Genome Biology and Evolution最新文献_第8页

A Consensus Genome Sequence for the Social Amoeba Dictyostelium giganteum. 社会变形虫巨盘齿骨虫基因组序列的共识。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-08-01 DOI: 10.1093/gbe/evag198

Aditya Sharma, Kumari Khushi, Febina Ravindran, Jayarama S Kadandale, Bibha Choudhary, Subha Srinivasan, Vidyanand Nanjundiah

{"title":"A Consensus Genome Sequence for the Social Amoeba Dictyostelium giganteum.","authors":"Aditya Sharma, Kumari Khushi, Febina Ravindran, Jayarama S Kadandale, Bibha Choudhary, Subha Srinivasan, Vidyanand Nanjundiah","doi":"10.1093/gbe/evag198","DOIUrl":"10.1093/gbe/evag198","url":null,"abstract":"The dictyostelid or cellular slime molds (CSMs) are recognized as models in cell, developmental, and human disease biology. Their unusual life cycle alternates between a free-living solitary phase and an aggregative social phase. We generated short Illumina reads and assembled a consensus genome, comprising nuclear and mitochondrial genomes, representative of six naturally occurring strains of the CSM Dictyostelium giganteum. The nuclear genome has an AT content of 75.76%, accounting for 38.52 Mb with an N50 of 3.01 Mb and L50 of 5, and resolves into five chromosome-scale scaffolds consistent with the karyotype. BUSCO analysis recovered 95.5% complete single-copy orthologs and 0.6% duplicated orthologs, corresponding to an overall completeness of 96.1%, with 0.3% fragmented and 3.6% missing orthologs. Approximately 5,500 deduced gene sequences from a publicly available transcriptome further validate the genome assembly and completeness. The genome encodes 13,251 predicted proteins, including ABC transporters, polyketide synthases, Ras/Rho GTPases, and expanded families of protein kinases. A comparative analysis shows extensive conservation of syntenic blocks with Dictyostelium. discoideum and Dictyostelium. firmibasis. About 18% of the nuclear genome is made up of repetitive DNA, mostly in the form of simple repeats. Comparative proteome-level orthology analysis across Dictyostelium species and Entamoeba identifies a conserved Amoebozoan core and a substantial dictyostelid-specific gene repertoire. Domain-level comparisons indicate widespread conservation of intracellular signaling and cytoskeletal modules with animals, whereas canonical metazoan extracellular adhesion domains are absent.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13487327/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148663713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Protein Structure Characters in the Light of Phylogenetic Systematics. 从系统发育系统学角度看蛋白质结构特征。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-08-01 DOI: 10.1093/gbe/evag168

Nicholas J Matzke, Changhao Li

{"title":"Protein Structure Characters in the Light of Phylogenetic Systematics.","authors":"Nicholas J Matzke, Changhao Li","doi":"10.1093/gbe/evag168","DOIUrl":"10.1093/gbe/evag168","url":null,"abstract":"Protein structure characters have great potential for improving phylogenetic inference, especially for deep nodes where amino acid sequences are highly diverged. The combination of AlphaFold structure predictions and Foldseek's \"3Di\" structural alphabet makes it relatively easy to conduct model-based phylogenetic inference that includes a partition of slow-evolving 3Di characters. However, we show that even identical amino acid sequences can produce substantially different 3Di characters, depending on the source of the structural model and whether inter-chain interactions are considered. We argue that such variability can be addressed with key concepts from traditional organism-based phylogenetic systematics: semaphoront, hypodigm, and character ascertainment method. To illustrate this, we develop an analogy between organismal development, taphonomy, and subsequent description and character coding by a systematist, and the process of protein synthesis, folding, and interaction and subsequent extraction, experimentation, and structural modeling by a biochemist. We conclude that differences in 3Di characters between semaphoronts are not intrinsically a problem, but they do require that the researcher uses the same replicable method on all proteins in the phylogenetic analysis. The guiding principle should be to maximize the chance that character differences in the data matrix are the results of underlying evolutionary changes, rather than artifacts due to differences in the methods used for obtaining semaphoronts and coding characters.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148630322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Emergence Biases in Molecular Evolution. 分子进化中的涌现偏差。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-08-01 DOI: 10.1093/gbe/evag195

