Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Duplication events”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed2025

Gene and Genome Duplication in Spiders.

Gene and genome duplications are widely observed across various organisms, including plants, yeasts, and animals. Numerous studies link gene duplications to the emergence of novel phenotypes, supporting the hypothesis that duplication events are advantageous for adaptive evolution. Whole-genome duplications (WGD) are especially prevalent in plants and have also occurred ancestrally in vertebrates. However, large-scale duplication events in other animal groups remain understudied, partly due to limited genomic resources. Arthropods, particularly insects, represent one of the most diverse animal clades in terms of both species and phenotypic diversity. With increasing availability of chromosome-level genomes, large-scale duplications appear to be rare in insects but are more frequent in chelicerates (e.g. spiders, scorpions, and horseshoe crabs). This makes chelicerates an intriguing group for comparing the mechanisms, fates, and evolutionary impacts of large-scale duplications with those seen in plants and vertebrates. In this review, we synthesize and discuss current research on WGD in spiders and discuss different scenarios for genes following gene duplication events (conservation, nonfunctionalization, subfunctionalization, specialization, drift, neofunctionalization) in the context of experimental studies. We hypothesize if there might be common trajectories after duplication and how these could be tested.

Animals↗
PubMed2026

Episode clustering in phylogenetic networks.

MOTIVATION: The classical duplication episode clustering (EC) model introduced by Guigó et al. in the 1990s provides a foundational approach for inferring genomic duplication events crucial to understanding genome evolution. This model clusters single gene duplications from a collection of gene trees at locations in the species tree to minimize the total number of such locations, called duplication episodes. However, it does not capture reticulate evolutionary histories. RESULTS: Here, we introduce NetEC, a novel extension of this problem to phylogenetic networks. To solve NetEC, we first develop a polynomial-time dynamic programming (DP) algorithm for testing whether a given set of network nodes can serve as episode locations. We then propose a main inference algorithm that utilizes this DP component to optimize the episode count; while the feasibility test runs in polynomial time, the full optimization has exponential worst-case complexity, and an optional heuristic mode is provided for larger instances. We also propose an extended episode analysis procedure that identifies additional genomic duplication candidates below reticulation nodes, complementing the main algorithm by resolving potential upward clustering of duplications induced by reticulation. We evaluate our method on simulated data and on an empirical Pandanales dataset comprising over 29 000 gene trees, demonstrating exact and accurate inference of genomic duplication events even in the presence of multiple reticulations. AVAILABILITY AND IMPLEMENTATION: All experiments were conducted using the NetEC tool (https://github.com/ppgorecki/netec), with all input data, scripts, and parameter settings for reproduction available in the same repository.

Phylogeny↗
PubMed2026

Genome-wide cyclin gene evolution in Arabidopsis and Brassica reveals polyploidization-driven duplication and flowering-time associations.

Cyclin genes are plant cell cycle regulators that play essential roles in growth, development, and reproduction. However, the evolutionary dynamics and genomic organization of cyclin genes across the Brassicaceae family remain poorly understood, particularly in the context of allotetraploid genome evolution. Here, we investigated the diversity, expansion mechanisms, and potential functional diversification of cyclin genes across ten Brassicaceae genomes, including four Arabidopsis and six Brassica species. A total of 1087 cyclin genes representing 23 cyclin types were identified. Comparative genomic analyses revealed that cyclin gene expansion was strongly influenced by polyploidization in Brassica species, with 1845 duplication events involving 1063 genes. Whole-genome duplication was the predominant mechanism driving expansion, while both inter- and intra-genomic duplications contributed to gene retention in tetraploid Brassica species, with the highest duplication frequency observed in Brassica juncea. Across genomes, 120 physical gene clusters were identified, including homogeneous and heterogeneous types. Ortholog analysis between progenitor and allotetraploid species identified 852 orthologous pairs involving 366 genes, indicating extensive conservation following allotetraploid formation. Phylogenetic analysis resolved cyclins into three major clades, while expression-based clustering in Brassica napus grouped genes into four major clusters, suggesting functional diversification. Integration of pan-genomic and flowering-time QTL analyses further identified two cyclin genes, Bna21cycA2 and Bna113cycD4, which contain amino acid polymorphisms and represent putative candidate variations potentially associated with flowering-time variation across multiple genomes. These findings provide new insights into the evolutionary expansion, retention, and potential functional divergence of cyclin genes in Brassicaceae and highlight candidate loci for future functional studies and crop improvement.

