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Kcnma1-tdtomato floxed allele sequence

BK large conductance calcium-activated K+ channels (KCa1.1) are expressed widely across many tissues, contributing to systemic regulation of cardiovascular, neurological, and other specialized physiological functions. The pore-forming α subunit is encoded by the Kcnma1 gene, originally named mSlo1 in mouse and slowpoke in Drosophila. Global deletion in mouse (Kcnma1−/−) produces a plethora of defects in neuron and muscle excitability, as well as other phenotypes related to channel function in nonexcitable cells. While homozygous null mice are viable, the ubiquitous loss of BK function has complicated the interpretation of phenotypes involving the interaction of multiple cell types which independently express BK channels. Here, we report the generation of a targeted allele for conditional inactivation of Kcnma1 using the Cre-loxP system (Kcnma1fl-tdTomato). Cre-mediated recombination generates a null allele, and BK currents were not detectable in neurons and muscle cells from Nestin-Cre; Kcnma1fl/fl and SM22α-Cre; Kcnma1fl/fl mice, respectively. tdTomato expression was detected in Cre-expressing tissues, but not in Cre-negative controls. These data demonstrate the utility of Kcnma1fl-tdTomato for conditional deletion of the BK channel, facilitating the understanding of tissue-specific contributions to physiological function in vivo.

Low-coverage whole-genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)

Atlantic cod (Gadus morhua, Linnaeus 1758) in the western Gulf of Maine are managed as a single stock despite several lines of evidence supporting two spawning groups (spring and winter) that overlap spatially, while exhibiting seasonal spawning isolation. Low-coverage whole genome sequencing was used to evaluate the genomic population structure of Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank using 222 individuals collected over multiple years. Results indicated low total genomic differentiation, while also showing strong differentiation between spring and winter spawning groups at specific regions of the genome. Guided regularized random forest and ranked FST methods were used to select panels of single nucleotide polymorphisms (SNPs) that could reliably distinguish spring and winter-spawning Atlantic cod (88.5% assignment rate), as well as males and females (95.0% assignment rate) collected in the western Gulf of Maine. These SNP panels represent a valuable tool for fisheries research and management of Atlantic cod in the western Gulf of Maine that will aid investigations of stock production and support accuracy of future assessments.

A new approach using targeted sequence capture for phylogenomic studies across Cactaceae

Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.

Matched Oxford Nanopore Technologies and Bisulfite Sequencing of the GM24385 Cell Line

One of the most widespread genomic modifications is 5-methylcytosine (5mC), which most frequently occurs at <a href="https://en.wikipedia.org/wiki/CpG_site">CpG</a> dinucleotides. Compared to whole-genome bisulfite sequencing, the traditional method of 5mC detection, nanopore technology can offer many advantages such as simplicity of sample prep and subsequent analysis. In order to demonstrate the utility and convenience of Oxford Nanopore Technologies’ sequencing platform for performing detection and analysis of 5mC, we have sequenced the HG002 Genome in a Bottle Sample GM24385 with both traditional bisulfite sequencing and using nanopore sequencing. Both technologies, old and new, were applied to the same sample from a single DNA extraction. Bisulfite sequencing Bisulfite sequencing was performed by a commercial provider and processed with the commonly used <a href="https://www.bioinformatics.babraham.ac.uk/projects/bismark/">bismark</a> package to obtain the proportion of reads displaying methylation at CpG sites throughout the whole genome.  Nanopore sequencing Nanopore sequencing was performed using the same sample of GM24385 material sent for bisulfite sequencing. Sequencing was performed on the MinION platform, across multiple flowcells, as part of ongoing platform development activities. The sequencing was not performed explicitly for the analysis presented here; we are making available all sequencing runs undertaken with this sample for the benefit of the community. Data Access Data is available as part of the Registry of Open Data on AWS: https://registry.opendata.aws/ont-open-data/. This dataset can be accessed through the S3 prefix: <blockquote> s3://ont-open-data/gm24385_mod_2021.09/ </blockquote> Further Information <ul> <li>https://labs.epi2me.io/gm24385-5mc/</li> <li>https://labs.epi2me.io/gm24385-5mc-remora</li> </ul>

Draft Genome Sequence of Pseudomonas sp. Strain MWU13-2922, Isolated from a Wild Cranberry Bog in Truro, Massachusetts

Annotated genome of Pseudomonas sp. MWU13-2922

opencc-by-3.0-usMar 2022View details →

Draft Genome Sequences of Aquitalea sp strain MWU-14.2238

Annotated genome of Aquitalea sp MWU-14.2238.

