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Fig. 4 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Fig. 4 Comparison of the diatom assemblages heterogeneity inside each lake, obtained with HTS and microscopy. Inside lake assemblage heterogeneity is the sum of the Bray-Curtis distances between the three samples of a lake. Correlation is significant (Pearson correlation p <0.001) and follows a linear model (p <0.001, R 2 = 50.8%) (see black line)

Fig. 6 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Fig. 6 Correlations of diversity indices obtained with microscopy and HTS. All correlations are significant and follow linear models (see Table 1)

Fig. 2 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Fig. 2 Correlation between both distance matrices (Bray-Curtis distances) calculated between diatom compositions of samples obtained with microscopy and HTS

Fig. 5 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Fig. 5 Comparison of diversity indices obtained with microscopy and HTS. Classes boundaries for α diversity: c1 <0.675 ≤ c2 <1.100 ≤ c3 <1.525 ≤ c4 <1.950 ≤ c5 <2.375 ≤ c6 <2.800 ≤ c7 <3.225 ≤ c8 <3.650 ≤ c9 <4.075 ≤ c10. For β diversity: c1 <0.7 ≤ c2 <0.8 ≤ c3 <0.9 ≤ c4 <1.0 ≤ c5 <1.1 ≤ c6 <1.2 ≤ c7 <1.3 ≤ c8 <1.4 ≤ c9 <1.5 ≤ c10. For ϒ diversity: c1 <1.04 ≤ c2 <1.48 ≤ c3 <1.92 ≤ c4 <2.36 ≤ c5 <2.80 ≤ c6 <3.24 ≤ c7 <3.68 ≤ c8 <4.12 ≤ c9 <4.56 ≤ c10

opencc-zeroDec 2012View details →

Data from: Who's for dinner? High-throughput sequencing reveals bat diet differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed

Effective management and conservation of biodiversity requires understanding of predator–prey relationships to ensure the continued existence of both predator and prey populations. Gathering dietary data from predatory species, such as insectivorous bats, often presents logistical challenges, further exacerbated in biodiversity hot spots because prey items are highly speciose, yet their taxonomy is largely undescribed. We used high-throughput sequencing (HTS) and bioinformatic analyses to phylogenetically group DNA sequences into molecular operational taxonomic units (MOTUs) to examine predator–prey dynamics of three sympatric insectivorous bat species in the biodiversity hotspot of south-western Australia. We could only assign between 4% and 20% of MOTUs to known genera or species, depending on the method used, underscoring the importance of examining dietary diversity irrespective of taxonomic knowledge in areas lacking a comprehensive genetic reference database. MOTU analysis confirmed that resource partitioning occurred, with dietary divergence positively related to the ecomorphological divergence of the three bat species. We predicted that bat species' diets would converge during times of high energetic requirements, that is, the maternity season for females and the mating season for males. There was an interactive effect of season on female, but not male, bat species' diets, although small sample sizes may have limited our findings. Contrary to our predictions, females of two ecomorphologically similar species showed dietary convergence during the mating season rather than the maternity season. HTS-based approaches can help elucidate complex predator–prey relationships in highly speciose regions, which should facilitate the conservation of biodiversity in genetically uncharacterized areas, such as biodiversity hotspots.

opencc-zeroDec 2012View details →

Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci was similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.

opencc-zeroDec 2015View details →

Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing

High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data.

opencc-zeroDec 2015View details →

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.