Evolution, Molecular↗
PubMed2026

Genome-wide identification and expression analysis of the UGT gene family in honeysuckle.

BACKGROUND: The UGT gene family plays critical roles in regulating plant growth, development, stress responses, and secondary metabolite synthesis. Although UGT proteins have been studied in numerous plant species, research on the UGT family in honeysuckle (Lonicera japonica Thunb.) remains limited. RESULTS: In this study, a comprehensive genome-wide analysis of the UGT gene family was performed in honeysuckle. A total of 224 unique LjUGT genes were identified and classified into 21 distinct subfamilies (T71-T92 without T77) based on the phylogenetic analysis. These genes were unevenly distributed on the 9 chromosomes. Eighteen segmental duplication events and 61 tandem duplications were identified, of which only 3 were positive selection. Integrated analysis of promoter cis-acting elements, transcription factors, targeted miRNAs, and interacting proteins suggested that the expression and function of the LjUGT genes may be regulated by transcription factors and proteins through binding to the various binding sites and cis-acting elements, thereby putatively participating in diverse biological processes, including hormone signaling, stress response, and metabolism. The expression pattern analysis of LjUGTs in different tissues and under stress conditions indicated that Lj2A1135G32, Lj5A236T61, Lj6A350T83, and Lj7A737T47 emerged as candidate genes potentially associated with development, 46 genes showed expression changes under all 6 abiotic stresses, suggesting broad stress responsiveness. Additionally, there 7 genes were identified as candidate hub genes that may correlate with the low temperature stress tolerance in honeysuckle according to the WGCNA results, and further verification by qRT-PCR confirmed that Lj4A99G61 and Lj9A591T82 can be regarded as key candidate genes for in-depth research. CONCLUSIONS: This study systematically identified 224 LjUGT genes in honeysuckle for the first time and characterized their physicochemical properties, phylogenetic relationship, and expression patterns. These findings provide a foundational resource for hypothesis-driven investigations into the functions and action mechanisms of LjUGTs.

Lonicera↗
PubMed2025

Molecular evolution of the members of the Snq2/Pdr18 subfamily of Pdr transporters in the Hemiascomycete yeasts.

The transporters of the ATP-Binding Cassette (ABC) Superfamily involved in the Multidrug Resistance (MDR) phenomena are also known as ABC-Pleiotropic Drug Resistance (PDR) proteins. The homologs of the Saccharomyces cerevisiae SNQ2 and PDR18 genes were identified in 171 yeast genomes, representing 68 different hemiascomycetous species. All early-divergent yeast species analyzed in this work lack Snq2/Pdr18 homologs, suggesting that the origin of these ABC-PDR genes in hemiascomycete yeasts resulted from a horizontal transfer event. The evolutionary pathway of the Snq2/Pdr18 protein subfamily in pathogenic Candida species was also reconstructed, revealing a main gene lineage leading to the Candida albicans SNQ2 gene. The results indicate that, after the gene duplication event at the origin of the SNQ2/PDR18 paralogs, the PDR18 ortholog has been under strong diversifying selection and suggest that a small portion of the sequence of the SNQ2 ancestral ortholog might have been under mild positive selection. The results also showed that strong positive selection was exerted over one of the two paralogs generated by the Whole Genome Duplication (WGD) event, corresponding to the duplicate at the origin of a "short-lived" WGD sublineage.

Evolution, Molecular↗
PubMed2025

Comparative genomic analysis of Artemisia argyi reveals asymmetric expansion of terpene synthases and conservation of artemisinin biosynthesis.

Artemisia argyi, a perennial herb of the Asteraceae family, possesses significant therapeutic and economic value. We present a 7.88 Gb chromosome-level haplotype-resolved genome assembly, revealing its unique evolutionary trajectory. The karyotype (2n = 34) of A. argyi is that of an autotetraploid, which underwent gametic chromosome fusion prior to species-specific whole-genome duplication (WGD-3). The genome exhibits pronounced multivalent chromosome pairing and frequent recombination among homologous groups. Asymmetrical evolution following WGD-3 is a hallmark feature, evidenced by imbalanced allelic gene loss and widespread neofunctionalization. The terpene synthase (TPS) gene family exemplifies this pattern, having expanded through four duplication events in A. argyi. Recent tandem duplications and allelic functional differentiation have generated substantial gene functional diversity. Notably, we identified a tandem-duplicated six-copy ADS homolog (AarADS)-a key TPS gene in the artemisinin biosynthetic pathway of Artemisia annua (AanADS)-localized exclusively to a single chromosome in A. argyi. Unlike AanADS, which converts farnesyl pyrophosphate (FPP) to amorpha-4,11-diene, AarADS catalyzes FPP to α-bisabolol. Evolutionary analysis suggested that AanADS acquired its specialized function via a derived mutation in the A. annua lineage. This study elucidates the genomic evolution underpinning A. argyi's distinctive medicinal properties.

