Molecular biology and evolution最新文献

Functional and structural determinants of long- and short-term evolution of herpesvirus proteins. 疱疹病毒蛋白长期和短期进化的功能和结构决定因素。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-10-09 DOI: 10.1093/molbev/msaf256

Rotem Fuchs, Alessandra Mozzi, Diego Forni, Bar Naim, Ofir Schor, Manuela Sironi, Tzachi Hagai

{"title":"Functional and structural determinants of long- and short-term evolution of herpesvirus proteins.","authors":"Rotem Fuchs, Alessandra Mozzi, Diego Forni, Bar Naim, Ofir Schor, Manuela Sironi, Tzachi Hagai","doi":"10.1093/molbev/msaf256","DOIUrl":"https://doi.org/10.1093/molbev/msaf256","url":null,"abstract":"Understanding the factors that shape viral protein evolution is a central question in evolutionary virology. However, these determinants are poorly characterized for the majority of viruses, because functional data is scarce and because most viruses encode few proteins, limiting comparisons between them. Here, we focus on the Orthoherpesviridae family whose related viruses, including human-infecting herpesviruses, allow evolutionary investigation at different timescales. We employ different models to estimate evolutionary rates of numerous herpesvirus proteins and residues, and assess their relationship to a set of structural, cellular and functional characteristics. Core genes whose orthologs are found in distant genera, evolve at similar rates within genera, despite their evolutionary distance and their differences in viral replication and environments. This likely stems from constraints imposed to maintain the structural fold across viruses, and is corroborated by the finding that fold complexity is a major determinant of evolutionary rates. Focusing on the evolution of specific protein regions, we show that surface and disordered regions are enriched with positively selected residues. However, motifs embedded in disordered regions, important for binding host proteins, have conserved occurrences across viruses. Additionally, viral proteins predicted to form biomolecular condensates often evolve slowly despite having high disordered content. In summary, our analyses reveal short- and long-term evolutionary constraints of herpesvirus proteins. These include constraints imposed by the protein structural fold and by elements within disordered regions important for host-virus interactions. These constraints are relevant when considering potential pathways of virus evolvability and for developing new antiviral treatments.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145258742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Navigating sampling bias in discrete phylogeographic analysis: assessing the performance of an adjusted Bayes factor. 导航抽样偏差在离散系统地理分析：评估一个调整贝叶斯因素的性能。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-10-07 DOI: 10.1093/molbev/msaf253

Fabiana Gámbaro, Maylis Layan, Guy Baele, Bram Vrancken, Simon Dellicour

{"title":"Navigating sampling bias in discrete phylogeographic analysis: assessing the performance of an adjusted Bayes factor.","authors":"Fabiana Gámbaro, Maylis Layan, Guy Baele, Bram Vrancken, Simon Dellicour","doi":"10.1093/molbev/msaf253","DOIUrl":"https://doi.org/10.1093/molbev/msaf253","url":null,"abstract":"Bayesian phylogeographic inference is widely used in molecular epidemiological studies to reconstruct the dispersal history of pathogens. Discrete phylogeographic analysis treats geographic locations as discrete traits and infers lineage transition events among them, and is typically followed by a Bayes factor (BF) test to assess the statistical support. In the standard BF (BFstd) test, the relative abundance of the involved trait states is not considered, which can be problematic in the case of unbalanced sampling. Existing methods to correct sampling bias in discrete phylogeographic analyses using continuous-time Markov chain (CTMC) model, often require additional epidemiological information to balance the sampling effort among locations. As such data is not necessarily available, alternative approaches that rely solely on available genomic data are needed. In this perspective, we assess the performance of a modification of the BFstd, the adjusted Bayes factor (BFadj), which incorporates information on the relative abundance of samples by location when inferring support for transition events and root location inference without requiring additional data. Using a simulation framework, we assess the statistical performance of BFstd and BFadj under varying levels of sampling bias, estimating their type I and type II error rates. Our results show that BFadj complements the BFstd by reducing type I errors at the cost increasing type II errors for inferred transition events, while improving type I and type II errors in root location inference. Our findings provide guidelines for implementing the complementary BFadj to detect and mitigate sampling bias in discrete phylogeographic inference using CTMC modelling.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The genomic imprint of chromosomal inversions and demographic history in island populations of deer mice. 鹿鼠岛种群染色体倒位的基因组印记和人口统计学历史。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-10-07 DOI: 10.1093/molbev/msaf254

