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PubMed2004

Conserved function of medaka pink-eyed dilution in melanin synthesis and its divergent transcriptional regulation in gonads among vertebrates.

Medaka is emerging as a model organism for the study of vertebrate development and genetics, and its effectiveness in forward genetics should prove equal to that of zebrafish. Here, we identify by positional cloning a gene responsible for the medaka i-3 albino mutant. i-3 larvae have weakly tyrosinase-positive cells but lack strongly positive and dendritic cells, suggesting loss of fully differentiated melanophores. The region surrounding the i-3 locus is syntenic to human 19p13, but a BAC clone covering the i-3 locus contained orthologs located at 15q11-13, including OCA2 (P). Medaka P consists of 842 amino acids and shares approximately 65% identity with mammalian P proteins. The i-3 mutation is a four-base deletion in exon 13, which causes a frameshift and truncation of the protein. We detected medaka P transcripts in melanin-producing eyeballs and (putative) skin melanophores on embryos and an alternatively spliced form in the non-melanin-producing ovary or oocytes. The mouse p is similarly expressed in gonads, but not alternatively spliced. This is the first isolation of nonmammalian P, the functional mechanism of action of which has not yet been elucidated, even in mammals. Further investigation of the functions of P proteins and the regulation of their expression will provide new insight into body color determination and gene evolution.

Amino Acid Sequence↗
PubMed2025

Genome-wide identification, characterization, and expression pattern analysis of the glyoxalase gene family in Phyllostachys pubescens during abiotic stresses.

BACKGROUND: The glyoxalase pathway comprising of three enzymes i.e., glyoxalase I (GLYI), glyoxalase II (GLYII), and glyoxalase III (GLYIII), which play vital role in mitigating abiotic stresses by detoxifying the stress induced cytotoxic metabolite methylglyoxal (MG). Phyllostachys pubescens an ecologically and economically important forest species, plays vital roles in carbon sequestration and climate change mitigation. A genome-wide study was conducted to identify and characterize GLYI, GLYII, and unique DJ-1/GLYIII gene candidates in P. pubescens. The identified members were evaluated based on phylogenetic analysis, gene structure, chromosomal distribution, gene duplication, presence of conserved domain(s) and cis regulatory region. RESULTS: A total of 19 GLYI, 18 GLYII, and 15 GLYIII members were identified, each featuring characteristic domains: glyoxalase, metallo-β-lactamase, and DJ-1/PfpI, respectively. The presence of different cis-elements in the promoter region of the glyoxalase genes gives insights into their role and regulation under hormonal response, developmental processes and stress adaptation. Besides this, stress responsive transcription factors binding sites also dominated the promoter regions of glyoxalase genes. Expression analysis of various glyoxalase genes demonstrated significant variability under different stress conditions, underscoring their potential roles in stress modulation. Significant upregulation of all of the PhGLYI, PhGLYII, and PhGLYIII were observed under cold, drought, heavy metal and salinity stress suggesting their involvement in oxidative stress management, osmotic regulation and remodelling cellular redox homeostasis. Among the glyoxalase genes, PhGLYI-15, PhGLYII-9, and PhGLYIII-3 showed consistent upregulation under various abiotic stresses. CONCLUSIONS: Our findings reveal that glyoxalase genes crucially contribute towards the improvement of cellular osmotic potential in moso bamboo under different abiotic stresses. This study enhances our understanding of glyoxalase genes' evolution and functional roles in plants and opens new avenues for developing stress resilient crop varieties for sustainable agriculture.

Lactoylglutathione Lyase↗
PubMed2025

Fishing for a reelGene: evaluating gene models with evolution and machine learning.

Assembled genomes and their associated annotations have transformed our study of gene function. However, each new annotated assembly generates new gene models. Inconsistencies between annotations likely arise from biological and technical causes, including pseudogene misclassification, transposon activity, and intron retention from sequencing of unspliced transcripts. To evaluate gene model predictions, we developed reelGene, a pipeline of machine learning models focused on (1) transcription boundaries, (2) mRNA integrity, and (3) protein structure. The first two models leverage sequence characteristics and evolutionary conservation across related taxa to learn the grammar of conserved transcription boundaries and mRNA sequences, while the third uses the conserved evolutionary grammar of protein sequences to predict whether a gene can produce a protein. Evaluating 1.8 million transcript models in Zea mays ssp. mays (maize), reelGene classified 28% as incorrectly annotated or non-functional. We find that reelGene classifies 92.2% of genes in the maize proteome and 99.2% of genes within the maize classical gene list as functional. reelGene also provides a way to further investigate genome biology- for instance, reelGene indicates that 10.3% of dispensable genes in B73 are functional, and within retained duplicate genes, reelGene identifies a 30% bias toward the retention of the M1 subgenome when one copy is functional and the other is non-functional. As an annotation-evaluating tool, reelGene is directly applicable to species of the Andropogoneae tribe, including other important crops like sorghum and miscanthus. As a community resource, reelGene has been integrated onto MaizeGDB both as a browser track and as an individual Shiny App, allowing researchers to evaluate gene model accuracy and further investigate genome biology.