Alkyl and Aryl Transferases↗
PubMed2026

Haplotype-resolved genome of Forsythia suspensa reveals the reticulate evolution in Oleaceae and a novel gene cluster regulating stamen development.

The olive family (Oleaceae) comprises numerous species of economic, horticultural, and medicinal importance. Despite its significance, the evolutionary history of this complex family remains enigmatic. Here, we generated a high-quality haplotype-resolved genome of Forsythia suspensa, a distylous species that occupies a key phylogenetic position in Oleaceae. The 2 haplotypes exhibit significant allelic divergence with potential allele-specific regulation. We reconstructed the polyploidization history of Oleaceae by confirming and precisely dating a shared whole-genome triplication and an independent whole-genome duplication event. We revealed a complex reticulate evolution that gave rise to the tribe Oleeae: an initial hybridization between Forsythieae (♂) and Jasmineae (♀), a subsequent backcrossing event, and a final whole-genome duplication. We identified a novel tandemly duplicated pectin methylesterase inhibitor gene cluster that regulates filament length and pollen size via restricting cell elongation in the long-styled morph. Dosage augmentation via stepwise cluster formation (0.99 to 3.83 Mya) may contribute to maintaining stamen traits of the long-styled morph. These FsPMEIs are co-expressed with many cell wall-related genes, suggesting a functional link in cell wall modification. Our study reveals the reticulate evolution in Oleaceae and a novel gene cluster controlling stamen development in F. suspensa and provides valuable haplotype-resolved genomic resources for heterostylous species, offering novel framework and molecular pathways to understand plant adaptive evolution.

Forsythia↗
PubMed1978

Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci.

Several groups of fishes, including salmonids and catastomids, appear to have originated through genome duplication events. However, these two groups retain approximately 50% of the loci examined as functioning duplicates, despite the passage of 50 million years or more of mutation and selection. Although other effects are not excluded, this apparently slow rate of duplicate silencing can be explained in terms of the effects of selection against defective double homozygotes to unlinked duplicates. We have derived a computer simulation of genetic drift that affords direct evaluation of the effects of population size (N), mutation rate (micron), initial allele frequencies, back mutation, fitness, and time on the probability of fixation for null alleles at unlinked duplicate loci. The results show that this probability is approximately linearly related to population size for N greater than or equal to 10(3). Specifically, for naive populations, the time for 50% probability of gene silencing is approximately equal to 15N + micron-3/4 generations. The retention of 50% of the loci as functional duplicates may therefore result from the large effective size of salmonid and catastomid populations. The results also show that, under most conditions for populations of 2000--3000 or larger, unlinked duplicate loci will be sustained in the functional state longer than tandem (linked) duplicates and hence are available for evolution of new functions for a longer time.

Alleles↗
PubMed2025

doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.

SUMMARY: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface. AVAILABILITY AND IMPLEMENTATION: doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.

Software↗
PubMed2026

From neuropeptides to toxins: illuminating the origins of venom complexity in cone snails.

New genes and gene functions are key drivers of evolutionary innovation. Venomous animals, such as cone snails, provide striking examples of gene innovation, yet the mechanisms by which toxins arise remain poorly understood. Using the Conus textile genome, we uncover how neuropeptide genes were recruited into the venom and neofunctionalized as doppelgänger toxins. We identify over 20 independent recruitment events that evolved dynamically across the Conus lineage. Rather than arising from ohnologs of a whole-genome duplication event ∼200 mya, these toxins evolved through diverse mechanisms, including exon shuffling, alternative splicing, and ectopic recombination, often facilitated by lineage-specific transposable elements. Our findings reveal a dynamic interplay between genome architecture and molecular innovation, offering broad insight into the evolution of complex gene repertoires in venoms and beyond.

Animals↗
PubMed2026

Evolutionary Conservation and Reproductive Expression of ABC Transporter Genes in Two Sphenomorphus Skinks.

