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Data from: Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing
Background: Lactobacillus represents a large genus with different implications for the human host. Specific lactobacilli are considered to maintain vaginal health and to protect from urogenital infection. The presence of Lactobacillus species in carious lesions on the other hand is associated with progressive caries. Despite their clinical significance, species-level identification of lactobacilli still poses difficulties and mostly involves a combination of different phenotypic and genotypic methods. This study evaluated rapid MALDI-TOF MS analysis of vaginal and oral Lactobacillus isolates in comparison to 16S rDNA analysis. Results: Both methods were used to analyze 77 vaginal and 21 oral Lactobacillus isolates. The concordance of both methods was at 96% with five samples discordantly identified. Fifteen different Lactobacillus species were found in the vaginal samples, primarily L. iners, L. crispatus, L. jensenii and L. gasseri. In the oral samples 11 different species were identified, mostly L. salivarius, L. gasseri, L. rhamnosus and L. paracasei. Overall, the species found belonged to six different phylogenetic groups. For several samples, MALDI-TOF MS analysis only yielded scores indicating genus-level identification. However, in most cases the species found agreed with the 16S rDNA analysis result. Conclusion: MALDI-TOF MS analysis proved to be a reliable and fast tool to identify lactobacilli to the species level. Even though some results were ambiguous while 16S rDNA sequencing yielded confident species identification, accuracy can be improved by extending reference databases. Thus, mass spectra analysis provides a suitable method to facilitate monitoring clinically relevant Lactobacillus species.
Data from: Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence
Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), thus contributing to the evolution of endogenous genetic barriers and eventually cause population divergence. We investigated differential TE abundance among conspecific populations of the non-biting midge Chironomus riparius and evaluated their potential role in causing endogenous genetic incompatibilities between these populations. We focussed on a Chironomus-specific TE, the minisatellite-like Cla-element, whose activity is associated with speciation in the genus. Using a newly generated and annotated draft genome for a genomic study with five natural C. riparius populations, we found highly population-specific TE insertion patterns with many private insertions. A significant correlation of the pairwise FST estimated from genome-wide single nucleotide polymorphisms (SNPs) and the FST estimated from TEs, is consistent with drift as the major force driving TE population differentiation. However, the significantly higher Cla-element FST level due to a high proportion of differentially fixed Cla-element insertions also indicates selection against segregating (i.e. heterozygous) insertions. With reciprocal crossing experiments and fluorescent in-situ hybridisation of Cla-elements to polytene chromosomes, we documented phenotypic effects on female fertility and chromosomal mispairings. We propose that the inferred negative selection on heterozygous Cla-element insertions may cause endogenous genetic barriers and therefore acts as DMI among C. riparius populations. The intrinsic genomic turnover exerted by TEs may thus have a direct impact on population divergence that is operationally different from drift and local adaptation.
Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA
Over the last decade, protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been widely developed. Their use is however limited to DNA of relatively high molecular weight. During the last year, several methods exploiting hybridization capture using probes based on RAD-sequencing loci have circumvented this limitation and opened avenues to the study of samples characterized by degraded DNA, such as historical specimens. Here, we present a major update to those methods, namely Hybridization capture from RAD-derived probes obtained from a reduced eXome template (hyRAD-X), a technique applying RAD-sequencing to messenger RNA from one or few fresh specimens to elaborate bench-top produced probes, i.e., a reduced representation of the exome, further used to capture homologous DNA from a samples set. In contrast to previous hybridization-capture methods, the reference catalog on which reads are aligned does not rely on de novo assembly of anonymous RAD-sequencing loci, but on an assembled transcriptome obtained from RNAseq data, thus increasing the accuracy of loci definition and Single-Nucleotide-Polmorphisms (SNP) call, and targeting, specifically, expressed genes. Finally, the capture step of hyRAD-X relies on RNA probes, increasing stringency of hybridization, making it well suited for low-content DNA samples. As a proof of concept, we applied hyRAD-X to subfossil needles from the coniferous tree Abies alba, collected in lake sediments (Origlio, Switzerland) and dating back from 7200-5800 years before present (BP). More specifically we investigated genetic variation before, during, and after an anthropogenic perturbation that caused an abrupt decrease in Abies alba population size, 6500-6200 years BP. HyRAD-X produced a matrix encompassing 524 exome-derived SNPs. Despite a lower observed heterozygosity was observed during the 6.500-6.200 years BP time slice, genetic composition was nearly identical before and after the perturbation, indicating that re-expansion of the population after the decline was driven by autochthonous specimens. To the best of our knowledge, this is the first time a population genomic study incorporating ancient DNA samples of tree subfossils is conducted at a moderate cost using reproducible exome-reduced complexity.
