Hubbard, Alfred · Solares, Edwin · Hemming-Schroeder, Elizabeth

88 rows · 18 KB · fasta

These are the files needed to run the Broad Institute's malaria amplicon pipeline for the PvGAP Plasmodium vivax panel, described in detail here . They consist of FASTA files containing the forward and reverse primers and another FASTA file containing reference sequences for each target, derived from the PvP01 reference genome.

Yuan, Guangyuan

72 rows × 13 cols · 6.0 KB · csv, fasta

11 numeric · 2 categorical

This dataset supports the findings of the manuscript "Root anatomical traits modulate the assembly and nitrogen transformation potential of root-associated microbiomes in a temperate steppe" (NPH-MS-2026-55667). It contains root traits data, bacterial 16S rRNA gene absolute abundances, functional genes relative abundances, DNA extraction metadata, and phylogenetic marker sequences for 37 plant species from a temperate steppe ecosystem. The dataset includes the following files: 1. root traits.csv - Root traits including average diameter (AD), specific root length (SRL), specific root area (SRA), root tissue density (RTD), root nitrogen content (RNC), root carbon content (RCC), carbon‑nitrogen ratio (RCN), cortex layer number (CLN), cortex thickness (CT), and the ratio of cortex thickness to root diameter (CTRD). The first column lists plant species names. 2. Absolute abundance of 16S rRNA gene.csv - Quantitative PCR (qPCR) derived absolute abundances of bacterial 16S rRNA gene copies (copies/ng DNA) across different root compartments (rhizosphere, rhizoplane, endosphere), host species, root orders, and cotyledon classes (monocot/dicot). 3. DNA extraction sample weight.csv - Fresh weight (grams) of root material used for DNA extraction for each sample, linked by SampleID to the abundance data. 4. DNA extraction concentration.csv - Qubit‑measured DNA concentrations (ng/μL) and the sample volume (μL) used for quality control, together with sample metadata. 5. 37species.fasta - DNA sequences of two chloroplast markers (matK and rbcL) for the 37 plant species included in the study. The sequences are in FASTA format with headers formatted as ">Species". These were used for host phylogeny construction and Pagel's λ analyses. 6. Quantitative PCR results of functional gene.csv - Quantitative PCR (qPCR) derived relative abundances of bacterial 16S rRNA gene and functional genes across different root compartments (rhizosphere, rhizoplane, endosphere), host species, root orders, and cotyledon classes (monocot/dicot). 7. README.md - A detailed description of each file, column headers, abbreviations, units, and any missing value codings (NA). All data are provided to ensure transparency and reproducibility of the analyses. For methodological details, please refer to the Materials and Methods section of the associated publication. These data are under embargo until the associated research article is published. After that date, they will be freely available under a Creative Commons Attribution 4.0 International (CC BY 4.0) license. During the embargo period, the metadata (title, authors, abstract) and the DOI remain publicly visible, but the data files are not accessible. For access requests before the embargo expires, please contact the corresponding author.

Requena Rolanía, Jose María · Greif, Gonzalo · ROBELLO, CARLOS

1 files · 8.0 MB · fasta

This dataset contains the genome sequence for Trypanosoma cruzi (strain Dm28c). This genome sequence was de novo assembled using PacBio Hi-Fi and Illumina sequencing platforms by Greif et al (2026. PMID: 41501640). The genome was assembled into 32 contigs, which represent complete chromosomes. The provided Fasta file also contains an additional contig corresponding to the maxicircle (mitochondrial genome) sequence. The Fasta files included in this dataset were downloaded from GenBank (assembly GCA_044048535.1; May 22, 2026). Additional information about the Dm28cT2T genome assembly and gene annotations may be accessed through the link: https://cruzi.pasteur.uy/

Burman, Nathaniel · Buyukyoruk, Murat · Wiegand, Tanner · et al.

4 files · 8.0 MB · fasta

This folder contains a multiple sequence alignment of Cas7 homologs in .fasta format, the domain-level annotations from PFAM and CasFinder, and an associated phylogenetic tree in .newick format.

Aalborg, Trine

7 files · 8.0 MB · csv, gzip

README - Data for "Genomic constraint and hypervariability in tetraploid potatoes" Trine Aalborg, May 2026 The data applied in the study includes phenotypic and genotypic information on the MASPOT panel (768 F1 progeny of an 18-parent diallel cross - property of Danespo A/S). The genotypic data was generated using genotyping-by-sequencing technology as described in the paper. Following genotype calling and filtration (5-60x read depth, < 50 % missing rate, > 1 % MAF), the total SNP set includes 151,164 biallelic SNPs. Coordinates of these SNPs relative to the DMv6.1 potato reference genome are provided. In addition to genotypes across the clones, the estimated GERP score of that SNP from (Wu et al., 2023) is reported. The manuscript analyses only consider markers with reliable GERP scores (MSA alignment depth > 50, and neutral score > 2), which corresponded to 97,815 of the total 151,164 biallelic SNPs. SNPeff annotations of the markers (based on the DMv6.1 reference genome) are also appended. The phenotypes were collected across 1-2 field trials, depending on the traits, and includes a minimum of two replicates per clone from a randomized block design. There are phenotypes for eight traits: dry matter content [%], yield (hkg/ha), senescence [1-9], flesh color [1-9], tubers/plant, tuber length [mm], tuber diameter [mm], and tuber size [mm^3]. Metadata includes phenotyping year and block location of the plot as well as pedigree of the diallel offspring. File descriptions: gt_MASPOT.csv - .csv file of the non-imputed genotypic data of 151,164 SNPs for the 768 F1 clones (those with GERP scores). Columns 1-3 are SNP coordinates and SNP IDs. Column names from column 4 and onwards are clone IDs. gt_MASPOT_imputed.csv - .csv file holding the imputed (random forest, missRanger algorithm) genotypic data of 151,164 SNPs for the 768 F1 clones. gt_MASPOT_recoded.csv - .csv file of the recoded, imputed genotypic data of 151,164 SNPs for the 768 F1 clones. The SNPs are recoded from original MASPOT ref/alt allele (based on AF in the MASPOT panel) to the alternative allele = the derived allele in the 100-Solanaceae panel. pt_MASPOT.csv - .csv file holding the phenotypic data (eight traits) of the 768 F1 clones (Clone_ID). The number of observations varies across traits. Also including metadata: year of phenotyping (Year), block number (Block, Line_in_block), clone parents (Mother, Father, Family). GERP_MASPOT.csv - .csv file holding the GERP scores (including alignment depth, neutral scores, and a marker annotation based on GERP score thresholds (deleterious, neutral, hypervariable, or low quality)), SNPeff annotations, and the derived allele in the 100-Solanaceae panel from (Wu et al., 2023) [MASPOT_Alt_Allele_Is_Sol_Derived_Allele - used for recoding of the genotypes] of the MASPOT SNPs with GERP scores. snps.MASPOT_F1.vcf.gz - zipped .vcf file of the GBS MASPOT genotypic data (both discrete genotype calls and allele frequencies) called to the DMv6.1 potato reference genome. Filtered to read depth 5x, MQ > 30. A total of 160,920 biallelic SNPs. Includes the 768 F1 progeny analyzed. Literature: Wu, Y., Li, D., Hu, Y., Li, H., Ramstein, G. P., Zhou, S., et al. (2023). Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 186, 2313-2328.e15. doi: 10.1016/j.cell.2023.04.008

Omukuti, Rodney

1 files · 8.0 MB · vcf