Emma K Howell, Felix Baier, Hopi E Hoekstra, Bret A Payseur

{"title":"The genomic imprint of chromosomal inversions and demographic history in island populations of deer mice.","authors":"Emma K Howell, Felix Baier, Hopi E Hoekstra, Bret A Payseur","doi":"10.1093/molbev/msaf254","DOIUrl":"https://doi.org/10.1093/molbev/msaf254","url":null,"abstract":"Populations that colonize islands experience novel selective pressures, fluctuations in size, and changes to their connectivity. Owing to their unique geographic setting, islands can function as natural laboratories in which to examine the interactions between demographic history and natural selection replicated across isolated populations. We used whole genome sequences of wild-caught deer mice (Peromyscus maniculatus) from two islands (Saturna and Pender) and one mainland location (Maple Ridge) in the Gulf Islands region of coastal British Columbia to investigate two primary determinants of genome-wide diversity: chromosomal inversions and non-equilibrium demographic history. We found that segregating inversions produce characteristic, large-scale distortions in allele frequencies and linkage disequilibrium that make it possible to identify and characterize them from short-read sequence data. Patterns of variation within and between karyotypes indicate that six inversion polymorphisms have been maintained by a shared history of balancing selection in both island and mainland populations. Whereas the estimated timing of contemporary population splits is consistent with the isolation of island populations from each other following the Last Glacial Maximum, ancestral island and mainland lineages are inferred to have diverged much earlier. These aspects of demographic history suggest that shared inversions existed long ago in a common ancestor or spread via limited gene flow between ancestral island and mainland lineages. Our results raise the possibility that inversions segregating among Gulf Islands populations are on similar evolutionary trajectories, providing a contrast to previous findings in mainland P. maniculatus and contributing to the emerging portrait of inversion evolution in this species.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comprehensive Mutational Landscape of Yeast Mutator Strains Reveals the Genetic Basis of Mutational Signatures in Cancer. 酵母突变株的综合突变景观揭示了癌症突变特征的遗传基础。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-10-06 DOI: 10.1093/molbev/msaf252

Lei Liu, Danyang Sun, Haoxuan Liu

{"title":"Comprehensive Mutational Landscape of Yeast Mutator Strains Reveals the Genetic Basis of Mutational Signatures in Cancer.","authors":"Lei Liu, Danyang Sun, Haoxuan Liu","doi":"10.1093/molbev/msaf252","DOIUrl":"https://doi.org/10.1093/molbev/msaf252","url":null,"abstract":"Spontaneous mutation rates and spectra are influenced by an intricate interplay of processes including DNA replication, proofreading, and diverse DNA damage repair pathways. Although significant progress has been made in characterizing the functions of individual genes involved in these processes, their direct effects on mutation rates and spectra remain unclear. In this study, we employed a systematic gene knockout approach coupled with mutation accumulation (MA) experiments and whole-genome sequencing (WGS) to investigate the mutational landscape of Saccharomyces cerevisiae. We targeted 136 gene-deletion strains encompassing nearly all known genes associated with DNA replication and repair. Analysis of 1,081 MA lines revealed that 114 of the 136 genes significantly influenced at least one type of mutation rate. Furthermore, deletions of specific genes led to marked shifts in mutational biases and spectra, with some deletions amplifying existing biases and others reversing them entirely. In contrast, mitochondrial mutation rates were notably less affected, with no significant impact detected. Importantly, comparative analysis revealed striking similarities between yeast mutational spectrum and those observed in human cancers with the same pathway deficiencies, suggesting conserved functional roles across species. In conclusion, our findings provided critical insights into the genetic underpinnings of these signatures and underscoring the utility of yeast as a model for studying the molecular basis of cancer-associated mutational processes.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145233000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic Insights into Convergent Evolution: Adaptation to Rocky Habitats in Rock-inhabiting Fungi. 趋同进化的基因组见解：岩石真菌对岩石栖息地的适应。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-10-06 DOI: 10.1093/molbev/msaf249