Draft Genome Sequences of Pseudomonas sp. Strain MWU12-2233, Isolated from a Wild Cranberry Bog in Provincetown, Massachusetts

Annotated genome of Pseudomonas sp. MWU12-2233.

opencc-by-3.0-usMar 2022View details →

Draft Genome Sequences of Pseudomonas sp strain MWU-15.20650

Annotated genome of Pseudomonas sp. MWU 15-20650.

opencc-by-3.0-usMar 2022View details →

Draft Genome Sequences of Aquitalea sp strain MWU-14.2238

Annotated genome of Aquitalea sp MWU-14.2238.

Raw sequence of: Field investigation- and dietary metabarcoding-based screening of arthropods that prey on primary tea pests

Predatory natural enemies play key functional roles in biological control. Abundant predatory arthropod species have been recorded in tea plantation ecosystems. However, few studies have comprehensively evaluated the control effect of predatory arthropods on tea pests in the field. We performed a one-year field investigation and collected predatory arthropods and pests in the tea canopy. Total 7,931 predatory arthropod individuals were collected, and Coleosoma blandum (Araneae, Theridiidae) was the most abundant species in the studied tea plantation. The population dynamics between C. blandum and four main tea pest species (Aleurocanthus spiniferus, Empoasca onukii, Ectropis grisescens and Scopula subpunctaria) were established using the individual number of predators and pests in each month. The results showed that the occurrence of C. blandum showed high synchronism with the occurrence of A. spiniferus, Em. onukii and Ec. grisescens. The prey spectrum of C. blandum was further analyzed using DNA metabarcoding. Among prey species, A. spiniferus, Em. onukii and Ec. grisescens were included, and the relative abundance and positive rates of target DNA fragments of A. spiniferus were obviously greater than those of other two pests.

Draft Genome Sequence of Pseudomonas sp. strain MWU13.2105, isolated from Wild Cranberry Bog in Truro, Massachusetts

Annotated genome of Pseudomonas sp. strain MWU13.2105.

Draft Genome Sequence of Pseudomonas sp. strain MWU13.2100, isolated from Wild Cranberry Bog in Truro, Massachusetts

Annotated genome of Pseudomonas sp. strain MWU13.2100.

Computational validation of clonal and subclonal copy number alterations from bulk tumour sequencing

Somatic variant identification from WGS data is a crucial step in the analysis of cancer genomes. Several tools are available to perform mutations calling, however, the noisiness of data requires appropriate quality control assessment. In the preprint work available at https://doi.org/10.1101/2021.02.13.429885 we present CNAqc, an R package devised to assess the quality of allele-specific Copy Number Alterations (CNA), somatic mutations, and tumor purity estimates. In order to test the model, we ran CNAqc on 2778 single-sample PCAWG whole-genomes and 48 TCGA whole-exomes. We uploaded the results of our analysis using the release of the tool available at https://github.com/caravagnalab/CNAqc/releases/tag/rr_22_0.1 in the form of .rds files. All the necessary details for the reproduction of our results are reported in the Supplementary Materials of the above-mentioned manuscript.

opencc-zeroApr 2022View details →

Color and W-chromosome sequence data from study on maternal inheritance of egg mimicry

<div>This dataset supports a study demonstrating that host-specific egg mimicry in the brood-parasitic African cuckoo finch Anomalospiza imberbis is maternally inherited. It includes egg reflectance spectra for the background colour of 188 cuckoo finch eggs from four host species in Zambia, and consensus sequences for 68 W-linked ddRAD-seq loci derived from 80 female cuckoo finches belonging to four different host-specific maternal lineages from three host species in Zambia. These data derive from two partially overlapping samples of eggs: some eggs with genetic data lacked egg spectral data, and vice versa. W-linked genetic data were all of offspring origin as they derived from embryonic or nestling tissue. Additional phenotypic data (host nest species and descriptions of egg phenotype), date and location data associated with each egg spectrum are provided in a separate file. Data on the origin of the individuals contributing to the W-linked loci are provided in Table S1 of the associated publication.</div>

Modeling Sequences of Earthquakes and Aseismic Slip (SEAS) in Elasto-Plastic Fault Zones With a Hybrid Finite Element Spectral Boundary Integral Scheme

This repository contains the results of 2D simulations of the earthquake cycles accounting for off-fault plasticity. Folder Case1 contains the slip rate and time history for all simulations with cohesion c = 47 MPa Folder Case2 contains the slip rate and time history for all simulations with cohesion c = 25 MPa the mat files contain equivalent plastic strain of each element stored at the start and end of each event with element connectivity and node coordinates.