Machine Learning↗
PubMed1976

Estimation of age and rate of increase of rare variants.

The problem considered is that of estimating the age or rate of increase of a variant on the basis of the present number of replicates observed in a population. In place of previous diffusion equation analyses of age probability distributions, the likelihood for the age is studied on the basis of a discrete branching process model. It is shown that variations inherent in the process of gene evolution in natural populations make it impossible to provide a reliable point estimate of the age of a specified variant, although the likelihood analysis provides a confidence interval which may place useful bounds on the period in which a variant originated. The observed distribution of numbers of several variants may also provide useful information. The problems of estimation are discussed with reference to rare variants arising in American Indian populations.

Alleles↗
PubMed2026

Intra-colony divergence and global allele sharing reflect purifying selection and recombination at the Botryllus histocompatibility factor locus.

Urochordates, the closest relatives of vertebrates, lack adaptive immunity. However, some taxa, such as the colonial species Botryllus schlosseri, provide a unique model for studying innate self/non-self recognition through natural allogeneic transplantation responses. In this species, interactions between colonies are controlled by a highly polymorphic locus, with the Botryllus histocompatibility factor (BHF) being the only gene known to predict tissue fusion or rejection outcomes with complete accuracy. Here, we analyzed full-length BHF alleles from 19 laboratory-born and wild colonies and found that highly divergent alleles tend to coexist within individuals, whereas identical alleles can be shared across continental-scale distances. Despite extensive length variation, evidence of intragenic recombination, and pronounced nucleotide diversity, BHF exhibits limited protein divergence, with 33 alleles encoding only 17 distinct protein variants. Contrary to expectations for polymorphic recognition genes, no evidence of balancing or directional selection was detected. Instead, signatures of purifying selection were observed. We propose that this contrast between nucleotide and protein diversity arises from the combined effects of recombination, human-mediated gene flow, and linkage to nearby loci under balancing selection, while functional constraints maintain protein stability. These findings suggest that extensive protein diversification may not be a universal driver of allorecognition gene evolution.

Animals↗
PubMed2026

Highlights from the 14th International Conference for Plant Mitochondrial Biology: Current Trends and Future Directions.

Plant mitochondrial biology is undergoing a rapid transformation driven by advances in genomics, structural biology, quantitative imaging, and genome engineering. Once focused primarily on respiration and bioenergetics, the field now encompasses diverse areas including genome evolution, gene expression, organelle dynamics, stress signaling, metabolism, and biotechnology. The 14th International Conference for Plant Mitochondrial Biology (ICPMB), held in Kagoshima, Japan, from 18-22 May 2026 (Fig. 1), brought together researchers to discuss recent advances across these rapidly expanding research areas. This meeting report summarizes the major scientific advances presented at ICPMB 2026 and highlights emerging directions that are defining the future of plant mitochondrial biology.

Cytoplasmic male sterility (CMS)↗
PubMedDate not supplied

[Evolution of the gene in energy space].

General idea of a gene as a part of the hereditary molecule DNA permits to correlate various alleles states of a gene to various energy states of the hereditary molecule. Hereditary molecule under the action of a random force moves along its energy states. So far as the number of individuals in a population usually is very big, such motion of a gene in energy space resembles random motion of the Brownian particle in liquid. Here the process of striving hereditary molecule for minimum potential energy will correspond to the slow precipitation of particles under the effect of the force of gravity. Therefore, gene diffusion in energy space is described by the Focker--Plank's equation. The solution of this equation shows the time evolution of the distribution of genes alleles states within the limits of an isolated population.

Alleles↗
PubMed1975

The organization, expression, and evolution of antibody genes and other multigene families.