Rong Fu, Luwen Yan, Shunxian Wang, Dongsheng Wei, Qi Wu, Xingzhong Liu, Meichun Xiang

{"title":"Genomic Insights into Convergent Evolution: Adaptation to Rocky Habitats in Rock-inhabiting Fungi.","authors":"Rong Fu, Luwen Yan, Shunxian Wang, Dongsheng Wei, Qi Wu, Xingzhong Liu, Meichun Xiang","doi":"10.1093/molbev/msaf249","DOIUrl":"https://doi.org/10.1093/molbev/msaf249","url":null,"abstract":"Rock-inhabiting fungi (RIF), obligate colonizers of bare rocks, are primarily distributed across two major phylogenetic classes: Dothideomycetes and Eurotiomycetes. These fungi display striking convergence in morphology and physiology, characterized by meristematic growth, melanized cell walls, and extreme stress tolerance. However, the genomic underpinnings of this adaptive convergence remain poorly understood. Here, through comparative genomic analysis of nine RIF and eighteen non-RIF fungi, we revealed that RIF possess compact, gene-dense genomes marked by contraction of genes involved in nutrient uptake and secondary metabolism, alongside expansions in cell wall biosynthesis, lipid metabolism, and stress-responsive pathways. We identified two genes under positive selection across multiple RIF lineages: Ino80 ATPase (chromatin remodeling) and the ER chaperone BiP (protein folding). Further evidence of convergence was found in the mannosyltransferase Mnn9, a key enzyme in cell wall assembly, where two RIF-specific amino acid substitutions were predicted to enhance protein stability. Additionally, a unique Mnn9-like clade has expanded exclusively in RIF. RNAi-mediated knockdown of an Mnn9-like gene in Rachicladosporium sp. confirmed its role in cell wall mannosylation, osmotic stress response, and the transition from meristematic to filamentous growth. Our findings elucidate a set of common genomic adaptations and highlight the specialized evolution of the Mnn9 family in driving the convergent success of phylogenetically diverse RIF in rocky environments.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Interpreting supervised machine learning inferences in population genomics using haplotype matrix permutations. 使用单倍型矩阵排列解释种群基因组学中的监督机器学习推断。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-10-06 DOI: 10.1093/molbev/msaf250

Linh N Tran, David Castellano, Ryan N Gutenkunst

{"title":"Interpreting supervised machine learning inferences in population genomics using haplotype matrix permutations.","authors":"Linh N Tran, David Castellano, Ryan N Gutenkunst","doi":"10.1093/molbev/msaf250","DOIUrl":"https://doi.org/10.1093/molbev/msaf250","url":null,"abstract":"Supervised machine learning methods, such as convolutional neural networks (CNNs), that use haplotype matrices as input data have become powerful tools for population genomics inference. However, these methods often lack interpretability, making it difficult to understand which population genetics features drive their predictions-a critical limitation for method development and biological interpretation. Here we introduce a systematic permutation approach that progressively disrupts population genetics features within input test haplotype matrices, including linkage disequilibrium, haplotype structure, and allele frequencies. By measuring performance degradation after each permutation, the importance of each feature can be assessed. We applied our approach to three published CNNs for positive selection and demographic history inference. We found that the positive selection inference CNN ImaGene critically depends on haplotype structure and linkage disequilibrium patterns, while the demographic inference CNN relies primarily on allele frequency information. Surprisingly, another positive selection inference CNN, disc-pg-gan, achieved high accuracy using only simple allele count information, suggesting its training regime may not adequately challenge the model to learn complex population genetic signatures. Our approach provides a straightforward, model-agnostic, and biologically-motivated framework for interpreting any haplotype matrix-based method, offering insights that can guide both method development and application in population genomics.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-Level Genome Assembly of Eden's Whale Clarifies the Taxonomy and Speciation of Bryde's Whale Complex. 伊登鲸染色体水平的基因组组装阐明了布莱德鲸复合体的分类和物种形成。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-10-01 DOI: 10.1093/molbev/msaf234

Yi-Tao Lin, Fan Hui, Wentao Han, Yi-Xuan Li, Bonnie Yuen Wai Heung, Chun Ming How, Shi Wang, Jian-Wen Qiu