Data from: Whole genome sequencing shows sleeping sickness relapse is due to parasite regrowth and not reinfection
The trypanosome Trypanosoma brucei gambiense (Tbg) is a cause of human African trypanosomiasis (HAT) endemic to many parts of sub-Saharan Africa. The disease is almost invariably fatal if untreated and there is no vaccine, which makes monitoring and managing drug resistance highly relevant. A recent study of HAT cases from the Democratic Republic of the Congo reported a high incidence of relapses in patients treated with melarsoprol. Of the 19 Tbg strains isolated from patients enrolled in this study, four pairs were obtained from the same patient before treatment and after relapse. We used whole genome sequencing to investigate whether these patients were infected with a new strain, or if the original strain had regrown to pathogenic levels. Clustering analysis of 5938 single nucleotide polymorphisms supports the hypothesis of regrowth of the original strain, as we found that strains isolated before and after treatment from the same patient were more similar to each other than to other isolates. We also identified 23 novel genes that could affect melarsoprol sensitivity, representing a promising new set of targets for future functional studies. This work exemplifies the utility of using evolutionary approaches to provide novel insights and tools for disease control.
Sample data for sequencing reads alignment
<p>These data are used for learning sequencing reads alignment and cluster usage</p>
Data from: Genotyping-by-sequencing reveals genomic homogeneity among overwintering Pacific Dunlin (Calidris alpina pacifica) aggregations along the Pacific coast of North America
Information on how migratory populations are genetically structured during the overwintering season of the annual cycle can improve our understanding of the strength of migratory connectivity and help identify populations as units for management. Here, we use a genotype-by-sequencing approach to investigate whether population genetic structure exists among overwintering aggregations of the Pacific Dunlin subspecies (Calidris alpina pacifica) sampled at two spatial scales (i.e. within and among overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses of 874 single nucleotide polymorphisms across 80 sampled individuals revealed no evidence for genetic differentiation among aggregations overwintering at three locations within the Fraser River Estuary (FRE) of British Columbia. Similarly, comparisons of aggregations in the FRE and those overwintering in southern sites in California and Mexico indicated no genetic segregation between northern and southern overwintering areas. These results suggest that Pacific Dunlin residing within the FRE, Sacramento Valley (California) and Guerrero Negro (Mexico) are genetically homogeneous, with no evident genetic structure between sampled sites or regions across the overwintering range. Despite no evidence for differentiation among aggregations, we identified a significant effect of geographical distance between sites on the distribution of individual genotypes in a redundancy analysis; however, a small proportion of the total genotypic variance (R2 = 0.036, P = 0.011) was explained by the combined effect of latitude and longitude, suggesting weak genomic patterns of isolation-by-distance that are consistent with chain-like migratory connectivity between breeding and overwintering areas. Our study represents the first genome-scale investigation of population structure for a Dunlin subspecies and provides essential baseline estimates of genomic diversity and differentiation within the Pacific Dunlin.
Data from: Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing
Genetic variation is of key importance for a species' evolutionary potential, and its estimation is a major component of conservation studies. New DNA sequencing technologies have enabled the analysis of large portions of the genome in nonmodel species, promising highly accurate estimates of such population genetic parameters. Restriction site-associated DNA sequencing (RADseq) is used to analyse thousands of variants in the bumble bee species Bombus impatiens, which is common, and Bombus pensylvanicus, which is in decline. Previous microsatellite-based analyses have shown that gene diversity is lower in the declining B. pensylvanicus than in B. impatiens. RADseq nucleotide diversities appear much more similar in the two species. Both species exhibit allele frequencies consistent with historical population expansions. Differences in diversity observed at microsatellites thus do not appear to have arisen from long-term differences in population size and are either recent in origin or may result from mutational processes. Additional research is needed to explain these discrepancies and to investigate the best ways to integrate next-generation sequencing data and more traditional molecular markers in studies of genetic diversity.
