li> </ul> Figure 5e: <ul> <li>assoc_err_linear.txt.zip - - Results of linear regression genome-wide association study with the ERR estimates for all 198 samples, using the mean of the posterior ERR estimates from Crellen et al. (2016) as a quantitative trait.</li> </ul> Supplementary figure 1: <ul> <li>median.coverage.txt - Normalised depth of read coverage (column 4) calculated in 25 kb windows (columns 2&3) across all samples for all chromosomes (column 1).</li> </ul> Supplementary figure 2a-f:  <ul> <li>cohort.genotyped.txt.zip -  - Variant quality site values (used to inform variant site retention or removal). </li> </ul> Supplementary figure 2g: <ul> <li>hard_filtered.imiss.txt -  Per sample variant missingness (used to inform quality control).</li> </ul> Supplementary figure 2h: <ul> <li>hard_filtered_filtindv.lmiss.txt.zip - Per site missingness (used to inform quality control).</li> </ul> Supplementary figure 3a, 4a, 4b: <ul> <li>prunedData.eigenvec - PCA eigenvectors</li> <li>prunedData.eigenval - PCA eigenvalues</li> </ul> Supplementary figure 3b: <ul> <li>pruned_data.mdist.csv - Distance matrix used as the basis for the neighbour joining phylogeny.</li> </ul> Supplementary figure 5: <ul> <li>cv_scores.txt - ADMIXTURE coefficient of variation scores (column 2) for each population size (1).</li> </ul> Supplementary figure 6: <ul> <li>*_SMC_SE.csv - SMC++ results (from 25 subsampled replicates) for each school subpopulation and outgroup samples. </li> </ul> Supplementary Figure 7: <ul> <li>smcpp.csv - SMC++ results for each school subpopulation and outgroup samples. </li> </ul> Supplementary Figure 8a-d <ul> <li>pi.per_host.txt.zip - Nucleotide diversity values for each host infrapopulation. </li> </ul> Supplementary Figure 9: <ul> <li>sexing.csv - inferred sex (based on differential read coverage over pseudoautosomal and Z-specific regions of the Z chromosome). </li> </ul> Supplementary Figure 10b: <ul> <li>sfs_res.csv - residuals for the SFS analysis in 3a/10a.</li> </ul> Supplementary Figure 11: <ul> <li>MAYUGE_TAJIMA_D.Tajima.D.2kb.txt.zip - Tajima's D values calculated for the Mayuge population in 2kb windows. </li> <li>Tororo_TAJIMA_D.Tajima.D.2kb.txt.zip - Tajima's D values calculated for the Tororo population in 2kb windows. </li> </ul> Supplementary Figures 13-18: <ul> <li>genes.bed - Coordinates of gene models (S. mansoni v7 annotation).</li> <li>KOCOGE_SITE_PI.sites.pi.txt.zip - Per site nucleotide diversity values</li> <li>MAYUGE_TORORO_sites.weir.fst.txt.zip - Per site FST values between Mayuge and Tororo populations. </li> <li>coverage_5kb.windows.txt.zip - Per sample depth of read coverage in 5 kb windows. Columns 4,5,6 represent the median, mean and sstev of coverage for each 5kb window (columns 2&3) along each chromosome (column 1). </li> <li>median.sample.coverage.txt -  Median chromosomal depth of read coverage for each sample. </li> </ul> Supplementary Figure 19: <ul> <li>kocoge_median.ld.txt.zip -  - The decay of linkage disequilibrium with genomic distance between all sites within 50 kb for the Kocoge parasite samples. Chromosomes are shown in column 1, distance in column 2, median values in column 3. </li> <li>mayuge_median.ld.txt.zip - The decay of linkage disequilibrium with genomic distance between all sites within 50 kb for the Mayuge parasite samples. Chromosomes are shown in column 1, distance in column 2, median values in column 3. </li> </ul> Misc files: schools.list - List of samples and schools where they were sampled.

opencc-by-4.0Jul 2021View details →

Machine learning models, and training, validation and test datasets for: "Sequence determinants of human gene regulatory elements"

This record contains the training, test and validation datasets used to train and evaluate the machine learning models in manuscript: Sahu, Biswajyoti, et al. "Sequence determinants of human gene regulatory elements." (2021). This record contains also the final hyperparameter-optimized models for each training dataset/task combination described in the manuscript. The README-files provided with the record describe the datasets and models in more detail. The datasets deposited here are derived from the original raw data (GEO accession: GSE180158) as described in the Methods of the manuscript.

opencc-by-4.0Jul 2021View details →

Data and software associated with the paper "Bayesian Inference of Joint Coalescence Times of Sampled Sequences"

1. Data files and run logs produced for the paper "Bayesian Inference of Joint Coalescence Times of Sampled Sequences". 2. Software script versions used in the above.

dryad40/100

Simultaneous genotyping of snails and infecting trematode parasites using high-throughput amplicon sequencing.

