DNA replication during cell proliferation is ‘vertical’ copying, which reproduces an initial amount of genetic information. Polyploidy, which results from whole-genome duplication, is a fundamental complement to vertical copying. Both org...
The AUTS2 gene plays major roles during brain development and is associated with various neuropathologies including autism. Data in non-mammalian species are scarce, and the aim of our study was to provide a comprehensive analysis of auts2 evolution...
The human genome produces a large repertoire of non-coding RNAs (ncRNAs) with important regulatory roles in development, physiology, and most of diseases. Among these, long non-coding RNAs (lncRNAs) have emerged as key modulators of gene expression,...
Despite the recognized involvement of TTC39 family genes in metabolism related to pigment deposition, their evolutionary features and potential roles in body coloration in teleost fish remain largely unexplored. We identified three TTC39 genes in Ple...
Arginine vasotocin (AVT) is well known for its role in steroidogenesis and estradiol biosynthesis during early brain development in Epinephelus coioides. Despite its hormonal functions, the biological significance of AVT across different taxa remains...
Strictosidine synthases (STRs) are catalytic enzymes involved in terpenoid indole alkaloid biosynthesis, whereas STR-like (STRL) genes in cereal crops remain poorly understood. Previous studies of the maize STR-like (STRL) gene family have mainly pro...
Transposable elements subvert host cellular functions to ensure their survival. Their interaction with the host DNA replication machinery indicates that selective pressures lead them to develop ancestral and convergent evolutionary adaptations aimed...
The study of protein–protein interactions (PPIs) is of significant importance for elucidating biological processes, clarifying pathological mechanisms, and promoting drug development. In this study, we proposed a method to predict PPIs based on...
ATP-binding cassette (ABC) transporters are one of the largest superfamilies of membrane proteins, but little is known about the structural and evolutionary features of their non-domain regions. To clarify the diversity of these non-canonical regions...
The genus Desmidorchis Ehrenb. (Apocynaceae) is a characteristic component of the succulent flora of the Arabian Peninsula, where high levels of endemism and increasing environmental pressures highlight the need for integrated genomic and conservatio...
Background: Traditional morphology-based classification of the Oriental Plover (Anarhynchus veredus) is inconsistent with molecular evidence, underscoring the necessity of incorporating molecular data to elucidate its evolutionary relationships withi...
The cell wall is a crucial feature that allows ancestral streptophyte green algae to colonize land. Expansin, an extracellular protein that mediates cell wall loosening in a pH-dependent manner, could be a powerful tool for studying cell wall evoluti...
Alternative splicing (AS) is a widely recognized post-transcriptional regulatory mechanism that plays a crucial role in plant evolution and environmental adaptation. In this study, five representative Panax species were systematically analyzed to exa...
Conservation and long-term management plans of marine species need to be based upon the universally recognized key-feature of species identity. This important assignment is particularly challenging in skates (Rajiformes) in which the phenotypic simil...
Gibberellic Acid-Stimulated Arabidopsis (GASA) proteins are cysteine-rich peptides broadly conserved in plants and implicated in growth regulation, stress adaptation, and hormone signaling. Here, we identified 13 GASA genes in the maize genome, distr...
Sinojackia Hu. comprises five to eight Chinese endemic species with high ornamental and medicinal value. However, the generic limits, interspecific relationships and evolutionary history of the genus remain unresolved. In this study, we newly sequenc...
SMXL genes constitute a conserved gene family that is ubiquitous in angiosperms and involved in regulating various plant processes, including branching, leaf elongation, and anthocyanin biosynthesis, but little is known about their molecular function...
Our evolutionary and structural analyses revealed that the severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) spike gene is a complex mosaic resulting from several recombination events. Additionally, the fixation of variants has main...
The wealth of biological databases provides a valuable asset to understand evolution at a molecular level. This research presents the machine learning approach, an unsupervised agglomerative hierarchical clustering analysis of invariant solvent acces...
To broaden the scope of research on the characteristics and evolutionary relationships within the heat shock protein 70 (Hsp70) family, encompassing its non-canonical members, amino acid sequences of Hsp70-12, Hsp70-13, and Hsp70-14, alongside those...
Mitochondrial codon usage and selective pressures drive adaptive evolution and translation efficiency. This study provides insights into the evolutionary constraints shaping 13 core mitochondrial proteins in Corvides, based on 117 species, including...
The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA w...
Mosses (Bryophyta) comprises a group of terrestrial plants that colonized land more than 450 million years ago that play fundamental ecological and evolutionary roles, particularly in polar and peatland ecosystems. The sequencing of Physcomitrium pat...
The variability in centrosome size, shape, and activity among different organisms provides an opportunity to understand both conserved and specialized actions of this intriguing organelle. Centrosomes in the model organism Dictyostelium sp. share som...
GATA transcription factors represent a conserved family of regulatory proteins that modulate plant growth and stress adaptation. While GATA families have been well characterized in model plants and Solanaceae crops, their evolutionary and functional...
