[This corrects the article DOI: 10.1093/hr/uhab077.].
[This corrects the article DOI: 10.1093/hr/uhab077.].
[This corrects the article DOI: 10.1093/hr/uhac105.].
Potato common scab (CS) is a worldwide disease, caused by Streptomyces spp., and its presence reduces the market value of potatoes. A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents. In this study, Bacillus atrophaeus DX9 was isolated and assessed for its ability to protect against CS. Through integrated metagenomic and metabolomic analyses, changes in the soil microbial community structure and soil properties were analyzed to understand the effects of Bacillus atrophaeus DX9 on CS. These studies revealed that DX9 inoculation could significantly decrease CS disease rate, disease index, and the number of CS pathogens, along with an increase in soil N and P content. Our metagenomic assays identified 102 phyla and 1154 genera, and DX9 inoculation increased the relative abundances of the phyla Pseudomonadota, Chloroflexota and Gemmatimonadota. Additionally, an increase in the relative abundance of genera, such as Bradyrhizobium, Agrobacterium, and Nitrobacter, were significantly and positively correlated with soil N and P. Metabolomic analysis revealed that DX9 inoculation significantly increased the soil levels of phytolaccoside A, 7,8dihydropteroic acid, novobiocin, and azafrin. These compounds were enriched in microbe pathway metabolites, including xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and metabolism of cofactors and vitamins. In summary, the use of Bacillus atrophaeus DX9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties. This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.
CRISPR/Cas is a simple, robust, versatile tool for plant biology studies and precision plant breeding. However, establishing a high-efficiency gene editing system for multiplex editing of the autotetraploid crop alfalfa (Medicago sativa L.), the most important forage legume worldwide, remains a formidable challenge. Here, we systematically identified endogenous U6 promoters in alfalfa through transient expression via Agrobacterium-mediated infiltration of alfalfa leaves. We further demonstrated the efficacy of the three most active promoters for genome editing using an optimized alfalfa hairy root system. Subsequently, we established an improved CRISPR/Cas9 multiplex system containing three or four tandemly arrayed MsU6-promoter-driven polycistronic tRNA-sgRNA (PTG) expression cassettes, each consisting of three tRNA-sgRNA units, to simultaneously edit three or four alfalfa genes, coupled with the visual reporter RH1 or RUBY. This toolkit showed efficient multiplex editing in the hairy root system with visual selection. We successfully obtained regenerated, red-colored shoots resulting from the stable transformation of alfalfa. These results highlight the potential application of the visual reporter system for the stable transformation of alfalfa. Our improved CRISPR/Cas9 multiplex system enables convenient, high-efficiency multiplex genome editing in alfalfa, providing a versatile toolset to facilitate functional studies of multiple genes and gene families for basic research and the genetic improvement of alfalfa.
The large-scale data generated by various omics technologies pose significant scientific challenges about how to rapidly and accurately analyze these data. It is essential to develop convenient tools that allow users to efficiently and precisely handle massive biological data. Based on new theories and mathematical models, as well as software engineering, this field is becoming an important research direction in bioinformatics and computational biology. In this review, we briefly review the development history of bioinformatics-related software. We also summarize the recent progress, focus on their application on evolutionary biology, and discuss three major ways of computer running mode and three paradigms of software programming. We also introduce the eGPS, a self-developed multi-functional evolutionary and omics analysis software platform, including the application of eGPS along with Conda and R for data analysis on individual genes, pathways, or genomes. We then propose new ideas for software development, use, and maintenance tailored to different users with varying scientific objectives. It posits that using a personal computer for evolutionary and multi-omics analysis is not only a necessity but also playing an important role.