{"title":"Chromosome-Level Genome Assembly of Eden's Whale Clarifies the Taxonomy and Speciation of Bryde's Whale Complex.","authors":"Yi-Tao Lin, Fan Hui, Wentao Han, Yi-Xuan Li, Bonnie Yuen Wai Heung, Chun Ming How, Shi Wang, Jian-Wen Qiu","doi":"10.1093/molbev/msaf234","DOIUrl":"10.1093/molbev/msaf234","url":null,"abstract":"Eden's whale (Balaenoptera edeni), a poorly understood baleen cetacean, has long been shrouded in taxonomic ambiguity due to limited genomic resources, obscuring its distinction from closely related species and its position within the cetacean Tree of Life. In this paper, we present a high-quality chromosomal-level genome of B. edeni and conduct comparative genomic analyses to address long-standing taxonomic confusion and elucidate speciation of balaenopterids. Our phylogenomic analysis and demographic reconstruction reveal that B. edeni is a distinct sister to Bryde's whale (Balaenoptera brydei), sharing a common ancestor that diverged approximately 7.84 million years ago during the late Miocene. Their genetic divergence exceeds typical intraspecific variation in whales, supporting the reinstatement of B. brydei as a valid species. Chromosomal syntenic analyses suggest that macro-fragment inversions contributed to speciation in balaenopterid whales and uncover unexpected large-scale complex genome rearrangements in Bryde's whale, offering novel insights into cetacean genome evolution. Functional enrichment analysis of inverted regions between B. edeni and Balaenoptera musculus indicates their predominant association with metabolism and biosynthesis, as well as responses to various substances, stress, and stimuli. These genomic resources for B. edeni not only lay a critical foundation for comparative genetic and evolutionary research of cetaceans but also advance our understanding of the taxonomy and evolutionary dynamics of the Bryde's whale complex, with broader implications for baleen whale conservation and biodiversity.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Distinct Evolutionary Signatures of Human Parainfluenza Viruses 2 and 4 Reveal Host Antagonism Divergence and Phylogenetic Discordance. 人类副流感病毒2和4的不同进化特征揭示宿主拮抗分化和系统发育不一致

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-10-01 DOI: 10.1093/molbev/msaf217

Stephanie Goya, Alexander L Greninger

{"title":"Distinct Evolutionary Signatures of Human Parainfluenza Viruses 2 and 4 Reveal Host Antagonism Divergence and Phylogenetic Discordance.","authors":"Stephanie Goya, Alexander L Greninger","doi":"10.1093/molbev/msaf217","DOIUrl":"10.1093/molbev/msaf217","url":null,"abstract":"Human parainfluenza virus 2 (HPIV-2) and human parainfluenza virus 4 (HPIV-4) are significant but underappreciated respiratory pathogens, particularly among high-risk populations including children, the elderly, and immunocompromised individuals. In this study, we sequenced 101 HPIV-2 and HPIV-4 genomes from respiratory samples collected in western Washington State and performed comprehensive evolutionary analyses using both new and publicly available sequences. Phylogenetic and phylodynamic analyses revealed that both HPIV-2 and HPIV-4 evolve at significantly faster rates compared to the mumps virus, a reference human orthorubulavirus. Notably, while HPIV-2 demonstrated the highest evolutionary rates in the surface glycoprotein HN, consistent with humoral immune-driven selection, the innate immune antagonist V/P gene evolved fastest in HPIV-4. We identified a hypervariable region within the HPIV-4V/P protein (residues 35 to 75), which structural modeling placed in a loop overlapping a known interferon antagonism domain in other paramyxovirus V proteins, though HPIV-4 is functionally incompetent in this activity. Expanded phylogenetic analysis across the Paramyxoviridae family uncovered a striking evolutionary discordance: while the HN glycoprotein and L polymerase of HPIV-4 and its 2 closest bat-derived viruses clustered within the Orthorubulavirus genus, their nucleoprotein (N), phosphoprotein (P), matrix (M), and fusion (F) proteins formed a distinct lineage outside the Rubulavirinae subfamily. Together, these findings highlight the distinct evolutionary trajectories of HPIV-2 and HPIV-4, raise hypotheses around complex Paramyxoviridae zoonotic events including recombination-like patterns, and demonstrate limitations of current L protein-based taxonomic classification schemes.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145033758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SegMantX: A Novel Tool for Detecting DNA Duplications Uncovers Prevalent Duplications in Plasmids. SegMantX：一种检测DNA复制的新工具，揭示了质粒中普遍的复制。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-10-01 DOI: 10.1093/molbev/msaf242

