Aspergillus fumigatus is a saprophytic filamentous fungus that is ubiquitous outdoors (soil decaying vegetation) and indoors (hospitals simulated closed habitats etc.). A. fumigatus can adapt to various environmental conditions and form airborne conidia that are the inoculum for a variety of diseases (e.g. non- and invasive pulmonary infections allergic bronchopulmonary aspergillosis etc.) in immunocompromised hosts. In an on-going Microbial Observatory Experiments on the International Space Station (ISS) molecular phylogeny of several fungal isolates were characterized. Two strains ISSF 21 and IF1SW-F4 were isolated from the HEPA filter and the surface of the Cupola of the ISS respectively. Using primers targeting the internal transcribed spacers ITS1 and 2 both isolates were identified as A. fumigatus. The whole genome sequence analysis of ISSF 21 revealed increased number of single nucleotide polymorphisms (SNPs) when compared to the reference A. fumigatus 293. Knowing that A. fumigatus is an opportunistic pathogen and microgravity highly influences the antibiotic susceptibility and pathogenicity of microorganisms we examined pathogenicity of both ISS isolates using the zebrafish larval model. The space station isolates (ISSF-021 and IF1SW-F4) were more virulent than two clinical strains (Af293 and CEA10) whose pathogenicity was highly characterized. Here the whole genome sequences of ISSF-021 strain are being deposited.

These data were compiled to support effective conservation for species within Astragalus sect. Humillimi. Two species, A. cremnophylax var. cremnophylax and A. humillimus are federally listed as endangered taxa. The data provided herein were used to resolve the relationaships among taxa, the population structure within taxa, and genetic diversity within taxa. The data are provided in a STRUCTURE-formatted file that includes taxa, individuals, sampling localities, and the genotype scores per individual for 690 Amplified Fragment Length Polymorphisms (AFLPs).

Genome sequencing and assembly of fungal isolates belonging to Penicilliium and Aspergillus genera isolated from International Space Station

Genomic and proteomic characterization of the Aspergillus niger isolate, JSC-093350089, collected from U.S. segment surfaces of the International Space Station (ISS) is reported, along with a comparison to the experimentally established strain ATCC 1015. Whole-genome sequencing of JSC-093350089 revealed enhanced genetic variance when compared to publicly available sequences of A. niger strains. Analysis of the isolate’s proteome revealed significant differences in the molecular phenotype of JSC-093350089, including increased abundance of proteins involved in the A. niger starvation response, oxidative stress resistance, cell wall integrity and modulation, and nutrient acquisition. Together, these data reveal the existence of a distinct strain of A. niger onboard the ISS and provide insight into the molecular phenotype that is selected for by melanized fungal species inhabiting spacecraft environments.

Genomic and proteomic characterization of the Aspergillus niger isolate JSC-093350089 collected from U.S. segment surfaces of the International Space Station (ISS) is reported along with a comparison to the experimentally established strain ATCC 1015. Whole-genome sequencing of JSC-093350089 revealed enhanced genetic variance when compared to publicly available sequences of A. niger strains. Analysis of the isolate xe2 x80 x9a xc3 x84 xc3 xb4s proteome revealed significant differences in the molecular phenotype of JSC-093350089 including increased abundance of proteins involved in the A. niger starvation response oxidative stress resistance cell wall integrity and modulation and nutrient acquisition. Together these data reveal the existence of a distinct strain of A. niger onboard the ISS and provide insight into the molecular phenotype that is selected for by melanized fungal species inhabiting spacecraft environments.

These data were compiled to investigate the evolutionary history of Astragalus iselyi, A. sabulosus var. sabulosus, and A. sabulosus var. vehiculus. The data release consists of six text files. One file is a bash script (astragalus_MLE_msms.sh) for generating simulated genetic data. Four files contain individual-level (astragalus.fasta, astragalus.nothin.recode.vcf, astragalus.recode.vcf) or population-level (astragalus_dadi.txt) information on genetic variation. One file contains sampling site-specific data for various soil and climatic variables (astragalus_env.txt). The .vcf files contain the full sequence information that is contained in the other files, but the file structures vary based on the programs used for analysis. These files may be opened and edited in a text editor program, such as Notepad ++ (PC) or BBEdit (Mac). The .vcf file can be loaded into the Stacks population program (Catchen et al. 2013) or VCFtools (Danecek et al. 2011) to calculate genetic diversity statistics (astragalus.nothin.recode.vcf contains multiple genetic variants per locus, whereas astragalus.recode.vcf contains only one genetic variant per locus).The astragalus_dadi.txt file can be used as an input file with the program dadi (Gutenkunst et al. 2009) to infer population history. Finally, astragalus.fasta can be loaded as an input file into RAxML (Stamatakis 2008) to perform phylogenetic analyses.

,This collection contains supplementary data for the manuscript "Genotypic characterization of the U.S. Peanut Core Collection", which describes genotyping results for the USDA peanut core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of the core collection was replicated genotyped in replicate, using between two and five seeds per accession to assess heterogeneity within an accession. Supplementary files include: descriptive information about the genotyped accessions, SNP genotype calls in several formats, a phylogenetic tree calculated from the genotype data, Structure analysis, PCA analysis, and comparisons with the diploid progenitors.,This research was co-funded by the National Institute of Food and Agriculture and the National Peanut Board.,,

This study generated genetic 'barcode' data using high-throughput sequencing to characterize pollen collected by the endangered rusty-patched bumblebee, Bombus affinis. Pollen samples were associated with a single Bombus affinis colony within a structure in Red Wing, Minnesota, USA, as previously described by Boone et al. (2022). This data release consists of two tab-delimited files: 1) sample.metadata.txt includes sample identifiers and accessions assigned by the National Center for Biotechnology Information (NCBI), the authoritative repository for publicly funded genetic data in the United States. These accessions can be used individually to obtain raw sequencing data or sample information at www.ncbi.nih.nlm.gov. Alternatively, the BioProject accession PRJNA1045705 can be searched to retrieve the full set of data and sample accessions listed in the file. Entity and attribute metadata are provided for this file. 2) taxon.counts.txt includes the inferred counts, or number of sequences, attributable to each identified taxon in each sample. Taxa are in rows and sequencing libraries are in columns. Taxa are listed by scientific name and the taxonomic rank of that scientific name. A numeric taxonomic identifier used by NCBI for each taxon is also provided, as the taxonomic identifier is unique in the NCBI databases whereas scientific names may not be. Entity and attribute data are not provided for this file due to its size and repetitive content.