The multigene family is a unit of chromosomal organization. Its gene members are closely linked, homologous in sequence, and have overlapping functions. Multigene families can be divided into three catagories: simple-sequence, multiplicational, and informational-by a variety of structural and functional criteria. Multigene families exhibit two novel evolutionary features-coincidental evolution and rapid change in family size-that suggest that they all share one or more evolutionary mechanisms. Natural selection cannot act directly upon individual genes in a family because of their identical or overlapping functions; hence selection must operate upon the family as a whole or upon blocks of genes within the family. The mechanism(s) for coincidental evolution expands out variant genes within a family so they can be acted upon by natural selection and, accordingly, permits multigene families to evolve adaptively. The control mechanisms in multiplicational families appear to promote the rapid expression of many gene copies. In contrast, the regulatory mechanisms of informational families promote the selection, expression, and amplification of appropriate units of information. The close linkage of the genes in a family appears to be a consequence of the fact that their control and evolutionary mechanisms may only operate on tandemly linked genes. New multigene families may evolve from a single gene or from other multigene families. In addition to evolving new functions, the latter mode of evolution generates a new multigene family whose members are preadapted to interact with those of the old family. These family interactions can lead to the evolution of more sophisticated molecular machines or to the regulation of one family by a second. Multigene families may be large or small. The three catagories of multigene families allow potential multigene families to be identified, and they suggest specific experimental approaches for the study of new families. Some of the most interesting genetic systems under the investigation today are known or potential informational multigene families. This is not fortuitous in that many of the most interesting aspects of phenotype are complex ones with correspondingly complex genetic, evolutionary, and regulatory requirements. One of the frontiers in modern genetics is the identification, characterization, and understanding of informational multigene families.

Alleles↗
PubMed2025

Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.

Transposable elements (TEs) significantly influence genomic diversity and gene regulation in plants. Brassica rapa and B. oleracea, with their distinct domestication histories, offer excellent models to explore TE dynamics. Here, we developed a refined TE classification method and systematically analyzed TEs across 12 B. rapa and B. oleracea genomes, identifying 1878 TE families. Approximately half (49.5%) of these TE families were shared between the two species, reflecting a common evolutionary origin, whereas species-specific expansions, particularly among long-terminal repeat (LTR) retrotransposons, underscore their roles in genomic differentiation. We notably characterized a heat-responsive Ty1-copia family (Copia0035) in B. oleracea roots, distinguished by low GC content and the absence of CG and CHG methylation motifs, sharing regulatory similarities with the Arabidopsis heat-induced ONSEN element. Syntenic analyses of gene-TE associations highlighted significant intraspecies TE insertion variability, with more accession-specific insertions in B. rapa and more conserved insertions, often associated with distinct morphotypes in B. oleracea. Gene ontology enrichment indicated TE involvement in developmental, reproductive, and stress response pathways. Transcriptome analysis across diverse accessions revealed that genes proximal to TEs, particularly those regulating floral development and flowering time, exhibit increased expression variability. These findings advance our understanding of TE-mediated genome evolution in Brassica species and underscore their potential utility in breeding and genome engineering strategies for crop improvement.

DNA Transposable Elements↗
PubMed2026

Evolution and Expression Divergence of Legume PAL Genes Suggest Associations with Drought Response and Root Nodule Development.

Comparative genomic analyses provide insight into the mechanisms underlying gene-family evolution and crop adaptation. Here, we used the legume phenylalanine ammonia-lyase (PAL) gene family as a model and integrated pan-genomic, phylogenetic, molecular evolutionary, duplication-mode, and transcriptomic analyses, while developing GFtool for gene family identification. Across 45 genomes, we identified 302 PAL genes and classified them into five Groups. Groups 1-3 represented ancient lineages shared with outgroups, whereas Groups 4 and 5 were legume-specific. Molecular-clock analyses placed the divergence of Group 2 near the Paleocene-Eocene transition, while Groups 4 and 5 diversified from the middle Eocene to the early Oligocene. WGD/segmental duplication broadly contributed to PAL copy-number expansion, whereas tandem duplication was enriched in Group 5 of Papilionoideae. Group 2 genes showed drought-induced expression, whereas Group 5 genes were associated with early root nodule development. GFtool provides a scalable framework for gene-family studies.

Fabaceae↗
PubMed1978

Mutator genes--pacemakers of evolution.

Initially a genetic oddity, male recombination in Drosophilaelanogaster is now being viewed as a means of detecting mutator activity and chromosome breakage in hybridising populations and is causing us to reconsider the source and rate at which genetic variability may be generated in nature.

Animals↗
PubMed2026

Evolutionary architecture and lineage-specific diversification of Forkhead box transcription factors in Perna viridis.

The Forkhead box (Fox) transcription factors are evolutionarily conserved regulators of development, cell cycle, and apoptosis across metazoans. This study provides the first comprehensive genome-wide analysis of the Fox gene family in the Asian green mussel (Perna viridis). We identified 28 Fox genes distributed across 10 chromosomes. Comparative analysis reveals the absence of the FoxI, FoxQ1, FoxR and FoxS subfamily, consistent with other bivalves and indicative of lineage-specific gene loss during molluscan evolution. Notably, gene duplications in the FoxAB, FoxD, FoxH, FoxN1-4, FoxQ2 and FoxQD subfamilies may reflect functional diversification associated with environmental adaptation. Exon-intron structural variability, including intron loss in several paralogues, suggests structural diversification and potential regulatory variation. Phylogenetic reconstruction confirmed the monophyly of core Fox classes while highlighting divergent expansion patterns in lophotrochozoans. Selection analyses showed strong purifying selection across duplicated Fox paralogs, supporting functional conservation after lineage-specific expansion. Gene Ontology enrichment linked Fox genes to stress response, apoptosis, and transcriptional regulation. By integrating phylogenetic, structural, and transcriptomic analyses, this study provides a genomic framework for understanding Fox gene organisation, evolution, and tissue-associated expression patterns in Perna viridis and establishes a comparative resource for future functional studies in bivalves.

