Saccharomyces cerevisiae, as a Generally Recognized as Safe (GRAS) fungus, has become one of the most widely used chassis cells for industrial applications and basic research. However, owing to its complex genetic background and intertwined metabolic...
Phage therapy is still in its infancy, but it is increasingly promising as a future alternative for treating antibiotic-resistant bacteria. To investigate the effect of phages on Mycobacterium abscessus complex (MABC), we isolated 113 environmental p...
Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Environmental concerns about fossil fuel combustion led to a sharp move towards renewable and environmentally friendl...
Oncolytic virus (OV) therapy has emerged as a promising approach for cancer treatment with the potential to be less toxic and more efficient than classic cancer therapies. Various types of OVs in clinical development, including Vaccinia virus (VACV)-...
Cell responses are usually viewed as transitive events with fixed inputs and outputs that are regulated by feedback loops. In contrast, directed cycles (DCs) have all nodes connected, and the flow is in a single direction. Consequently, DCs can regen...
The genus Flavobacterium contains a large group of commensal bacteria identified in diverse terrestrial and aquatic habitats. We compared the genome of a new species Flavobacterium akiainvivens IK-1T to public available genomes of Flavobacterium spec...
The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not al...
The evolution of the karyotype and genome size was examined in species of Crepis sensu lato. The phylogenetic relationships, inferred from the plastid and nrITS DNA sequences, were used as a framework to infer the patterns of karyotype evolution. Fiv...
When discussing chromosomal instability, most of the literature focuses on the characterization of individual molecular mechanisms. These studies search for genomic and environmental causes and consequences of chromosomal instability in cancer, aimin...
The development of multicellular eukaryotes, according to their body plan, is often directed by members of multigene families that encode transcription factors. MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR)-box...
The universality of DNA methylation as an epigenetic regulatory mechanism belongs to all biological kingdoms. However, while eukaryotic systems have been the primary focus of DNA methylation studies, the molecular mechanisms in prokaryotes are less k...
Since the discovery of transposable elements (TEs) in maize in the 1940s by Barbara McClintock transposable elements have been described as junk, as selfish elements with no benefit to the host, and more recently as major determinants of genome struc...
The question whether evolution is blind is usually presented as a choice between no goals at all (‘the blind watchmaker’) and long-term goals which would be external to the organism, for example in the form of special creation or intelligent design....
All viruses, but especially RNA viruses, generate tremendous diversity in genome composition, including point mutations, duplications, deletions, and insertions. We used in vitro and in vivo models to perform natural and directed experimental evoluti...
The genus Geobacillus is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that Geobacillus evolved from Bacillus, relatively little knowledge has b...
The chloroplast genome, as an important evolutionary marker, can provide a new breakthrough direction for the population evolution of plant species. Actinidia deliciosa represents one of the most economically significant and widely cultivated fruit s...
Cell morphology is an essential and phenotypic trait that can be easily tracked during adaptation and evolution to environmental changes. Thanks to the rapid development of quantitative analytical techniques for large populations of cells based on th...
Genome size is a biodiversity trait that shows staggering diversity across eukaryotes, varying over 64,000-fold. Of all major taxonomic groups, land plants stand out due to their staggering genome size diversity, ranging ca. 2400-fold. As our underst...
Capsicum (pepper) is an economically vital genus in the Solanaceae family, with most species possessing about 3 Gb genomes. However, the recently sequenced Capsicum rhomboideum (~1.7 Gb) represents the first reported case of an extremely compact geno...
Bacteriophage genomes represent an enormous level of genetic diversity and provide considerable potential to acquire new insights about viral genome evolution. In this study, the genome sequences of sixteen Bacillus-infecting bacteriophages were expl...
LTR retrotransposons (RTEs) play a crucial role in plant genome evolution and adaptation. Although RTEs are generally silenced in somatic plant tissues under non-stressed conditions, some expressed RTEs (exRTEs) escape genome defense mechanisms. As o...
Formerly considered nonfunctional “junk DNA,” pseudogenes have been re-evaluated in light of technological advances in bioinformatics and high-throughput sequencing. The limited research to date on pseudogenes in hexaploid common wheat (T...
Large DNA fragment deletion (LDFD) provides a powerful means to reconfigure plant genomes at the kilobase to megabase scale, enabling the dissection of genome function, elucidation of non-coding regulatory elements, modulation of gene dosage, reorgan...
Background/Objectives: With advances in sequencing technology, whole genome sequences have become a valuable resource for deciphering species evolution. However, efficiently extracting phylogenetic information from such data remains a major challenge...
One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to advances in high throughput sequencing technologies it is no...
Directed evolution is a powerful approach for protein engineering and functional studies. However, directed evolution outputs from bacterial and yeast systems do not always translate to higher organisms. In situ directed evolution in plant and animal...