Several methodological issues currently hamper the study of entire trematode communities within populations of their intermediate snail hosts. Here we develop a new workflow using high-throughput amplicon sequencing to simultaneously genotype snail hosts and their infecting trematode parasites. We designed primers to amplify 4 snail and 5 trematode markers in a single multiplex PCR. While also applicable to other genera, we focused on medically and economically important snail genera within the Superorder Hygrophila and targeted a broad taxonomic range of parasites within the Class Trematoda. We tested the workflow using 417 Biomphalaria glabrata specimens experimentally infected with Schistosoma rodhaini, two strains of Schistosoma mansoni, and combinations thereof. We evaluated the reliability of infection diagnostics, the robustness of the workflow, its specificity related to host and parasite identification, and the sensitivity to detect co-infections, immature infections, and changes of parasite biomass during the infection process. Finally, we investigated its applicability in wild-caught snails of other genera naturally infected with diverse trematode assemblages. After stringent quality control the workflow allows the identification of snails to species level, and of trematodes to taxonomic levels ranging from family to strain. It is sensitive to detect immature infections and changes in parasite biomass described in previous experimental studies. Co-infections were successfully identified, opening the possibility to examine parasite-parasite interactions such as interspecific competition. Altogether, these results demonstrate that our workflow provides a powerful tool to analyze the processes shaping trematode communities within natural snail populations.

opencc-zeroJul 2021View details →

Fig. 3 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data

Fig. 3. — Strict consensus of 10,000 most parsimonious trees resulting from the analysis of 58 ITS sequences; tree length = 725 steps; consistency index = 0.518; retention index = 0.734. Clades denoted by brackets are those referred to in text. Values along branches are bootstrap percentages. Placement of Polyscias elegans (discussed in text) is denoted by an asterisk. Labels for the Tieghemopanax group and other clades in "Polyscias sensu lato" follow PLUNKETT et al. (2001).

Fig. 2 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data

Fig. 2. — The single most parsimonious tree resulting from the combined analysis of ITS + trnL-trnF + 5S spacer sequences, based on the identical 24-taxon sampling as used in Fig. 1; tree length = 349 steps; consistency index = 0.663; retention index = 0.770. Values along nodes are bootstrap percentages; nodes with dashed branches have bootstraps below 70%. Identical or near identical clades (labeled A-E) from Fig. 1 are also labeled, as is the placement of Polyscias sambucifolia and P. microbotrys (asterisks), as discussed in text. Outgroups indicated by "OG."

Fig. 4 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data

Fig. 4. — Strict consensus of 156 most parsimonious trees resulting from the analysis of 40 trnL-trnF sequences; tree length = 122 steps; consistency index = 0.938; retention index = 0.972. Values along branches are bootstrap percentages. Placement of Polyscias elegans (discussed in text) is denoted by an asterisk. Labels for the Tieghemopanax group and other clades in "Polyscias sensu lato" follow PLUNKETT et al. (2001).

Fig. 5 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data

Fig. 5. — Strict consensus of 156 most parsimonious trees resulting from the analysis of 26 5S spacer sequences; tree length = 147 steps; consistency index = 0.744; retention index = 0.849. Values along branches are bootstrap percentages.

opencc-by-4.0Aug 2021View details →

Sanger sequencing traces of specific exons of the Sm.TRPM_PZQ gene from schistosome field samples