Animals↗
PubMed1979

Evolution of the differential regulation of duplicate genes after polyploidization.

In the 50 million years since the polyploidization event that gave rise to the catostomid family of fishes the duplicate genes encoding isozymes have undergone different fates. Ample opportunity has been available for regulatory evolution of these duplicate genes. Approximately half the duplicate genes have lost their expressions during this time. Of the duplicate genes remaining, the majority have diverged to different extents in their expression within and among adult tissues. The pattern of divergence of duplicate gene expression is consistent with the accumulation of mutations at regulatory genes. The absence of a correlation of extent of divergence of gene expression with the level of genetic variability for isozymes at these loci is consistent with the view that the rates of regulatory gene and structural gene evolution are uncoupled. The magnitude of divergence of duplicate gene expressions varies among tissues, enzymes, and species. Little correlation was found with the extent of divergence of duplicate gene expression within a species and its degree of morphological "conservatism", although species pairs which are increasingly taxonomically distant are less likely to share specific patterns of differential gene expression. Probable phylogenetic times of origin of several patterns of differential gene expression have been proposed. Some patterns of differential gene expression have evolved in recent evolutionary times and are specific to one or a few species, whereas at least one pattern of differential gene expression is present in nearly all species and probably arose soon after the polyploidization event. Multilocus isozymes, formed by polyploidization, provide a useful model system for studying the forces responsible for the maintenance of duplicate genes and the evolution of these once identical genes to new spatially and temporally specific patterns of regulation.

Animals↗
PubMed2025

Comprehensive identification and analysis of clusters of tandemly duplicated genes reveal their contributions to adaptive evolution of green plants.

Tandem gene duplication occurred more frequently compared with the episodic whole-genome duplication (WGD), providing a continuous supply of genetic material for evolutionary innovation and adaptation to changing environments. The rising roles of clusters of tandemly duplicated genes (CTDGs) in the evolution of phenotypic diversity have been unraveled in mammals. However, the content and biological roles of CTDGs remain largely unknown in plants. Here, we comprehensively identified CTDGs in 220 published plant genomes representing major lineages of green plants. The number of CTDGs showed great variation across taxa, ranging from 0 to 6028. The size of CTDGs varied from 2 to 47 genes, with small clusters containing two members predominating. Interestingly, significant expansion of CTDGs was found in early-diverging land plants and is closely associated with the evolution of key traits (e.g., ABA response, plant cuticle, UV-B resistance) required for plants to conquer terrestrial environments. Functional enrichment analysis revealed conserved and specialized functional profiles among different sizes of CTDGs in both Arabidopsis thaliana and the bryophyte Physcomitrium patens. Small CTDGs were enriched in fundamental stress responses, including protein modification, signal transduction, and responses to diverse stress stimuli, while large CTDGs were enriched in more sophisticated processes such as plant hormone biosynthesis and signaling, plant-microbe interactions, and reproductive processes. Expression pattern analyses of CTDGs under different stress conditions in A. thaliana and P. patens revealed that the highest number of CTDGs showed differential expression under drought stress, suggesting important roles of CTDGs in the evolution of desiccation tolerance in early land plants. The results of this study provide new additions to our knowledge about the abundance of CTDGs across green plants and reveal their important contributions to enable plants to overcome stressful environments on land.

Gene Duplication↗
PubMedDate not supplied

Multilocus enzymes in man.

Two or more separate loci may be concerned in coding for enzyme proteins with the same or very similar catalytic properties. The phenomenon appears to be remarkably common and rough estimates suggest that perhaps 50% or more of structural loci coding for enzyme proteins are concerned with these so-called multilocus enzymes. The separate enzymes in such a multilocus set ressemble each other not only in their enzyme properties, but also in subunit structures and in molecular sizes. However there are often remarkable differences in expression of the several loci of a set from tissue to tissue. Such sets of loci probably arose in evolution by gene duplications with subsequent divergence by point mutations. Tissue differentiation in expression suggests that, pari passu with the divergence of the structural genes, there was an evolution of genetic regulating systems controlling their tissue expression.

Biological Evolution↗