Timothy Fuqua, Nikolaos Vakirlis

引用次数: 0

Network Properties Influence Covariance Between Gene Expression and Fecundity Fitness of Caenorhabditis elegans in a Novel Laboratory Environment. 在一个新的实验室环境中，网络特性影响秀丽隐杆线虫基因表达和繁殖力适应度之间的协方差。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-08-01 DOI: 10.1093/gbe/evag180

Tyler R Inskeep, Simon C Groen

{"title":"Network Properties Influence Covariance Between Gene Expression and Fecundity Fitness of Caenorhabditis elegans in a Novel Laboratory Environment.","authors":"Tyler R Inskeep, Simon C Groen","doi":"10.1093/gbe/evag180","DOIUrl":"10.1093/gbe/evag180","url":null,"abstract":"Gene expression bridges genotype and phenotype, shaping how organisms respond to their environments. Yet, it remains difficult to untangle how the architecture of gene regulatory networks (GRNs) influences the relationship between gene expression and fitness-especially in structured populations where genetic variants affecting both types of traits are inherited together. Here, we use publicly available data from wild Caenorhabditis elegans strains to link genome-wide gene expression levels to lifetime fecundity upon cultivation in a novel laboratory environment. Despite strong population structure caused by self-fertilization, selective sweeps, and hyperdivergent haplotypes, we find that a small subset of genes show significant covariance between their expression levels and fecundity fitness in laboratory cultivation conditions. These associations persist even after controlling for underlying genomic features. Genes that are older, show more tissue-specific expression patterns, and are particularly enriched in the germline and nervous system exhibit stronger covariance with fecundity in the new laboratory environment, consistent with known patterns of genetic divergence between wild and \"domesticated\" laboratory strains. Moreover, genes that are centrally positioned within GRNs, or are regulated downstream of certain transcription factors, show stronger associations with fitness. Together, these results suggest that genome structure and network topology jointly shape how variation in gene expression translates into fitness, shedding light on the early stages of adaptation to novel environments.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13429268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148445787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Molecular Drivers of Mutualistic Association Between Anemone and Anemonefish. 海葵和海葵鱼共生关系的分子驱动因素。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-08-01 DOI: 10.1093/gbe/evag197

Sneha Suresh, Daniele Romeo, Celia Schunter

{"title":"Molecular Drivers of Mutualistic Association Between Anemone and Anemonefish.","authors":"Sneha Suresh, Daniele Romeo, Celia Schunter","doi":"10.1093/gbe/evag197","DOIUrl":"10.1093/gbe/evag197","url":null,"abstract":"The anemone-anemonefish mutualism is one of the most iconic in the marine environment. While the evolution of this mutualistic relationship has contributed to the ecological success of both partners, the underlying molecular processes that establish and maintain it remain poorly understood, particularly how anemonefish tolerate anemone venom. Here, we characterize the transcriptional dynamics in both the anemonefish Amphiprion clarkii and its host anemone Entacmaea quadricolor 48 h after association, providing a rare insight into the coordinated molecular processes in both partners that underlie symbiosis establishment. Upon acclimation with an anemone, anemonefish showed differential regulation of sensory perception and memory genes in key brain regions, indicating activation of neural pathways that may facilitate host recognition and mutualism establishment. In the fish's skin, altered expression of genes involved in neurotransmitter release, cytoskeleton organization, and venom receptor proteins points to mechanisms of resistance to anemone venom. This resistance is particularly remarkable since anemone hosting fish exhibited increased expression of genes encoding mechanoreceptors, putative venom-associated proteins, and ion channels involved in nematocyst discharge, indicating the anemone does indeed mount an active response to their mutualistic partner. By simultaneously capturing the molecular responses of both symbiotic partners, our results reveal the complex, coordinated interplay of molecular events in both species that play a pivotal role in establishing this mutualistic relationship.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13481981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148630289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Selective Regimes and Evolutionary Dynamics of Z and W Gametologs Across an Expanded Avian Neo-Sex Chromosome. 扩展的鸟类新性染色体上Z和W配子学的选择机制和进化动力学。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-08-01 DOI: 10.1093/gbe/evag204