Chromosomes, as the fundamental unit of genetic material located within the cell nucleus, have undergone extensive and complex changes throughout the evolutionary history of eukaryotes. Many of these patterns and mechanisms of change share commonalities across various diseases, including cancer. For a long time, biologists were limited to research methods with relatively low resolution, such as fluorescence in situ hybridization (FISH). However, the rapid advancement of high-throughput sequencing technologies is revolutionizing our understanding of chromosomal variations across different species, among individuals of the same species, and even at the cellular level within a single individual. In this review, we focus on the chromosomal evolution in vertebrates, and provide an overview of the role of chromosom rearrangements in speciation, the molecular mechanisms of chromosomal rearrangements, the evolutionary patterns from ancestral chromosomes to extant chromosomes, and the significance of sex chromosomes as a general paradigm for studying chromosomal evolution. Finally, we discuss the new opportunities and challenges that synthetic biology brings to the field of chromosomal evolution research, with the aim of offering new insights and references for understanding and studying vertebrate chromosomal evolution.
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has significantly impacted human life safety and the global economy. The rapid mutation of the SARS-CoV-2 genome has attracted widespread attention, with almost every site in the genome experiencing single nucleotide variants (SNVs). Among these, the mutations in the spike (S) protein are of particular importance, as they play a more critical role in the virus's adaptive evolution and transmission. In this review, we summarize the phylogenetic relationships between SARS-CoV-2 and related coronaviruses in non-human animals, and delves into the lineage classification of SARS-CoV-2 and the impact of key amino acid variations on viral biological characteristics. Furthermore, it outlines the current challenges and looks forward to the promising application of deep mutational scanning (DMS) combined with artificial intelligence methods in predicting the prevalence trends of SARS-CoV-2 variants.
Gene duplication is the process of a gene copied via specific molecular mechanisms to form more duplicate genes. As an important approach to the origination of new genes, gene duplication contributes to around half of the genes in eukaryotic genomes, facilitating the adaptive evolution of species. Over the past fifty years, especially since entering the genomics era in the last two decades, there have been extensive and profound discussions on the mechanisms, evolutionary processes and forces behind the emergence of duplicate genes. Sequence similarity of duplicate genes often leads to functional redundancy, enhancing organismal robustness. Conversely, functional divergence can create novel functions and improve evolvability. In this review, we summarize the mechanism of gene duplication, the fate and the evolutionary models of duplicate genes. This article concludes by outlining how long-read sequencing technologies, gene editing, and various other high-throughput techniques will further advance our understanding of the role of duplicate genes in the genetics-development-evolution network.
During evolution, mutations occur randomly and are fixed by selection. At the same time, species gradually formed, producing various life forms. In the traditional evolutionary theory system, mutations are considered genetic mutations by default, and somatic mutations are usually applicable in specific scenarios such as carcinogenesis, immunity and aging. At the same time, selection plays a role at multiple levels of living systems, including genes, cells, tissues and organs, individuals, populations, species, and even ecosystems. The research community of modern life science expresses genetic mutations as genotypes and cellular and other level characteristics as phenotypes, and finds that phenotypes are determined by both genotypes and environmental factors. Currently, it is unclear how genotypic and environmental factors act at the cellular level to create and fix new cell types. In this review, we summarize that it's time to move forward from gene evolution to build the framework for cell type evolution and finally update the theoretical system for evolutionary biology.
Tumor itself is a complex microecosystem, with complex spatio-temporal dynamics and multi-dimensional interactions. Its unimaginable heterogeneity and evolvability have exceeded the cognition of traditional oncology medicine. How to systematically characterize the whole tumor cell ecosystem from the dynamics and interaction of material, energy and signal levels, in order to explore new cognition, new rules and new therapies for the occurrence and development of tumors, is a new proposition and goal of tumor ecology. In this review, we discuss the origin, occurrence and development of tumors from the perspective of evolutionary ecology. First, we discuss the application of some classical concepts of ecology with tumor evolution. Subsequently, through the integration of the frontier papers of tumor ecology, we highlight the importance of ecological interactions on the occurrence and development of tumors from multiple levels, such as between cancer cells, between cancer cells and other normal somatic cells, and the tumor ecosystem. Finally, we propose the concept of tumor cell ecosystem, discussed how to characterize the entire tumor ecosystem from the system theory and proposed possible innovative treatment directions.
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