遗传最新文献

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.

Echolocation is a complex biological traits that collaborated by multiple systems. Its origin can be traced back to 68 million years ago, and repeatedly appeared in multiple vertebrate groups in the subsequent biological evolution. The strong vitality has become a typical case of the convergence evolution in nature. However, it was not until the beginning of the 20th century that humans really opened the prelude to the research on animal echolocation, and became research hotspots in the fields of zoology, behavior, and genetics, and achieved rich results in the past 80 years. In this review, we summarize the development history of animal echo positioning, summarize different echo positioning animal groups in detail, and focuse on the research progress of echo positioning in sound mechanisms, acoustic characteristics, and high-frequency listening mechanisms in order to provide reference for comprehensive understanding of animal echo positioning.

The origin and evolution of sex chromosomes have long been a focus of research in biology. Two of the most studied systems are the XY system and the ZW system. Due to Y/W degeneration, heterozygous (XY/ZW) sex-linked genes are absent and their dosage is reduced when compared to autosomal genes and homozygous (XX/ZZ) sex-linked genes, creating an issue of dosage imbalance between sex chromosomes and autosomes. Multiple evolutionary models have been proposed to explain the evolutionary mechanism of dosage compensation that might resolve such dosage imbalance. In this review, we summarize the findings related to the dosage effect of sex chromosomes from a variety of perspectives, including transcriptomes, proteomes, haploid cells, and single cells. In addition, a summary of the dosage effect of sex chromosomes in major phylogenetic branches of multiple species is provided. Finally, we approved an overview of the related theoretical models and future research directions at the end of this paper.

Evolutionary developmental biology combines evolutionary biology and developmental biology, focusing on the evolution of developmental processes and the mechanisms of morphological diversification. Since the discovery of the homeobox gene in 1984, the genetic mechanisms of morphogenesis in multiple model organisms have been systematically studied. In contrast, non-model organisms are rich in complex evolutionary traits, yet their underlying genetic mechanisms have not yet been fully elucidated, so more relevant studies are still needed. Among non-model organisms, butterflies are rich in species diversity, with more than 18,700 species. In particular, butterfly wings have simple flat structures but exhibit diverse and complex patterns, likely associated with complex functions(e.g., defense and courtship) and subject to strong selective pressures, which makes them a classic system for evolutionary developmental biology studies. Early comparative morphological studies proposed the Nymphalid ground plan, providing a theoretical framework for the evolutionary developmental biology of butterfly wing patterns; a series of interference experiments on butterfly wing discs later confirmed the association between the wing developmental process and phenotypes. In recent years, by integrating genetics, developmental biology, and genomics research methods, genetic toolkit genes and loci involved in wing pattern regulation have been identified in several butterfly species, further improving the theoretical framework for studying butterfly wing pattern evolution and development. From the methodological perspective, experimental methods such as in situ hybridization and gene editing have played an important role in evolutionary developmental biology studies of butterfly wings, and the development of hybridization chain reaction technology and CRISPR/Cas9 gene editing technology has further advanced the feasibility of functional validation in butterflies. In the future, the development and optimization of lepidopteran RNA interference and gene editing technologies can promote functional studies, thus expanding the research systems of evolutionary developmental biology by comparing and analyzing complex traits. The above research can also be broadened to an ecological-evolutionary-developmental context to explore genetic and environmental factors that shape complex phenotypes(e.g., butterfly wing patterns), thereby deepening the understanding of key scientific issues such as the origin and evolution of biodiversity.