Dustin M Hanke, Tal Dagan

{"title":"SegMantX: A Novel Tool for Detecting DNA Duplications Uncovers Prevalent Duplications in Plasmids.","authors":"Dustin M Hanke, Tal Dagan","doi":"10.1093/molbev/msaf242","DOIUrl":"10.1093/molbev/msaf242","url":null,"abstract":"Segmental duplications play an important role in genome evolution via their contribution to copy-number variation, gene-family diversification, and the emergence of novel functions. The detection of segmental duplications is challenging due to heterogeneous amelioration of sequence similarity among duplicates, which hinders the reconstruction of continuous sequence alignment. Here we introduce SegMantX, a novel approach for the identification of diverged segmental duplications in prokaryote genomes using local alignment chaining. In this approach, local alignments resulting from a preliminary sequence similarity search (e.g. BLASTn) are chained into continuous segments. Evaluating the performance of SegMantX using simulated sequences shows that the tool can detect diverged duplications beyond the sensitivity limits of standard alignment-based methods. Applying SegMantX to 6,784 enterobacterial plasmids, we find that 65% plasmids contain duplicated regions and gene duplications, most of which correspond either to dispersed, noncoding regions or duplicated mobile genetic elements (MGEs; e.g. transposons and insertion sequences). Furthermore, we demonstrate the applicability of SegMantX for the identification of diverged gene transfers between replicons and plasmid hybridization events. Our findings highlight MGEs as drivers of segmental duplications in plasmid evolution, leading to the amplification of their cargo genes, including antibiotic resistance genes. SegMantX provides a powerful framework for reconstructing diverged segmental duplications and other alignment problems.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145150074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transposable Element-Mediated Cis-Regulation Drives the Evolution of dmrt1 as a Candidate Master Sex-Determining Gene in Black Carp. 转座因子介导的顺式调控驱动dmrt1作为一个候选的主要性别决定基因在黑鱼中的进化。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-10-01 DOI: 10.1093/molbev/msaf239

Jiamin Guo, Gen Hua Yue, Jiale Li, Chenglong Wu, Le Wang, Yubang Shen

{"title":"Transposable Element-Mediated Cis-Regulation Drives the Evolution of dmrt1 as a Candidate Master Sex-Determining Gene in Black Carp.","authors":"Jiamin Guo, Gen Hua Yue, Jiale Li, Chenglong Wu, Le Wang, Yubang Shen","doi":"10.1093/molbev/msaf239","DOIUrl":"10.1093/molbev/msaf239","url":null,"abstract":"Sex determination in vertebrates exhibits remarkable evolutionary plasticity, with diverse mechanisms and master sex-determining (MSD) genes arising independently across lineages. Among these, dmrt1, a dosage-sensitive gene, has repeatedly been recruited as an MSD gene through gene duplication or allelic diversification. However, the biochemical basis of such evolutionary transitions, particularly those driven by allelic diversification, remains largely unexplored. Here, we generated haplotype-resolved genome assemblies for both XX and XY black carp (Mylopharyngodon piceus) and identified a ∼40-kb region on chromosome 4, containing only dmrt1, as the candidate sex-determining locus. We discovered two Y-specific insertions in the dmrt1 promoter: a 13.4-kb highly repetitive element and an 11-bp motif. Functional assays revealed that these insertions act as enhancer and a promoter element, respectively, driving early, allele-specific upregulation of dmrt1 prior to gonadal differentiation. Notably, the 13.4-kb insertion contains transposable elements (TEs) functioning as cis-regulatory modules with transcription factor binding sites that mediate Y-specific activation. Our findings reveal a TE-mediated regulatory innovation that promoted dmrt1's evolution as a male-determining gene via allelic diversification, providing new insights into how mobile genetic elements drive the origin and diversification of sex-determining systems in vertebrates.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145150107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0