Identification of Disease-Related 2-Oxoglutarate/Fe (II)-Dependent Oxygenase Based on Reduced Amino Acid Cluster Strategy

Soybean genome‑wide association study of seed weight, protein, and oil content in the southeastern USA

Soybean is a globally significant legume crop, providing essential protein and oil for human and livestock nutrition. Improving oil and protein content simultaneously without compromising yield has been challenging due to the quantitative nature of these traits and their interrelationships. This study aims to deepen our understanding of the molecular basis soybean of seed weight, protein, and oil content to facilitate marker-assisted breeding to enhance these traits. In this research, a Genome-Wide Association Study (GWAS) was conducted utilizing 285 diverse soybean accessions from maturity group V, employing genotyping through the SoySNP50K platform. These accessions were tested in three environmental conditions of the southeast US for three traits: 100-seed weight, protein, and oil content. The study identified 18, 23, and 26 SNPs significantly associated with 100-seed weight, seed oil, and protein content. Colocalized protein and oil content regions were discovered on chromosomes 15, 16, and 20. Chromosomes 15 and 20 are well documented to have pleiotropic but opposite effects on oil and protein content, but both regions contain genes that affect individual traits, such as FAD2-1 and nodulin MtN21. A 1.92 Mb region on chromosome 11 exhibits a target region to improve oil and seed weight without affecting protein content. This study highlights key genomic regions and candidate genes influencing seed weight, protein, and oil content, with some regions affecting multiple traits. Hence, these findings provide a valuable foundation for marker-assisted selection to optimize seed weight and simultaneously enhance oil and protein content in soybean breeding programs.

Genomic diversity and biogeographic distributions of a novel lineage of bacteriophages that infect marine OM43 bacteria

The marine methylotrophic OM43 clade is considered an important bacterial group in coastal microbial communities. OM43 bacteria, which are closely related to phytoplankton blooms, have small cell sizes and streamlined genomes. Bacteriophages profoundly shape the evolutionary trajectories, population dynamics, and physiology of microbes. The prevalence and diversity of several phages that infect OM43 bacteria have been reported. In this study, we isolated and sequenced two novel OM43 phages, MEP401 and MEP402. These phages share 90% of their open reading frames (ORFs) and are distinct from other known phage isolates. Furthermore, a total of 99 metagenomic viral genomes (MVGs) closely related to MEP401 and MEP402 were identified. Phylogenomic analyses suggest that MEP401, MEP402, and these identified MVGs belong to a novel subfamily in the family Zobellviridae and that they can be separated into two groups. Group I MVGs show conserved whole-genome synteny with MEP401, while group II MVGs possess the MEP401-type DNA replication module and a distinct type of morphogenesis and packaging module, suggesting that genomic recombination occurred between phages. Most members in these two groups were predicted to infect OM43 bacteria. Metagenomic read-mapping analysis revealed that the phages in these two groups are globally ubiquitous and display distinct biogeographic distributions, with some phages being predominant in cold regions, some exclusively detected in estuarine stations, and others displaying wider distributions. This study expands our knowledge of the diversity and ecology of a novel phage lineage that infects OM43 bacteria by describing their genomic diversity and global distribution patterns. IMPORTANCE OM43 phages that infect marine OM43 bacteria are important for host mortality, community structure, and physiological functions. In this study, two OM43 phages were isolated and characterized. Metagenomic viral genome (MVG) retrieval using these two OM43 phages as baits led to the identification of two phage groups of a new subfamily in the family Zobellviridae. We found that group I MVGs share similar genomic content and arrangement with MEP401 and MEP402, whereas group II MVGs only possess the MEP401-type DNA replication module. Metagenomic mapping analysis suggests that members in these two groups are globally ubiquitous with distinct distribution patterns. This study provides important insights into the genomic diversity and biogeography of the OM43 phages in the global ocean.

Research progress of reduced amino acid alphabets in protein analysis and prediction

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A comprehensive summary of the literature on the reduced amino acid alphabets.

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A systematic review of the development history of reduced amino acid alphabets.

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Rich application cases of amino acid reduction alphabets are described in the article.

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A detailed analysis of the properties and uses of the reduced amino acid alphabets.

Proteins are the executors of cellular physiological activities, and accurate structural and function elucidation are crucial for the refined mapping of proteins. As a feature engineering method, the reduction of amino acid composition is not only an important method for protein structure and function analysis, but also opens a broad horizon for the complex field of machine learning. Representing sequences with fewer amino acid types greatly reduces the complexity and noise of traditional feature engineering in dimension, and provides more interpretable predictive models for machine learning to capture key features. In this paper, we systematically reviewed the strategy and method studies of the reduced amino acid (RAA) alphabets, and summarized its main research in protein sequence alignment, functional classification, and prediction of structural properties, respectively. In the end, we gave a comprehensive analysis of 672 RAA alphabets from 74 reduction methods.