Data from: Whole genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection
The prevailing demographic model for Drosophila melanogaster suggests that the colonization of North America occurred very recently from a subset of European flies that rapidly expanded across the continent. This model implies a sudden population growth and range expansion consistent with very low or no population subdivision. As flies adapt to new environments, local adaptation events may be expected. To describe demographic and selective events during North American colonization, we have generated a data set of 35 individual whole-genome sequences from inbred lines of D. melanogaster from a west coast US population (Winters, California, USA) and compared them with a public genome data set from Raleigh (Raleigh, North Carolina, USA). We analysed nuclear and mitochondrial genomes and described levels of variation and divergence within and between these two North American D. melanogaster populations. Both populations exhibit negative values of Tajima's D across the genome, a common signature of demographic expansion. We also detected a low but significant level of genome-wide differentiation between the two populations, as well as multiple allele surfing events, which can be the result of gene drift in local subpopulations on the edge of an expansion wave. In contrast to this genome-wide pattern, we uncovered a 50-kilobase segment in chromosome arm 3L that showed all the hallmarks of a soft selective sweep in both populations. A comparison of allele frequencies within this divergent region among six populations from three continents allowed us to cluster these populations in two differentiated groups, providing evidence for the action of natural selection on a global scale.
Data from: Whole genome sequencing and rare variant analysis in essential tremor families
Essential tremor (ET) is one of the most common movement disorders. The etiology of ET remains largely unexplained. Whole genome sequencing (WGS) is likely to be of value in understanding a large proportion of ET with Mendelian and complex disease inheritance patterns. In ET families with Mendelian inheritance patterns, WGS may lead to gene identification where WES analysis failed to identify the causative single nucleotide variant (SNV) or indel due to incomplete coverage of the entire coding region of the genome, in addition to accurate detection of larger structural variants (SVs) and copy number variants (CNVs). Alternatively, in ET families with complex disease inheritance patterns with gene x gene and gene x environment interactions enrichment of functional rare coding and non-coding variants may explain the heritability of ET. We performed WGS in eight ET families (n=40 individuals) enrolled in the Family Study of Essential Tremor. The analysis included filtering WGS data based on allele frequency in population databases, rare SNV and indel classification and association testing using the Mixed-Model Kernel Based Adaptive Cluster (MM-KBAC) test. A separate analysis of rare SV and CNVs segregating within ET families was also performed. Prioritization of candidate genes identified within families was performed using phenolyzer. WGS analysis identified candidate genes for ET in 5/8 (62.5%) of the families analyzed. WES analysis in a subset of these families in our previously published study failed to identify candidate genes. In one family, we identified a deleterious and damaging variant (c.1367G>A, p.(Arg456Gln)) in the candidate gene, CACNA1G, which encodes the pore forming subunit of T-type Ca(2+) channels, CaV3.1, and is expressed in various motor pathways and has been previously implicated in neuronal autorhythmicity and ET. Other candidate genes identified include SLIT3 which encodes an axon guidance molecule and in three families, phenolyzer prioritized genes that are associated with hereditary neuropathies (family A, KARS, family B, KIF5A and family F, NTRK1). Functional studies of CACNA1G and SLIT3 suggest a role for these genes in ET disease pathogenesis.
FIGURE 3 in Four new taxa of Ilyonectria and Thelonectria (Nectriaceae) revealed by morphology and combined ITS and -tubulin sequence data
FIGURE 3. One of thirty-six equally most parsimonious trees inferred from combined ITS and β-tubulin partial sequences. Abbreviations: Neo. = Neonectria, I. = Ilyonectria, T. = Thelonectria, N. = Nectria. Tree length = 1169, CI = 0.6296, HI = 0.3704, CI excluding uninformative characters = 0.5856, HI excluding uninformative characters = 0.4144, RI = 0.8426, Rescaled consistency index = 0.5305. Bootstrap values ≥50% from 1000 replicates are noted above internodes. Asterisks indicate sequences of ITS and β- tubulin gene were from different strains as shown in TABLE 1.