Praziquantel (PZQ) is the only drug available to treat schistosomiasis, which is caused by schistosome blood flukes. In Schistosoma mansononi, the transient receptor potential (TRP) channel Sm.TRPMPZQ is strongly suspected to be the target of PZQ. Our <a href="https://doi.org/10.1101/2021.06.09.447779">genetic analysis of S. mansoni response to PZQ</a> revealed a QTL on its chromosome 3 which contains the Sm.TRPMPZQ gene, strongly suggesting that Sm.TRPMPZQ could be responsible for PZQ resistance. Therefore, understanding the natural variation in this gene and identifying potential resistance alleles will be a valuable tool for monitoring mass treatment programs aimed at schistosomiasis elimination. We investigated our schistosome collection to examine mutations present in Sm.TRPMPZQ in natural schistosome populations. We analyzed exome sequencing data from 259 miracidia, cercariae or adult parasites from 3 African countries (Senegal, Niger, Tanzania), the Middle East (Oman) and South America (Brazil). We were able to sequence 36/41 exons of Sm.TRPMPZQ from 122/259 parasites on average (s.e. = 18.65). We identified several mutations in critical areas of the channel. However, these mutations were supported by a limited number of reads only and required confirmation by Sanger sequencing. The present dataset corresponds to the sequencing effort done on specific exons which carried the mutations to be confirmed. We generated PCR products which were sequenced on on ABI sequencer using Eurofins Genomics services. The SCF files were then analyzed using PolyPhred (see manuscript for details about PCR conditions and data analysis). The trace files are available in the traces folder. Each filename carries a barcode which corresponds to a combination of sample, exon, and primer. All the combinations and corresponding barcodes are listed in the barcode_list.tsv file. Table header details of the barcode list: <ul> <li>Sample: the name of sample. The sample coding is as follows: species.country_patientID. BR: Brazil, SN: Senegal, NE: Niger, TZ: Tanzania, OM: Oman.</li> <li>Exon: the exon targeted. The exon number corresponds to the exon number of isoform 5 and not the exon number of the gene.</li> <li>Barcode: the barcode provided by Eurofins Genomics.</li> <li>Primer: the primer used for sequencing. F: forward, R: reverse.</li> </ul>

Figures 14–19 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data

Figures 14–19. Automontage photographs of features of the Aleiodes buzurae-group. (14) Aleiodes kasenenei sp. n., habitus; (15)–(19) Aleiodes kanyawarensis sp. n., habitus, face, mesosoma, wings and metasoma, respectively.

Figure 3 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data

Figure 3. Bootstrap consensus tree from analysis of CO1 sequence data for Aleiodes reared from suspended mummies in Uganda plus another member of the A. buzurae-group and outgroups.

Figures 20–25 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data

Figures 20–25. Automontage photographs of features of Aleiodes trevelyanae sp. n. (20)–(24) Habitus, face, metasoma, mesosoma and wings of holotype; (25) metasoma of paratype.

Figures 10–13 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data

Figures 10–13. Automontage photographs of features of Aleiodes busutai sp. n., habitus, head lateral aspect, metasoma and mesosoma, respectively.

Figure 2 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data

Figure 2. Phylogram from analysis of CO1 DNA sequence data for individuals of the A. buzurae-group and related species, and also multiple representatives of four European species for comparison.

Figure 1 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data

Figure 1. Photograph of a suspended mummy showing J-shaped configuration with silk thread (arrowed) arising near larval mouth.

Figure 4 in Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data

Figure 4. Selected contiguous fragment of the CO1 gene in individuals of the Aleiodes buzurae-group from Uganda and Kenya with bold characters indicating substitutions. Asterisks show phylogenetically informative substitutions at species level; exclamation marks show apomorphies for individual species in the buzarae group and $ sites that have both unique and informative variation.

opencc-by-4.0Apr 2021View details →

Dataset for submitted manuscript "Temperatures and cooling rates recorded by the New Caledonia ophiolite: implications for cooling mechanisms in young forearc sequence"

original dataset for the manuscript "Temperatures and cooling rates recorded by the New Caledonia ophiolite: implications for cooling mechanisms in young forearc sequences" submitted to the journal "G3 Geophysics, Geochemistry, Geosystems"

opencc-by-4.0Dec 2017View details →

Figs 27–31. Palaeoplatyura johnsoni Johannsen, 1910 in Macrocera rohaceki sp. nov. and other interesting records of Keroplatidae (Diptera) from southern and central Europe, with DNA sequence data

Figs 27–31. Palaeoplatyura johnsoni Johannsen, 1910, male: 27 – wing; 28 – terminalia, ventral view; 29 – terminalia, dorsal view, tergite 9 removed; 30 – tergite 9 and cerci, external view; 31 – habitus.

opencc-by-4.0Dec 2017View details →

Figs 11–16 in Macrocera rohaceki sp. nov. and other interesting records of Keroplatidae (Diptera) from southern and central Europe, with DNA sequence data

Figs 11–16. Isoneuromyia pseudochracea (Landrock, 1925), male: 11 – wing; 12 – thorax dorsally; 13 – habitus; 14 – terminalia, ventral view; 15 – terminalia, dorsal view, tergite 9 removed; 16 – tergite 9 and cerci, external view.