opencc-zeroOct 2021View details →

A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations

An optimized, high-throughput and cost-effective genotyping method applicable to various crop breeding populations is very important in this genomic era. We have developed an optimized Nextera skim-sequencing (skim-seq) approach to genotype different populations that can be used for genetics studies and genomics-assisted breeding. We performed skim-seq on a variety of populations developed through doubled haploid (DH) technology, inter-specific recombinants developed through introgression, amphidiploid developed through wide crosses, and on known monosomic samples. 1. A doubled haploid (DH) population consisting of 48 lines from the cross of spring wheat (Triticum aestivum) cultivars CDC Stanley and CDC Landmark developed by the Crop Development Centre at the University of Saskatchewan. We genotyped these DH with skim-seq and identified the genomic segments contributed by each of the two parental lines. 2. A population of 335 back cross generation 1 (BC1) skim-seq samples for wheat-barley recombinants with group 7 translocations and 839 F1 wheat 5D monosomic lines (TA3059) along with 16 standard Chinese Spring lines as internal control. 3. A panel of 144 Thinopyrum intermedium x Triticum durum (IWG--durum) lines and 141 Thinopyrum intermedium (IWG) lines were evaluated to assess skim-seq genome coverage as well as amphiploidy levels. The demultiplexed FASTQ files for all samples tested in the experiment are available at NCBI SRA public repository with respective BioProject accessions; DH lines [PRJNA729723], 5D monosomic line [PRJNA742385], wheat-barley recombinants [PRJNA738484], IWG-durum and IWG [PRJNA736976]. An example key file for the 5D monosomic line is also attached. This study indicated that skim-seq is an efficient approach for genomic evaluation of a range of different populations and applications. The scripts have been provided to implement skim-seq data for variant calling, identification of genomic segment dosage and alien introgression. Each step of the pipeline is described and implemented with similar sequencing data from skim-seq libraries.

opennotspecifiedDec 2021View details →

Fig. 1 in High-Throughput Sequencing for Life-History Sorting and for Bridging Reference Sequences in Marine Gerromorpha (Insecta: Heteroptera)

Fig. 1. Representative images of Halobates species collected (rows), and their various life stages (columns). (Top row) Halobates calyptus: nymph (A), adult male (B), and adult female (C); (middle row) Halobates hayanus: nymph (D), adult male (E), and adult female (F); (bottom row) Halobates maculatus: nymph (G), adult male (H) and adult female (I). All images are scaled to size, and black scale bars represent 1 mm.

opennotspecifiedDec 2021View details →

Fig. 4 in High-Throughput Sequencing for Life-History Sorting and for Bridging Reference Sequences in Marine Gerromorpha (Insecta: Heteroptera)

Fig. 4. Maximum likelihood reconstruction (rooted to Rhagovelia antilleana) of 738 marine Gerromorpha samples using the 658-bp COI gene, collapsed into clades representing 10 species units (colored blocks) partitioned by ASAP (Puillandre et al. 2021) and PTP (Kapli et al. 2017; Zhang et al. 2013). mPTP posterior probabilities are denoted on the branches. Colors indicate the final species units (i.e., nine) delineated in this study after preliminary investigations found no morphological differences in H. maculatus clades.

Contribution of High-throughput Exome Sequencing in the Diagnosis of the Cause Fetal Polymalformation Syndromes

ClinicalTrials.gov study NCT02512354. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Medico-economic Evaluation of Different High-throughput Sequencing Strategies in the Diagnosis of Patients With Intellectual Deficiency

ClinicalTrials.gov study NCT03287206. IPD Sharing: Not stated. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

Precision Cancer Medicine for Advanced Cancer Through High-throughput Sequencing

ClinicalTrials.gov study NCT02090530. IPD Sharing: NO. Countries: 1. Publications: 1.

Evaluate and Understand Preferences and Representations in Families of Patients With Regard to High-throughput Sequencing Technology for Diagnostic Purposes

ClinicalTrials.gov study NCT02814747. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Evaluation of the Diagnostic Contribution of High-throughput Exome Sequencing for Patients With Convulsive Encephalopathy of Unknown Etiology: Pilot Study to Improve Genetic Counselling

ClinicalTrials.gov study NCT03652246. IPD Sharing: Not stated. Countries: 1. Publications: 0.

publicNov 2017View details →

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing.

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publicFeb 2015View details →

Data from: High-throughput sequencing of nematode communities from total soil DNA extractions

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publicAug 2016View details →

Data from: High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements

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