While it is well known that 98–99% of the human genome does not encode proteins, but are nevertheless transcriptionally active and give rise to a broad spectrum of noncoding RNAs [ncRNAs] with complex regulatory and structural functions, specif...
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led...
Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these funda...
In the dynamic field of gene therapy, recombinant adeno-associated viruses (rAAVs) have become leading viral vectors due to their safety, long-term expression, and wide-ranging cell and tissue tropism. With numerous FDA approvals and commercial produ...
Nemertea is a phylum consisting of 1300 mostly marine species. Nemertea is distinguished by an eversible muscular proboscis, and most of the species are venomous. Genomic resources for this phylum are scarce despite their value in understanding biodi...
Genomic characterization of circulating influenza type-A viruses (IAVs) directs the selection of appropriate vaccine formulations and early detection of potentially pandemic virus strains. However, longitudinal data on the genomic evolution and trans...
With the increasing power of DNA sequencing, the genomics-based approach is becoming a promising resolution to dissect the molecular mechanism of domestication of complex traits in trees. Genus Camellia possesses rich resources with a substantial val...
Retrotransposons can alter the regulation of genes both transcriptionally and post-transcriptionally, through mechanisms such as binding transcription factors and alternative splicing of transcripts. SINE-VNTR-Alu (SVA) retrotransposons are the most...
We sequenced the complete mitochondrial genomes of Lycosa shansia, and Lycosa singoriensis by combining Sanger and next-generation sequencing methods and analyzed the sequenced genomes in order to explore the phylogenetic placement and the mitogenome...
The Lauraceae family, a keystone group in subtropical evergreen broad-leaved forest ecosystems, exhibits exceptional diversity in sexual systems (including hermaphroditic flowers, functionally unisexual flowers, and pseudo-dioecy), serving as a natur...
The monotremes (platypuses and echidnas) represent one of only four extant venomous mammalian lineages. Until recently, monotreme venom was poorly understood. However, the availability of the platypus genome and increasingly sophisticated genomic too...
Aging in sexually reproducing organisms is shaped by the declining force of natural selection after reproduction begins. In Drosophila melanogaster, experimental evolution shows that altering the age of reproduction shifts the timing of aging. Using...
Olea europaea Geminivirus (OEGV) was recently identified in olive in Italy through HTS. In this work, we used HTS to show the presence of an OEGV isolate in Portuguese olive trees and suggest the evolution direction of OEGV. The bipartite genome (DNA...
Mitochondria are well known to participate in multiple aspects of tumor formation and progression. They indeed can alter the susceptibility of cells to engage regulated cell death, regulate pro-survival signal transduction pathways and confer metabol...
Begomovirus has become a potential threat to the agriculture sector. It causes significant losses to several economically important crops. Given this considerable loss, the development of tools to study viral genomes and function is needed. Infectiou...
The evolution and the emergence of new mutations of viruses affect their transmissibility and/or pathogenicity features, depending on different evolutionary scenarios of virus adaptation to the host. A typical trade-off scenario of SARS-CoV-2 evoluti...
In recent years, great advances have been made in the field of collection, storage, and analysis of biological samples. Large collections of samples, biobanks, have been established in many countries. Biobanks typically collect large amounts of biolo...
Copy number variations (CNVs), as an important structural variant in genomes, are widely present in plants, affecting their phenotype and adaptability. In recent years, CNV research has not only focused on changes in gene copy numbers but has also be...
Few genomes of the HF1-group of viruses are currently available, and further examples would enhance the understanding of their evolution, improve their gene annotation, and assist in understanding gene function and regulation. Two novel HF1-group hal...
This review focuses on CRISPR genome editing technology, particularly its application in the study of Macrobrachium rosenbergii (M. rosenbergii). It first elaborates on the basic principles and mechanisms of CRISPR–Cas9 technology, base editors...
In the search of theoretical models describing cancer, one of promising directions is chaos. It is connected to ideas of “genome chaos” and “life on the edge of chaos”, but they profoundly differ in the meaning of the term &ld...
This review initiates by outlining the clinical relevance of IA, underlining the pressing need to comprehend its foundational elements. We delve into the assorted risk factors tied to IA, spotlighting both environmental and genetic influences. Additi...
Bacteriophages are a key ecological factor in the legume rhizosphere, controlling bacterial populations and affecting introduced inoculant strains. Despite their importance, rhizobiophage genomic diversity remains poorly characterized. We report the...
Single nucleotide polymorphism was widely used to perform genetic and evolution research in pigs. However, little is known about the effect of copy number variation (CNV) on characteristics in pigs. This study performed a genome-wide comparison of CN...
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