ATP-binding cassette (ABC) transporters represent one of the largest membrane protein superfamilies in vertebrates, playing essential roles in translocating diverse substrates across membranes. However, knowledge of ABC transporter genes in reptiles remains limited. In this study, we conducted a comprehensive genome-wide identification and characterization of the ABC gene family in oviparous Sphenomorphus incognitus and viviparous Sphenomorphus indicus. A total of 45 ABC genes were identified in each species and classified into seven subfamilies (ABCA-ABCG). Comparative and phylogenetic analyses revealed a generally conserved gene repertoire, with limited duplication events observed mainly in the ABCA and ABCG subfamilies, whereas other subfamilies (e.g., ABCE, ABCF, and ABCD) remained highly conserved. Interestingly, a lineage-specific duplication of ABCC2 was identified in lizards. Oviductal expression profiling revealed distinct temporal patterns of ABC gene expression across reproductive stages. Several genes, including ABCG1, ABCC3, and ABCD4, exhibited conserved expression trajectories across both species, suggesting shared transcriptional regulation. In contrast, ABCA1, ABCB1, and ABCG2 showed species-specific expression patterns, indicating regulatory divergence between the two lizard species. Overall, ABC gene expression was more dynamic in S. incognitus than in S. indicus. In summary, although the ABC transporter family is structurally conserved, it exhibits lineage-specific evolutionary changes and divergent transcriptional regulation in lizard oviducts. This study provides a foundation for understanding the diversity and regulation of ABC transporter genes in reptiles.

Animals↗
PubMed2026

Tandem duplication-driven expansion and UV-B stress adaptation of the LHC gene family in Artemisia annua L.

BACKGROUND: Artemisia annua L., is the primary natural source of the antimalarial drug artemisinin. In nature, fluctuating light is a major environmental stress that affects plant growth and artemisinin biosynthesis. Although the light-harvesting chlorophyll a/b-binding (LHC) superfamily plays a key role in mediating plant responses to fluctuating light, systematic research of this gene family in A. annua has not yet been conducted, limiting our understanding of light adaptation in this medicinally important species. RESULTS: This study investigated the evolutionary dynamics and functional adaptation of the light-harvesting chlorophyll a/b-binding (LHC) superfamily in A. annua, with a focus on the early light‑induced protein (ELIP) subfamily. Comparative genomics of 24 plant species showed that the LHC superfamily recently expanded in the examined Asteraceae lineages through duplication events. In A. annua, 229 LHC genes identified from four haplotype genomes comprised 205 allelic and 24 haplotype-specific loci, with the ELIP subfamily expanding significantly via tandem duplication. Notably, compared to non-Asteraceae plants, ELIPs exhibited a uniform single-exon architecture, indicating it is a genomic feature unique to Asteraceae plants. Population genomics of 41 individuals showed dynamic copy number variations ranging from 1 to 4 copies per locus. Interestingly, a structurally disrupted ELIP allele remained transcriptionally active and produced long aberrant transcripts, showing that this subfamily is still actively evolving. Under UV-B stress, AaELIP loci showed synchronized induction trend but differed in expression levels, suggesting a division into major and auxiliary roles within the expanded tandem cluster. Overall, while the response of ELIPs to light stress is evolutionarily conserved, this dramatic expansion and structural streamlining of AaELIPs may represent a key evolutionary adaptation that enhances the plant's ability to cope with intense light and radiation stress. CONCLUSIONS: Collectively, this study demonstrates a significant expansion of the LHC superfamily in A. annua, especially within the ELIP subfamily, as well as its robust response to UV-B treatment, underscoring the essential role of ELIPs in mediating light stress responses. These findings provide a valuable foundation for future research to uncover the molecular mechanisms underlying A. annua's adaptation to complex light environments.

Artemisia annua↗
PubMed2026

Evolutionary adaptation of CCD4 enzymes in Buddleja alternifolia for crocetin biosynthesis.

