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opencc-by-4.0Jan 2021View details →

NEXUS file describing the taxonomic relationships of the 466 species for which genome sequencing was underway at Tree of Life, Wellcome Sanger Institute, at 31 December 2020

This NEXUS file shows the taxonomic relationships of 466 species of eukaryote. The taxonomy derives from the NCBI TaxonomyDB. The species are those for which genome sequencing is underway at the Tree of Life programme, Wellcome Sanger Institute, as of 31st Decemnber 2020. The NEXUS file includes a figtree block generated in FigTree [<a href="https://github.com/rambaut/figtree">https://github.com/rambaut/figtree</a>] that informs display of the data as a circular tree with species coloured by taxonomic Family, and Families with more than one species represented as triangles. The figure is used in publications and presentations describing the activities of the Tree of Life programme and the projects in which Tree of Life is involved, especially the Darwin Tree of Life project [https://darwintreeoflife.org].

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Morphological and DNA sequence data generated by Sanger sequencing and target capture methods for moss plants in the genus Fissidens from herbarium specimens

Morphological evolution in mosses has long been hypothesized to accompany shifts in microhabitats and can be tested using comparative phylogenetics. These lines of inquiry have developed substantially, in part, by target capture sequencing allowing for phylogenomic scale data generated from herbarium specimens. In the present study, we test the relationship between taxonomically important morphological characters in the moss genus Fissidens, using both a 400-locus dataset generated using a target-capture approach as well as a three-locus phylogeny generated using sanger sequencing. Phylogenetic trees were generated using ASTRAL and Bayesian Inference and used to test the monophyly of subgenera/sections and provided the basis for ancestral character reconstruction and phylogenetic correlation analyses among five morphological characters as well as habitat moisture scored from literature. The characters axillary hyaline nodules, limbidium, costa, and peristome morphology as well as sexual system, minimum habitat moisture, average habitat moisture, maximum habitat moisture, and habitat moisture niche breadth each exhibit statistically significant phylogenetic signal. Significant correlations were found between the limbidium (phyllid/leaf border) and habitat moisture niche breadth, which could be interpreted as a more extensive limbidium enabling species to survive across a wider variety of habitats. Correlations were also found between costa anatomy and the limbidum of the gametophyte and sporophyte peristome morphology, as well as average habitat moisture and sexual system. Continued exploration of the relationships between morphological evolution, life history, and habitat will enable us to expand our understanding of functional morphology in mosses.

opencc-zeroJun 2022View details →

opencc-zeroJan 2024View details →

Linked collectors and determiners for: Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae).

Natural history specimen data linked to collectors and determiners held within, "Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/bfb878f3-8a74-46d3-a104-36485c32aaba">https://bionomia.net/dataset/bfb878f3-8a74-46d3-a104-36485c32aaba</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/bfb878f3-8a74-46d3-a104-36485c32aaba">https://gbif.org/dataset/bfb878f3-8a74-46d3-a104-36485c32aaba</a>. Formatted as a Frictionless Data package.

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>

Figure S1 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure S1. Map of the Gigantometra gigas mitogenome using Sanger method (GenBank accession number: MF177288). Genes in the outer circle indicate the direction of transcription of the majority strand (J-strand), and those in the inner circle indicate that of the minority strand (N-strand). The GC content, GC skew+, and GC skew- are separately shown in the circle.

Figure 6 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure 6. Two examples of the heteroplasmic sites in Sanger sequencing which correspond to the differently sequenced sites. Panels A and B indicate the sites at which the second-peak is obviously higher than the third-peak and fourth-peak, and the base state of the second-peak can be obtained by at least one result of HTS. The different fluorescence densities of base situated at np 1923 in the cox1 are shown in the panel A, and the panel B shows the nucleotides with amino acids at np 1923 in the results of Sanger and HTS methods. The nucleotides are C in the results of HTS sequencing, while the corresponding nucleotides are T in the results of Sanger method in both positions, and the different nucleotides lead not to the amino acids changed. Panels C and D indicate the site at the unobvious second-peak, which is slightly higher than the third-peak and fourth-peak, and the base state of the second-peak can also be obtained by at least one result of HTS. Panel C shows the unobvious second-peak at np 7125, and the nucleotide and amino acid of the site in the results of Sanger and HTS methods are shown in panel D. The amino acids are listed using single-letter amino acid abbreviations.

Figure 4. Intraspecific pairwise K2P in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure 4. Intraspecific pairwise K2P distance of G. gigas based on barcode fragment size of cox1 (Sanger). The red boxplot shows the genetic distances of individuals in all three collecting sites, and the boxplots (blue, green, and yellow) separately show the distances of individuals within each place (HNYG, HNDL, and VIET). The pink boxplot shows the distances of the corresponding cox1 sequences obtained by the two sequencing methods. Abbreviation: HNYG—Yinggeling Nature Reserve, Hainan; HNDL— Diaoluoshan Nature Reserve, Hainan; VIET—northern Vietnam.

Figure S5 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure S5. The coverage of short fragments at each position in the assembly results of HTS. The three results of HTS method were separately used as reference sequences to be mapped back onto the corresponding HTS scaffolds, and the mitochondrial genes were shown below the corresponding coverage. The scale bar had an indicator at the mean coverage level and the coverage for each nucleotide position was indicated by the height of the blue line.

Figure 3 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure 3. The different nucleotides in the ITS-1 and ITS-2 regions are shown. The result shows the different nucleotides at nucleotide position np 1897 (G nucleotide and T nucleotide) and np 2790 (C nucleotide and T nucleotide) obtained by Sanger and HTS methods.

