Due to their high number and variety, simple sequence repeats in DNA are a valuable source of genetic markers widely used in population genetics, genetic diversity, and fingerprinting. is a cosmopolitan basidiomycete and a valuable object for biotechnology and mycology. It is often used as a model organism in genetic and population studies. Numerous genome sequences of are available in the National Center for Biotechnology Information (NCBI) database, allowing for a meticulous study of the distribution of simple tandem nucleotide repeats in the genomes of different strains, based on their origin. Analysis of the average density of simple tandem repeats in the genomes of fungi reveals the division of cultures into groups based on the USA, Ru (Russian Federation), and EA (South Korea, Japan, China) populations. Intensive point mutations lead to the accumulation and dominance of mononucleotide (C)n and dinucleotide (CG)n motifs in fungal genomes. Results show that the GCT motif contributes more to the divergence of the Ru population, whereas CTC, GAG, and GGA motifs contribute to the divergence of the USA population. Strains MG53 (China) and IUM1114-SS01 (South Korea: Incheon) from the EA population occupy a separate position, mainly because of the CGA motif. The divergence in quantitative traits of motifs between populations provides evidence of the evolutionary transformation of fungal genomes under environmental factors.
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http://dx.doi.org/10.1080/00275514.2023.2186742 | DOI Listing |
JAMA Netw Open
January 2025
Department of Medicine, Harvard Medical School, Boston, Massachusetts.
Importance: Disease characteristics of genetically mediated coronary artery disease (CAD) on coronary angiography and the association of genomic risk with outcomes after coronary angiography are not well understood.
Objective: To assess the angiographic characteristics and risk of post-coronary angiography outcomes of patients with genomic drivers of CAD: familial hypercholesterolemia (FH), high polygenic risk score (PRS), and clonal hematopoiesis of indeterminate potential (CHIP).
Design, Setting, And Participants: A retrospective cohort study of 3518 Mass General Brigham Biobank participants with genomic information who underwent coronary angiography was conducted between July 18, 2000, and August 1, 2023.
Funct Integr Genomics
January 2025
Children's Medical Center, Peking University First Hospital, No.5 Le Yuan Road, Daxing District, 100034, Beijing, China.
Long-read sequencing has emerged as a transformative technology in recent years, offering significant potential for the molecular diagnosis of unresolved genetic disorders. Despite its promise, the comprehensive detection and clinical annotation of genomic variants remain intricate and technically demanding. We present SUMMER, an integrated and structured workflow specifically designed to process raw Nanopore sequencing reads.
View Article and Find Full Text PDFPlant Mol Biol
January 2025
Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Biotechnology of Fujian Higher Education Institutes, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Int J Colorectal Dis
January 2025
Internal Medicine, Jilin Cancer Hospital, Changchun, China.
Purpose: This phase II study is designed to evaluate the combination therapy involving suvemcitug and envafolimab with FOLFIRI in microsatellite-stable or mismatch repair-proficient (MSS/pMMR) colorectal cancer (CRC) in the second-line treatment setting.
Methods: This study is a non-randomized, open-label prospective study comprising multiple cohorts (NCT05148195). Here, we only report the data from the CRC cohort.
Mol Biol Evol
January 2025
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China.
Nucleotide-binding leucine-rich repeat receptor (NLR) genes encode a pivotal class of plant immune receptors. However, their rampant duplication and loss have made inferring their genomic evolutionary trajectory difficult, exemplified by the loss of TNL family genes in monocots. In this study, we introduce a novel classification system for angiosperm NLR genes, grounded in network analysis of micro-synteny information.
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