INTRODUCTION: Carotenoid cleavage dioxygenase 4 (CCD4) enzymes play central roles in carotenoid turnover and apocarotenoid biosynthesis in plants. Despite their importance, the evolutionary mechanisms underlying diversification of CCD4 catalytic functions remain poorly understood. This study investigated the CCD gene family in Buddleja alternifolia, with particular emphasis on the expansion and functional evolution of the CCD4 subfamily. METHODS: A genome-wide identification and comparative analysis of CCD genes were performed in B. alternifolia. Genomic organization, phylogenetic relationships, and syntenic patterns were analyzed to investigate gene family expansion. Functional characterization of 11 BaCCD4 paralogs was conducted through biochemical assays, while structural analyses were used to identify sequence features associated with differences in substrate cleavage specificity. Gene expression profiling was performed to assess patterns of tissue-specific regulation. RESULTS: Twenty-three CCD genes were identified, including 12 CCD4 paralogs, representing one of the largest CCD4 expansions reported within Lamiales. Syntenic and genomic analyses revealed that recent tandem duplication events, particularly within a CCD4-rich region on chromosome 10, were the primary drivers of this expansion. The presence of pseudogenes in the same region supported an ongoing birth-and-death evolutionary process. Functional analyses demonstrated extensive biochemical diversification among BaCCD4 enzymes despite their high sequence similarity. Several paralogs catalyzed asymmetric carotenoid cleavage leading to citraurin production, whereas two paralogs, KAG8367281 and KAG8375220, exhibited symmetric zeaxanthin cleavage activity, producing crocetin dialdehyde, the direct precursor of crocins. Notably, these crocetin-producing enzymes belonged to closely related paralogous pairs whose counterparts displayed distinct cleavage specificities, indicating rapid neofunctionalization after duplication. Structural analyses suggested that subtle sequence variations, including indels affecting loop regions adjacent to the substrate access channel, may underlie changes in regioselectivity. Expression profiling further revealed tissue-specific expression patterns consistent with functional divergence among paralogs. DISCUSSION: These findings indicate that crocetin-forming activity in B. alternifolia likely evolved through progressive modifications of ancestral CCD4 functions rather than through a single evolutionary event. The remarkable expansion and diversification of the CCD4 subfamily provide evidence for the role of gene duplication and neofunctionalization in shaping carotenoid cleavage specificity. Collectively, this work establishes B. alternifolia as a valuable model for investigating the molecular evolution of CCD4 enzymes and the emergence of specialized apocarotenoid metabolism in plants.

CCD4 evolution↗
PubMed1978

Gene duplication in Saccharomyces cerevisiae.

Five independent duplications of the acid-phosphatase (aphtase) structural gene (acp1) were recovered from chemostat populations of S. cerevisiae that were subject to selection for in vivo hyper-aphtase activity. Two of the duplications arose spontaneously. Three of them were induced by UV. All five of the duplication events involved the transpositioning of the aphtase structural gene, acp1, and all known genes distal to acp1 on the right arm of chromosome II, to the terminus of an arm of other unknown chromosomes. One of the five duplicated regions of the right arm of chromosome II was found to be transmitted mitotically and meiotically with very high fidelity. The other four duplicated regions of the right arm of chromosome II were found to be unstable, being lost at a rate of about 2% per mitosis. However, selection for increased fidelity of mitotic transmission was effective in one of these strains. No tandem duplications of the aphtase structural gene were found.

Acid Phosphatase↗
PubMed2024

Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication.

The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Earlier versions of apple reference genomes were unphased, fragmented, and lacked comprehensive insights into the apple's highly heterozygous genome, which impeded advances in genetic studies and breeding programs. In this study, we assembled a haplotype-resolved telomere-to-telomere (T2T) reference genome for the diploid apple cultivar Golden Delicious. Subsequently, we constructed a pangenome based on 12 assemblies from wild and cultivated species to investigate the dynamic changes of functional genes. Our results revealed the gene gain and loss events during apple domestication. Compared with cultivated species, more gene families in wild species were significantly enriched in oxidative phosphorylation, pentose metabolic process, responses to salt, and abscisic acid biosynthesis process. Our analyses also demonstrated a higher prevalence of different types of resistance gene analogs (RGAs) in cultivars than their wild relatives, partially attributed to segmental and tandem duplication events in certain RGAs classes. Structural variations, mainly deletions and insertions, have affected the presence and absence of TIR-NB-ARC-LRR, NB-ARC-LRR, and CC-NB-ARC-LRR genes. Additionally, hybridization/introgression from wild species has also contributed to the expansion of resistance genes in domesticated apples. Our haplotype-resolved T2T genome and pangenome provide important resources for genetic studies of apples, emphasizing the need to study the evolutionary mechanisms of resistance genes in apple breeding.

Malus↗
PubMed2025

PAHG: the database of human multi-gene families.