FIGURE 2 in Four new taxa of Ilyonectria and Thelonectria (Nectriaceae) revealed by morphology and combined ITS and -tubulin sequence data
FIGURE 2. Thelonectria yunnanica (holotype). A. Median section of an ascoma; B. Structure of lateral perithecial wall; C. Colony on PDA; D−F. Macroconidia; G, H. Conidiophores and microconidia; I. Asci with ascospores.
FIGURE 1 in Four new taxa of Ilyonectria and Thelonectria (Nectriaceae) revealed by morphology and combined ITS and -tubulin sequence data
FIGURE 1. Thelonectria beijingensis (holotype). A. Median section of an ascoma; B. Colony on PDA; C. Conidiophores and macroconidia; D Asci with ascospores; E. Microconidia; F, G. Macroconidia.
Data from: SNP discovery in European lobster (Homarus gammarus) using RAD sequencing
The European lobster (Homarus gammarus) is a decapod crustacean with a high market value and therefore their fisheries are of major importance to the economies they support. However, over-exploitation has led to profound stock declines in some regions such as Scandinavia and the Mediterranean. To manage this resource sustainably, knowledge of population structure and connectivity is crucial to inform management about dispersal, recruitment, stock identification and food traceability. We used restriction-site associated DNA sequencing to develop novel SNP markers from 55 individuals encompassing much of the species range; SNPs were quality filtered, ranked using F-statistics and the top 96 SNPs adequate for primer design were retained. SNP markers were developed with the aim of maximising the power to detect genetic differentiation between: (i) Atlantic and Mediterranean lobsters and (ii) Atlantic lobsters. This panel of SNPs provides a useful resource for future studies of population genetic structure and assignment in H. gammarus.
epicPCR sequencing data, July 7 2021
<p>Samples: 1. Biolstd, Nomock, Nomag, 16S<br> 2. Biolstd, Nomock, Mag, 16S<br> 3. Biolstd, Nomock, Nomag, 18S<br> 4. Biolstd, Nomock, Mag, 18S<br> 5. Biolstd, Mock, Nomag, 16S<br> 6. Biolstd, Mock, Mag, 16S<br> 7. Biolstd, Mock, Nomag, 18S<br> 8. Biolstd, Mock, Mag, 18S<br> 9. Biolstd+WW, Nomock, Nomag, 16S<br> 10. Biolstd+WW, Nomock, Mag, 16S<br> 11. Biolstd+WW, Nomock, Nomag, 18S<br> 12. Biolstd+WW, Nomock, Mag, 18S<br> 13. Biolstd+WW, Mock, Nomag, 16S<br> 14. Biolstd+WW, Mock, Mag, 16S<br> 15. Biolstd+WW, Mock, Nomag, 18S<br> 16. Biolstd+WW, Mock, Mag, 18S<br> 17. WW, Nomock, Nomag, 16S<br> 18. WW, Nomock, Mag, 16S<br> 19. WW, Nomock, Nomag, 18S<br> 20. WW, Nomock, Mag, 18S<br> 21. WW, Mock, Nomag, 16S<br> 22. WW, Mock, Mag, 16S<br> 23. WW, Mock, Nomag, 18S<br> 24. WW, Mock, Mag, 18S</p>
Data from: High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements
Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27–43). On average, 66.2% of the reads mapped to the pseudo-reference genome of each species. Of these mapped reads, an average of 52.7% was identified as PCR or optical duplicates. We achieved deeper effective sequencing for historical samples (122.7×) compared to modern samples (23.5×). The number of nucleotide sites with at least 8× sequencing depth was high, with averages ranging from 0.89 × 106 bp (Arachnothera, modern samples) to 1.98 × 106 bp (Stachyris, modern samples). Linear regression revealed that the amount of sequence data obtained from each historical sample (represented by per cent of the pseudo-reference genome recovered with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013) related to how recently the sample was collected. We observed characteristic post-mortem damage in the DNA of historical samples. However, we were able to reduce the error rate significantly by truncating ends of reads during read mapping (local alignment) and conducting stringent SNP and genotype filtering.
Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), using multilocus Sanger sequence and genomic ddRADseq data
<p>The Rough Greensnake, <i>Opheodrys aestivus,</i> is a moderately-sized, semi-arboreal snake broadly distributed throughout eastern North America. While numerous taxa with similar distributions have been shown to be comprised of multiple species, <i>O. aestivus</i> has yet to be examined in a detailed phylogeographic context. Here, we use Sanger-sequence data of one mitochondrial and three nuclear loci for samples from throughout the distribution of <i>O. aestivus</i> to elucidate phylogeographic patterns in this species. We combine this with ddRADseq data for a subset of samples to test patterns on a more genomically comprehensive scale. In both datasets, we find strong support for three deeply divergent clades within <i>O. aestivus</i>: peninsular Florida, central Texas, and a main clade comprising the rest of the distribution, with the Florida clade the earliest diverging lineage of the three. Estimates of divergence time suggest that the central Texas and main clades diverged approximately 1.34 million years ago (Mya), while the peninsular Florida clade diverged from other lineages approximately 2.94 Mya, and these lineages diverged from the sister taxon, <i>O. vernalis</i>, approximately 6.43 Mya.<i> </i>These results also suggest that the historically recognized Florida subspecies, <i>O. a. carinatus</i>, could be elevated to species status. While the divergence of peninsular Florida or central Texas populations is not unique among squamates, nor is low levels of divergence from the Atlantic coast to eastern Texas, this combination of patterns is unusual, and yields important insight into the biogeography of North American biota. Further, our approach helps illustrate how dense geographic sampling with limited genomic sequencing can be used as a guide for the selection of samples to test phylogeographic patterns comprehensively.</p>
Data for morphometric analysis and DNA barcode sequence for the new fish species Polymixia hollisterae
<p>Two datasets are provided to support the journal article (https://doi.org/10.1643/i2020112) by T. C. Grande and M. V. H. Wilson naming the new Bermuda fish species <em>Polymixia hollisterae</em>. The first dataset is for 2-D multivariate morphometric comparisons of selected specimens and species of the fish genus <em>Polymixia</em>. The file is in TPS format, as a plain text file, for use in the application MorphoJ. The data are for 27 specimens with pixel coordinates for 34 landmarks digitized in ImageJ and used to generate Fig. 13 in the referenced publication. The second dataset, published here courtesy of Dr. R. Eytan, is a mitochondrial DNA barcode sequence in fasta format for the second paratype specimen, a small juvenile of the new species. The specimen is only the third one known of the new species and the only one not from Bermuda. It was collected in the north-central Gulf of Mexico and is now deposited in the Harvard University MCZ fish collection as catalog number MCZ 174218. The fasta file can be used as input to the barcode identification function at boldsystems.org, although its original identification in BOLD was incorrect.</p>
FIGURE 3 in Studies on Wrightoporia from China 3. Wrightoporia subavellanea sp. nov. based on morphological characters and rDNA sequence data
FIGURE 3. Strict consensus tree illustrating the phylogeny of Wrightoporia subavellanea and its related species generated by maximum parsimony based on ITS+nLSU sequences. Parsimony bootstrap values (before the slash markers) higher than 50% and bayesian posterior probabilities (after the slash markers) more than 0.95 were indicated along branches.
FIGURE 2 in Studies on Wrightoporia from China 3. Wrightoporia subavellanea sp. nov. based on morphological characters and rDNA sequence data
FIGURE 2. Microscopic structures of Wrightoporia subavellanea (Dai 11484). a Basidiospores. b Basidia and basidioles. c Cystidioles. d Hyphae from trama. e Hyphae from subiculum.
Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing
<p>Studies of structural variation (SV) have been challenging due to technological contraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examime SV in the <em>EGFR </em>landscape of four haplotypes derived from two human samples. We analyzed the <em>EGFR</em> gene and its landscape (+/- 500,000 base pairs) using this sequencing approach and were able to identify regions of non-coding DNA which had relatively high similarity to the most common activating <em>EGFR</em> mutation in non-small cell lung cancer. We discovered that reverse complements to the exon 19 deletion mutation which had at least 60% homology to the <em>EGFR</em> exon 19 canonical deletion and were within ± 421,000 bp of the deletion varied across the five haploid genomes examined (4 patient landscapes and hg38). Although the sample size is limited in this study, the estimated variation observed in genomic stability between the five <em>EGFR</em> haplotypes examined is novel and encourages further work to examine structural variation in larger cohorts.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.