Simon J Ellerstrand, Bengt Hansson

{"title":"Selective Regimes and Evolutionary Dynamics of Z and W Gametologs Across an Expanded Avian Neo-Sex Chromosome.","authors":"Simon J Ellerstrand, Bengt Hansson","doi":"10.1093/gbe/evag204","DOIUrl":"10.1093/gbe/evag204","url":null,"abstract":"Sex chromosome evolution is characterized by Y/W degeneration and its consequences for selection on X/Z-linked recessive mutations in the heterogametic sex, yet how functional constraints modulate the evolutionary dynamics of Z-W gametologs remains poorly resolved. We addressed this question in larks (Alaudidae), a lineage carrying enlarged neo-sex chromosomes with multiple evolutionary strata formed through repeated translocations and successive recombination-suppression events. Using whole-genome sequences of males and females of two Alauda species, we analysed 1,759 Z-W gametologs. We found that W-gene degeneration was governed primarily by evolutionary time and intrinsic gene features: long genes were lost earliest, although this tendency was mitigated by gene essentiality, as indicated by high haploinsufficiency scores. Z-linked genes lacking a functional W counterpart exhibited higher nonsynonymous divergence than Z genes retaining a functional W, consistent with selection-driven faster-Z evolution. The strongest signature of purifying selection, comparable to that of pseudoautosomal genes, was observed in haploinsufficient Z-linked genes, which were also more likely to retain W gametologs. Although W genes generally diverged faster, their selection signatures covaried with those of Z and with haploinsufficiency, suggesting partially shared Z-W evolutionary dynamics. Notably, a small subset of W genes showed intensified or positive selection, including several genes associated with putative female-specific functions. Together, our results demonstrate that gene essentiality slows functional divergence on both Z and W, modulates faster-Z dynamics and enables key W genes to remain functional-and potentially advantageous for females-for millions of generations after recombination cessation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13524101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148706343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Not All Roads Lead to Red: The Genetics of Sexual Dichromatism in the Northern Cardinal (Cardinals cardinalis). 并非所有的道路都通向红色：北方红衣主教（红衣主教）的性别二色性遗传学。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-08-01 DOI: 10.1093/gbe/evag201

Miranda J Wade, Sara M Patton, Elizabeth C Scheer, Rebecca E Koch, Yufeng Zhang, Matthew B Toomey, Geoffrey E Hill, Simon Yung Wa Sin

{"title":"Not All Roads Lead to Red: The Genetics of Sexual Dichromatism in the Northern Cardinal (Cardinals cardinalis).","authors":"Miranda J Wade, Sara M Patton, Elizabeth C Scheer, Rebecca E Koch, Yufeng Zhang, Matthew B Toomey, Geoffrey E Hill, Simon Yung Wa Sin","doi":"10.1093/gbe/evag201","DOIUrl":"10.1093/gbe/evag201","url":null,"abstract":"Sexual dichromatism, characterized by sex-specific differences in coloration, is widespread among birds and often involves carotenoid-based pigmentation. Despite extensive research on the social and ecological environments favoring sexual dichromatism, the molecular mechanisms underlying its development and evolution remain largely unexplored. In this study, we investigated the genetic and molecular processes giving rise to sexual dichromatism in the red ketocarotenoid-based plumage of northern cardinals (Cardinalis cardinalis). We quantified carotenoid concentrations in plasma and feather follicles, confirmed that homologs of CYP2J19, BDH1L, and TTC39B catalyze the production of C-4 ketocarotenoids, and performed gene expression analyses across tissues. Males showed significantly higher plasma and feather ketocarotenoid concentrations, upregulated CYP2J19 and TTC39B expression in liver and feather tissues, and upregulated carotenoid transport gene expression in the gut and feather follicles. Females exhibited a dramatic upregulation of BCO2 in their feather follicles, facilitating carotenoid degradation and attenuating red pigmentation. Additionally, sex-biased expression of hormonal regulators, such as HSD17B4 and ZNF131, in the feather follicle suggests hormonal modulation influences dichromatism. These findings indicate that sex-specific regulation of carotenoid processing genes underpins the vivid red coloration in males and the drab phenotype in females, likely maintained by a balance between natural and sexual selection, with mechanisms of sexual antagonism affecting divergent gene expression. This work advances understanding of the molecular basis of avian sexual dimorphism, highlighting key genetic pathways involved in carotenoid-based coloration and providing a foundation for further research into the evolution of sexually dichromatic traits.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13494560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148706328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Beyond Invariable Sites: Using Evolutionary Stasis to Map Multilayered Constraints on the Evolution of Viral and Mammalian Genomes. 超越不变位点：利用进化停滞来绘制病毒和哺乳动物基因组进化的多层约束。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-08-01 DOI: 10.1093/gbe/evag184

