In this article, we present the draft genome sequence of strain Marseille-P3344, isolated from a human fecal sample. The genome described here is composed of 2,464,704 nucleotides, with 2,230 protein-coding genes and 76 RNA genes.
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http://dx.doi.org/10.1128/genomeA.01459-17 | DOI Listing |
Mol Phylogenet Evol
January 2025
Department of Ecology and Evolutionary Biology and University of Michigan Herbarium, University of Michigan, Ann Arbor, MI 48109, USA.
Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
The Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia.
Background: Plasma phospho-tau biomarkers, such as p217+tau, excel at identifying Alzheimer's Disease (AD) neuropathology. However, questions remain regarding their capacity to inform AD biological PET stages at group level and maintain the same precision at individual patient level.
Method: Participants included 248 cognitively unimpaired (CU) and 227 cognitively impaired (CI) individuals, with Janssen plasma p217+tau Simoa® assay, F-NAV4694 Aβ PET (A) and F-MK6240 tau PET (T) data.
NAR Genom Bioinform
March 2025
Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
Recent advancements in viral metagenomics and single-virus genomics have improved our ability to obtain the draft genomes of environmental viruses. However, these methods can introduce virus sequence contaminations into viral genomes when short, fragmented partial sequences are present in the assembled contigs. These contaminations can lead to incorrect analyses; however, practical detection tools are lacking.
View Article and Find Full Text PDFJ Genomics
January 2025
Université de Lorraine, INRAE, UMR 1136 Interactions Arbres/Microorganismes, 54280, Champenoux, France.
The earthball , an ectomycorrhizal basidiomycete belonging to the Sclerodermataceae family, serves as a significant mutualistic tree symbiont globally. Originally, two genetically sequenced strains of this genus were obtained from fruiting bodies collected under chestnut trees (). These strains were utilized to establish ectomycorrhizal roots of chestnut seedlings.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Korea Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
Given the presence of highly repetitive genomic regions such as subtelomeric regions, understanding human genomic evolution remains challenging. Recently, long-read sequencing technology has facilitated the identification of complex genetic variants, including structural variants (SVs), at the single-nucleotide level. Here, we resolved SVs and their underlying DNA damage-repair mechanisms in subtelomeric regions, which are among the most uncharted genomic regions.
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