BACKGROUND: In the early vertebrate history, gene duplications, including single-gene, segmental-gene (SSD), and whole-genome duplication (WGD), formed multigene families. Despite efforts to classify metazoan multigene families hierarchically for evolutionary insight, a gap exists in accessible, curated resources for human/vertebrate multigene families. RESULTS: Addressing this, we present the Phylogenomic Analysis of Human Genome (PAHG) database. It focuses on curated multigene families in the human genome, particularly within four paralogons: HOX-bearing (Hsa:2/7/12/17), FGFR-bearing (Hsa:4/5/8/10), MHC-bearing (Hsa:1/6/9/19), and chromosomes 1/2/8/20. CONCLUSION: The current PAHG version details the phylogenetic history of 221 human multigene families (1247 gene members) with 15,231 protein sequences from diverse metazoans. It provides insights into gene duplication timings, co-duplication events, and their relationships with human genome syntenic organization. The PAHG database addresses the lack of accessible resources, offering valuable information on human/vertebrate multigene family evolution. Access the PAHG database at: https://www.pahgncb.com/ and http://pahg.qau.edu.pk/ . This resource enriches our understanding of vertebrate genetic evolution.

Humans↗
PubMed2026

Genome-wide identification and functional analysis of the BES1-like (VfBES1) gene family in Vernicia fordii reveals its role in floral development.

BACKGROUND: Vernicia fordii Hemsl (also known as Tung tree), an significant commercial oil-producing tree species, is a monoecious and diclinous species with male and female flowers on the same inflorescence; however, the molecular mechanisms governing its floral sex determination remain elusive, particularly the genetic basis underlying the skewed female-to-male flower ratio and the evolutionary dynamics of sex-related gene families, which severely restrict targeted breeding for yield enhancement. In the model plant Arabidopsis, the BRI1 EMS SUPPRESSOR 1 (BES1) transcription factor family plays a crucial role in Brassinosteroid (BR) signaling and reproductive development. However, its function remains largely unexplored in woody perennials. RESULTS: In this study, we introduce the genome-wide identification and functional characterization of the BES1-like (VfBES1) gene family in the Tung tree for the first time. Integrative multi-omics approaches reveal seven VfBES1 genes that are clustered into three phylogenetically distinct clades, each characterized by clade-specific motifs and structural simplicity. Segmental duplication events (VfBES1-1/VfBES1-5 and VfBES1-4/VfBES1-7) and promoter cis-element enrichment (hormone-responsive and abiotic stress-related motifs) highlight evolutionary innovation and functional diversification. Spatiotemporal expression profiling reveals VfBES1 genes' tissue- and stage-specific roles. VfBES1-1 predominantly expresses in female flowers and fruits, suggesting its possible roles in late-stage sex maintenance or ovule and fruit development. VfBES1-2 and VfBES1-6 exhibit male flower-specific and early floral developmental activation, respectively. Nuclear-localized VfBES1-6 displays co-expression with VfMYB35-1 gene, which is a regulator of male structure degeneration. CONCLUSIONS: Findings in this study shed light on the regulatory roles of VfBES1 genes in the floral development of the Tung tree, providing a reference for its precision breeding to enhance flowering synchrony and seed productivity. This study also provides a comparative framework for understanding the functional diversity of BES1-like genes in non-model woody plants.

Flowers↗
PubMed2026

Diversification of Cellulose Synthase (CESA) Genes in Mosses Suggests Both Ancient and Recent Gene duplications.

Cellulose is an important polysaccharide that constitutes all plant cell walls, giving them strength and stability. The plant cellulose synthase (CESA) gene family, which encodes the catalytic subunits of cellulose synthesis complexes (CSCs), has diversified independently in several plant lineages, providing an interesting model for understanding selection for gene duplication. Here we quantified the presence of CESA genes across mosses to understand how the process of gene family diversification occurred in this group and how it parallels diversification in other groups. We first examined the CESA gene family in eight species of mosses across seven families for which whole genome assemblies were available. We then identified CESA genes from additional species, for which only short-read sequence data was available, by using BLAST searches and targeted gene assemblies. We validated this approach by comparing the assembled paralogs from the short-read data to the genes identified from whole genome assemblies in the eight reference species. This approach allowed us to identify paralogs directly from short-read data and greatly expand our sample set. Results from the combined empirical data support the hypothesis that CESA genes diversified within the moss lineage at least as early as the mesozoic period, during or possibly even prior to the onset of moss diversification, but also continue to diversify within modern species. In addition, we found evidence for purifying selection as the dominant force shaping these genes and observed that different lineages experienced different levels of evolutionary constraint. Lastly, our approach to assemble paralogs has the potential to allow researchers to improve analyses of gene duplication events.

Physcomitrium patens↗