Supplementary Information of Amplicon-based nanopore sequencing of patients with COVID-19 omicron (B.1.1.529) variant from India

We report sequencing of  omicron variants from SARS-CoV-2 in 75 patients, using Nanopore long-read sequencing chemistry. We highlight the nature of mutations in spike glycoprotein that are unique and common to other populations.

opencc-zeroApr 2022View details →

Blast output from: Lost in dead wood? Environmental DNA sequencing from dead wood shows little signs of saproxylic beetles

eDNA metabarcoding has become a standard method for assessing wood-inhabiting fungi and bacteria, yet determination of dead-wood-inhabiting beetles still relies on time-consuming collection of beetle specimens. We thus tested whether beetle species can be identified by eDNA sequencing of wood in a mesocosm experiment that manipulated species assemblages. Dead wood samples were taken at exit holes of beetles and DNA was extracted and analyzed using two comparative methods: (i) metabarcoding with standard arthropod primers (421 bp) and (ii) using short species-specific primers (120-264 bp) with Sanger sequencing. Results showed that beetle DNA was amplified by each of the two approaches, however, with (i) we detected only one non-target saproxylic beetle species. In addition, we identified 80 different OTUs with four non-targeted species of arthropods. For (ii) we detected the targeted species in two fresh beetle exit holes out of 20 samples. We suggest that, in contrast to fungi and bacteria, this eDNA metabarcoding approach is not able to reliably detect saproxylic beetles from wood samples, likely due to rapid degradation of their target DNA. Adapting such an approach for large scale analyses thus requires a better knowledge of degradation processes affecting DNA quality and quantity in wood.

opencc-zeroApr 2022View details →

The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding the origin of domestic goat

The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat Radiation-Hybrid map (RH map). The existing whole-genome re-sequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.

Substitution mutational signatures in whole-genome-sequenced cancers in the UK population, Mutational Signatures Data

This uploads contains the mutational signature data from the article Substitution mutational signatures in whole-genome-sequenced cancers in the UK population, Science, doi:10.1126/science.abl9283, 2022.

Source data and code for manuscript 'An executive network for the control of sequence-behavior in pigeons'

The contents of this folder are part of the submission of the manuscript entitled 'An executive network for the control of sequence-behavior in pigeons', by Lukas Alexander Hahn & Jonas Rose Contact: lukas.hahn@ruhr-uni-bochum.de Data and code have been compressed into a .zip folder each. Unpack the contents of the folders to use the dataset. The dataset is split into two main folders and one Matlab file: 'code' contains all analysis code to produce all figures and reported statistics of the manuscript (refer to the MATLAB live script 'manuscriptResultsLiveScript.mlx' to run the analysis, please adjust the path information of where the data is stored on your computer). 'RESULTSSTATISTICS.mat' contains all reported statistical values (generated by 'manuscriptResultsLiveScript.mlx') 'sourceData' Contains all required source data files (i.e. pre-processed data) required to run the analyses stored in 'code'. Data related to animal behavior was recorded using MATLAB (R2016b). Electrophysiological data was recorded by NeuroNexus microelectrodes and an INTAN RHD2000 headstage on an INTAN USB-Interface board, with a sampling rate of 30 kHz and was subsequently filtered for spike sorting at bandpass 0.5 - 7.5 kHz. Data format is the MATLAB '.mat' type (which can be loaded in by MATLAB, or alternatively by the freely available Octave Software (https://www.gnu.org/software/octave)). Data is organized in MATLAB structures, one file per session for behavioral results, one file per neuron for different alignments and preprocessing conditions (refer to manuscriptResultsLiveScript). Structures contain individual matrices (labelled by a descriptive name) that contain numerical values or character strings. Matrices labelled by the keyword 'Info' contain character strings that give a brief description of the loaded data. Source data contains two separate folders containing data of animal 1 ('P855'), and animal 2 ('T1003'). Data was sorted into different subsets, for analysis of individual task phases. Subfolder 'NCL' refers to 'nidopallium caudolaterale', 'NIML' refers to 'nidopallium intermedium mediale pars laterale', the recorded brain regions.