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dryad40/100

Supplementary materials to: Nano-Strainer: a workflow for identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads

In the paper associated with this dataset, a workflow is presented which enables the identification of single-/low-copy nuclear molecular markers for a plant group of interest, by mining data from a small representative target capture experiment done using a commercial probe kit and Oxford Nanopore long-read sequencing. The proposed pipeline first assesses sequence variability contained in the data from targeted loci and assigns reads to their respective genes, via a combined BLAST/clustering procedure. Cluster consensus sequences are then examined based on four pre-defined criteria presumably indicative for absence of paralogy. This is done by calculating four specialized indices; loci are ranked according to their performance in these indices, and top-scoring loci are considered putatively single- or low-copy. The approach can be applied to any probe set. As it relies on long reads, the contribution also provides template workflows for processing Nanopore-based target capture data. Identified loci can be used for NGS amplicon sequencing. For detection of possibly remaining paralogy in these data, which might occur in groups with rampant paralogy, the long-read assembly tool CANU is employed. The presented workflow can be useful for researchers dealing with reticulate or polyploidization phylogenetic histories in plants. The present dataset contains several documents supplementing the original paper. Its most important elements are a detailed description (alongside two graphical workflow figures) of all methods employed in the study, suitable for reproducing the steps of the workflow and also the wet-lab work. The workflow employs a collection of BASH, Python and R scripts which is available here, together with a detailed account on command line use in Linux. Also, reference sequences for the identified markers can be found as well as sequence alignments derived from the amplicon sequencing.

opencc-zeroJun 2023View details →

zenodo40/100

Dataset for indoor carbon dioxide readings using low-cost sensors

The dataset was originated from four sensors: 2 units of MG–811, a Metal Oxide Semiconductor, and 2 units of MH–Z16, a Non-Dispersive Infra-Red Sensor.

opencc-by-4.0Jul 2023View details →

dryad40/100

Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF

The long-term persistence of species in the face of climate change can be evaluated by examining the interplay between selection and genetic drift in the contemporary evolution of populations. In this study, we focused on spatial and temporal genetic variation in four populations of the cold-water kelp Laminaria digitata using thousands of SNPs (ddRAD-seq). These populations were sampled from the center to the south margin in the North Atlantic at two different time points, spanning at least two generations. By conducting genome scans for local adaptation from a single time point, we successfully identified candidate loci that exhibited clinal variation, closely aligned with the latitudinal changes in temperature. This finding suggests that temperature may drive the adaptive response of kelp populations, although other factors, such as the species' demographic history should be considered. Furthermore, we provided compelling evidence of selection through the examination of allele frequency changes over time, by taking into the impact of genetic drift. Specifically, we detected candidate loci exhibiting temporal differentiation that surpassed the levels typically attributed to genetic drift at the south margin, confirmed through simulations. This finding was in sharp contrast with the lack of detection of outlier loci based on temporal differentiation in a population from the North Sea, exhibiting low and decreasing levels of genetic diversity. These contrasting evolutionary scenarios among populations can be primarily attributed to the differential prevalence of selection relative to genetic drift. In conclusion, our study highlights the potential of temporal genomics to gain deeper insights into the contemporary evolution of marine foundation species in response to rapid environmental changes.

opencc-zeroJun 2023View details →

dryad40/100

Cacao gene atlas: Additional file 13 (CPM normalized read counts) and Additional file 14 (fractional counts)

A large dataset of replicated transcriptomes was developed to accelerate Theobroma cocoa genomics research with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao. RNAs were extracted and transcriptomes were sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3-5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. We describe the creation of the atlas,and its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. To promote wider use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. A gene expression browser with a graphical user interface was developed to display gene expression patterns and to provide easy access of raw data and statistical analyses.

opencc-zeroAug 2023View details →

zenodo40/100

Simulated reads for benchmarking SARS-CoV-2 lineage abundance estimation

To evaluate the accuracy of lineage abundance estimates from amplicon-based and whole genome-based sequencing, we simulated paired-end reads from amplicons determined by AmpliDiff, and reads spanning full genomes. Abundances of lineages are based on the relative abundance of a lineage within the dataset. The data consists of the following 8 independent datasets: <ul> <li>200 bp reads from the Netherlands based on AmpliDiff amplicons (1, 2, 5 or 10 amplicons) at 1000x coverage,</li> <li>400 bp reads from the Netherlands based on AmpliDiff amplicons (1, 2, 5 or 10 amplicons) at 1000x coverage,</li> <li>200 bp reads from the Netherlands based on whole genome sequencing at 100x coverage,</li> <li>400 bp reads from the Netherlands based on whole genome sequencing at 100x coverage,</li> <li>200 bp reads from Texas based on AmpliDiff amplicons (1, 2, 5 or 10 amplicons) at 1000x coverage,</li> <li>400 bp reads from Texas based on AmpliDiff amplicons (1, 2, 5 or 10 amplicons) at 1000x coverage,</li> <li>200 bp reads from Texas based on whole genome sequencing at 100x coverage,</li> <li>400 bp reads from Texas based on whole genome sequencing at 100x coverage.</li> </ul> Every independent dataset contains 20 sets of reads (generated with different random seeds). The genomes used for the Netherlands-based simulations can be obtained via GISAID through accession id <a href="https://doi.org/10.55876/gis8.230825fe">EPI_SET_230825fe</a>, and the genomes used for the Texas-based simulations can be obtained via GISAID through accession id <a href="https://doi.org/10.55876/gis8.230825pe">EPI_SET_230825pe</a>.

opencc-by-4.0Aug 2023View details →

zenodo40/100

Simulated reads for the MMBDTP novel genome

Simulated read data for use in the "Microbes, Microbiomes and Bioinformatics" doctoral training program. The long read dataset required an update   https://mmbdtp.github.io/

opencc-by-4.0Oct 2022View details →

dryad40/100