Sergei L Kosakovsky Pond, Hannah Verdonk, Steven Weaver, Gallean Brown, Danielle Callan, Anton Nekrutenko, Darren P Martin

{"title":"Beyond Invariable Sites: Using Evolutionary Stasis to Map Multilayered Constraints on the Evolution of Viral and Mammalian Genomes.","authors":"Sergei L Kosakovsky Pond, Hannah Verdonk, Steven Weaver, Gallean Brown, Danielle Callan, Anton Nekrutenko, Darren P Martin","doi":"10.1093/gbe/evag184","DOIUrl":"10.1093/gbe/evag184","url":null,"abstract":"The quantification of genomic conservation has progressed from foundational statistical modeling of evolutionary rates to state-of-the-art deep learning architectures. However, a major resolution gap remains at the zero-rate origin, where standard selection inference tools fail to distinguish between sites that are invariant due to chance (stochastic invariance) or low substitution opportunity and those that are invariant due to extreme purifying selection. We present B-STILL (Bayesian Significance Test of Invariant Low Likelihoods), a hierarchical Bayesian framework designed to resolve the selective landscape of protein-coding genes near the zero-rate limit. By leveraging gene-level rate distributions (prior calibration) and modeling codon-site-specific substitution opportunities (determined by genetic-code degeneracy and nucleotide substitution biases), B-STILL quantifies the statistical significance of observed stasis. We define a rate-based stasis threshold to identify evolutionary stasis anchors (ESAs)-sites where the upper bound on the evolutionary rate is statistically constrained relative to the background rate of the gene due to extreme purifying selection. Validation against clinical and pathogen datasets confirms that ESAs are strong predictors of biological fitness and pathogenicity. Applying B-STILL across viral and mammalian genomes, we identify thousands of significantly clustered ESAs that map to known functional domains and uncharacterized structural motifs. These results establish B-STILL as a scalable, statistically rigorous framework for high-resolution genomic annotation, converting previously uninformative invariant sites into precise markers of extreme evolutionary constraint.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13427764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148602148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

NOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species Complex. nod样受体基因在真菌物种复合体中经历了多样性增强的进化。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-08-01 DOI: 10.1093/gbe/evag185

S Lorena Ament-Velásquez, Sven J Saupe

{"title":"NOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species Complex.","authors":"S Lorena Ament-Velásquez, Sven J Saupe","doi":"10.1093/gbe/evag185","DOIUrl":"10.1093/gbe/evag185","url":null,"abstract":"Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria. Some fungal NLRs are known to control regulated cell death in the context of allorecognition, the capacity to recognize conspecific nonself. However, the function of most fungal NLR genes remains unknown. Here, we characterize the evolution of the NLRs repertoire in the Podospora anserina species complex. We show that the vast majority of the NLRs display effector domains known to be involved in regulated cell death execution. Moreover, NLRs undergo more rapid gene turnover than random genes, show higher dN/dS values, and faster evolutionary rates. A subgroup of NLRs, distinguished by superstructure-forming repeats with very high sequence identity (high internal conservation), evolved independently multiple times. We found that high internal conservation NLRs are more associated with transposable elements, exhibit higher nucleotide diversity partially driven by repeat-induced point mutation, and show elevated Tajima's D values indicative of balancing selection. Furthermore, high internal conservation NLR phylogenies do not recapitulate species relationships, which we determined is caused by both balancing selection and introgression. In addition, we identified cases of repeat exchange between distinct high internal conservation NLR genes, implying that novel binding specificities may evolve through repeat shuffling, thereby increasing allelic diversity. Finally, we determined that NLR genes with high internal conservation repeats exist outside of the fungal realm, arguing for similar dynamics in other taxa. Overall, these findings suggest that fungal NLRs evolve under diversity-enhancing mechanisms and display selective signatures consistent with a general immune function.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148561359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

CAPHEINE, or Everything and the Kitchen Sink: A Workflow for Automating Selection Analyses Using HyPhy. CAPHEINE，或一切和厨房水槽：使用HyPhy自动化选择分析的工作流程。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-08-01 DOI: 10.1093/gbe/evag173

Hannah Verdonk, Danielle Callan, Sergei Pond

引用次数: 0