Figure 1. Gigantometra gigas. A. Female, dorsal view. B. Male, dorsal view. C in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods

Figure 1. Gigantometra gigas. A. Female, dorsal view. B. Male, dorsal view. C. The narrow distribution of G. gigas.

publicJun 2022View details →

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Morphological and DNA sequence data generated by Sanger sequencing and target capture methods for moss plants in the genus Fissidens from herbarium specimens

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opencc-zeroMar 2024View details →

Data from: Genomic footprint of cladogenesis revealed through RADseq and Sanger sequencing demonstrates congruent patterns in the velvet worm Peripatopsis sedgwicki species complex (Onychophora: Peripatopsidae)

In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1259 - 11,468 SNPs, in order to assess the species diversity and phylogeographic of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, statistically well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY, and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq and COI data suggests that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.

opencc-by-4.0Mar 2024View details →

UnCoVar: Benchmarking dataset for SARS-CoV-2 sequence processing software pipelines, Sanger sequences

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opencc-zeroApr 2022View details →

Rare and widespread: Integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma

Premise Genera that are widespread but have a geographically discontinuous distribution and are represented by few species are intriguing. Did they achieve their disjunct distribution recently, or is it ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale floristic pattern in which closely related species appear co-distributed in isolated regions over the edges of Africa and nearby archipelagos. Genus Camptoloma (Scrophulariaceae) is the most notable example, comprising three species isolated from each other at the ends of the African continent: C. canariense in the west, endemic to the Canary Islands; C. lyperiiflorum in the east, endemic to the Horn of Africa - Southern Arabia; and C. rotundifolia, restricted to Southern Africa. Methods Here, we employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of Camptoloma within Scrophulariaceae, using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian MCMC approaches. Population history was estimated with phylogeographic structured coalescent methods. Key Results Our results support C. rotundifolia as sister to the disjunct clade formed by C. canariense and C. lyperiiflorum. Stem divergence was dated in the Late Miocene, while the origin of extant diversification within the genus was inferred as Early Pliocene. Conclusions We show that the current disjunct distribution of Camptoloma across Africa was likely the result of fragmentation and extinction/population bottlenecking events associated to historical aridification cycles, consistent with the "climatic refugia" hypothesis.

opencc-by-4.0Jun 2022View details →

Supplementary material (Sanger sequencing photo) of the case of THRB mosaicism presented in Clinically Symptomatic Resistance to Thyroid Hormone β Syndrome Because of THRB Gene Mosaicism of Donnars et al. (https://doi.org/10.1210/clinem/dgac347)

Supplementary material (Sanger photo) of the case of THRB mosaicism presented in "Clinically Symptomatic Resistance to Thyroid Hormone β Syndrome Because of THRB Gene Mosaicism", by Donnars et al. (https://doi.org/10.1210/clinem/dgac347)

opencc-zeroJun 2022View details →

Data for a preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): exploring the combination of targeted enrichment data and legacy Sanger sequence data

The purpose of this study is to provide a proof-of-concept that the use of molecular data, particularly targeted enrichment data, and statistically supported methods of analysis can result in the construction of a stable phylogenetic framework for the microcaddisflies (Trichoptera: Hydroptilidae). Here, we use a combination of targeted enrichment data for ca. 300 nuclear protein-coding genes and legacy (Sanger-based) sequence data for the mitochondrial COI gene and partial sequence from the 28S rRNA gene.

opencc-zeroOct 2022View details →

Raw Sanger sequences of the tyr fragment from crispant and control zebrafish embryos

Thanks to the amenability to genetic modifications, the minimal or non-invasive phenotyping possibilities in early embryos and larvae and the presence of a high percentage of genes orthologous to humans, zebrafish is a successful alternative vertebrate to validate new disease genes and variants and to study mechanisms underlying human diseases. We developed an optimized method allowing early and gentle genotype detection to reduce further possible suffering associated with the generation of genetically modified zebrafish and valid to strategize the employment of "surplus" animals (e.g., those needed solely for line generation or without the desired genotype). The method is based on minimally-invasive tissue (fin) scratching (FS) to obtain genomic DNA material and perform genotyping in early zebrafish embryos. We showcase the method's usefulness for various genotyping needs, including screening both F0 and stable CRISPR/Cas9 lines and obtaining genomic material compatible with Sanger sequencing. Here we provide the raw sequences obtained from FS-derived genomic DNA of single mutant F0 embryos carrying mutations in the tyr gene generated with Base editor (BE) CRISPR/Cas9 technology. We compared the sequencing outcome of FS- vs whole embryos (WE)-based genomic DNA preparation (the WE sequencing results are also provided here). Sequences show the successful C>T (G>A) conversion generating crispant tyr mutants that FS-derived genomic DNA can capture. The resulting dataset demonstrates the compatibility of the method developed with sequencing-based genotyping of early crispant embryos.

opencc-by-4.0Aug 2019View details →

Sanger sequencing of F1 mice from Y647S founder

Sanger sequencing from genomic DNA from two F1 pups of WTB6M crossed to founder 258F3 Demonstrates germline transmission of mutant allele 7 heterozygotes and 7 wildtype littermates will be shipped from NIH to U of T in September

opencc-by-4.0Oct 2024View details →

Sanger sequencing traces experimental evolution rVSV-SADS

A recombinant vesicular stomatitis virus (VSV) expressing the spike glycoprotein of swine accute diarrhea syndrome virus (SADS) (rVSV-SADS) was serially passaged in three human cell lines (Huh-7, H23, OVCAR-8). The wild-type (WT), initial virus (P0) and final viruses at passage 10 (P10) were sequenced using Sanger sequencing. The seuquence traces are attached.