The GLABROUS1 Enhancer Binding Protein (GeBP) gene family plays a crucial role in plant growth, development, and stress responses. In this study, 28 GeBP genes were identified in Brassica oleracea using HMMER and validated through multiple conserved...
A chimeric protein produced from the fusion of a type-P4 ATPase, also called flippase, and a guanylate cyclase (P4GC) was originally described in ciliates and malaria parasites. An extensive search for P4GC homologs was carried out, and the protein&r...
Chloroplast genomes are valuable tools for exploring plant evolution, photosynthesis, and molecular systematics due to their relatively conserved structure and gene content. Here, I present a comprehensive comparative analysis of complete chloroplast...
While most patients with degenerative rotator cuff tears respond to conservative treatment, a minority progress to surgery. To anticipate these cases under class imbalance, we propose a sensitivity-constrained evolutionary feature selection framework...
Hippophae rhamnoides ssp. sinensis Rousi a species of significant ecological and economic value that is native to the Qinghai–Tibet Plateau and arid/semi-arid regions. Investigating the mitochondrial genome can elucidate stress adaptation mecha...
Heterotrimeric G-proteins are fundamental signal transducers highly conserved in plant species, which play crucial roles in regulating plant growth, development, and responses to abiotic stresses. Identification of G-protein members and their express...
While the concept of “evolutionary conservation” has enabled biologists to explain many ancestral features and traits, it has also frequently been misused to evaluate the degree of changes from a common ancestor, or “derivedness&rdq...
Colletotrichum spp. are the causative agents of anthracnose of rubber trees, one of the most destructive diseases, resulting in substantial economic losses. To investigate the evolutionary characteristics of these pathogenic species, we first assembl...
Mitochondrial genome sequences have been used in diverse fields of biology. In this study, we sequenced the complete mitochondrial genomes (mitogenome) of two pear pests: Cacopsylla jukyungi, the most damaging insect pest to commercial pears in South...
Clethra fargesii, an essential ecological and endemic woody plant of the genus Clethra in Clethraceae, is widely distributed in Central China. So far, there have been a paucity of studies on its chloroplast genome. In the present study, we sequenced...
Low complexity regions (LCRs) in proteins are characterized by amino acid frequencies that differ from the average. These regions evolve faster and tend to be less conserved between homologs than globular domains. They are not common in bacteria, as...
Bioinformatics and biophysical studies of intrinsically disordered proteins and regions (IDRs) note the high entropy at individual sequence positions and in conformations sampled in solution. This prevents application of the canonical sequence-struct...
Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguicul...
Feline coronaviruses (FCoVs) are evolutionarily dynamic alphacoronaviruses whose diversification has been driven by extensive genetic exchange and long-term adaptation. However, how genome plasticity is balanced with the evolutionary constraints requ...
The dung beetle family Geotrupidae (Scarabaeoidea) plays a vital ecological role in nutrient cycling and soil health, yet the scarcity of complete mitochondrial genome (mitogenome) data has hindered phylogenetic and comparative studies within this fa...
Sestrins are a conserved family of stress-responsive proteins that play a crucial role in cellular metabolism, stress response, and ageing. Vertebrates have three Sestrin genes (SESN1, SESN2, and SESN3), while invertebrates encode only one. Initially...
Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cel...
Human metapneumovirus genotype B (HMPV-B) is an important respiratory pathogen, requiring detailed elucidation of the evolutionary and antigenic features of its fusion (F) gene. Using 500 sequences collected between 1982 and 2024, we investigated the...
Anguillid herpesvirus 1 (AngHV-1) is a pathogen of eels and a member of the genus Cyprinivirus in the family Alloherpesviridae. We have compared the biological and genomic features of different AngHV-1 strains, focusing on their growth kinetics in vi...
The Kelch-like ECH-associated protein 1 (KEAP1)/Nuclear factor E2-related factor 2 (NRF2) pathway is a key mechanism that responds to oxidative stress and xenobiotic stimuli in vertebrates. However, knowledge of its evolutionary origins remains limit...
Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated cereals worldwide, holding significant agricultural, historical, and evolutionary importance. However, our genomic knowledge of it is rather limited at present, hampering fur...
Paeonia ludlowii, a critically endangered species endemic to Tibet, China, possesses significant ornamental, culinary, and medicinal value. However, its mitochondrial genome remains understudied, limiting insights into its evolutionary mechanisms and...
Resilin is an elastic protein that is vital to insects’ vigorous movement. Canonical resilin proteins possess the R&R Consensus, a chitin-binding domain conserved in a family of cuticular proteins, and highly repetitive sequences conferring...
The adaptive immune system arose around 500 million years ago in jawed fish, and, since then, it has mediated the immune defense against pathogens in all vertebrates. Antibodies play a central role in the immune reaction, recognizing and attacking ex...
The calmodulin-binding protein 60 (CBP60) family comprises essential Ca2+-responsive transcription factors that orchestrate salicylic acid (SA)-mediated immunity and broader stress responses. Despite being extensively characterized in model species,...
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