Molecular biology and evolution最新文献_第9页

Where Did the Y Chromosome in the Spiny Rat Go, and How Did It Get There? 多刺鼠的Y染色体去了哪里？它是如何到达那里的？

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf102

Miki Okuno, Kentaro Matsuoka, Yuta Mochimaru, Takahiro Yamabe, Mayou Okano, Takamichi Jogahara, Atsushi Toyoda, Asato Kuroiwa, Takehiko Itoh

{"title":"Where Did the Y Chromosome in the Spiny Rat Go, and How Did It Get There?","authors":"Miki Okuno, Kentaro Matsuoka, Yuta Mochimaru, Takahiro Yamabe, Mayou Okano, Takamichi Jogahara, Atsushi Toyoda, Asato Kuroiwa, Takehiko Itoh","doi":"10.1093/molbev/msaf102","DOIUrl":"10.1093/molbev/msaf102","url":null,"abstract":"The XX/XY sex chromosome system is highly conserved across mammals, with rare exceptions where males lack a Y chromosome. Among these is the genus Tokudaia, a group of spiny rats comprising three species with unique sex chromosome systems deviating from the typical XX/XY pattern. While Tokudaia osimensis and Tokudaia tokunoshimensis have completely lost the Y chromosome, they retain some Y-linked genes on the X chromosome. In contrast, Tokudaia muenninki retains large sex chromosomes where both the X and Y chromosomes have fused with an autosome pair, carrying multi-copied Y-linked genes, including Sry. In this study, we generated chromosome-level genome assemblies for male individuals of all three Tokudaia species. By investigating loci typically associated with rodent Y-linked genes, we characterized sequences derived from the Tokudaia Y-chromosomal most recent common ancestor (Tokudaia Y-MRCA) and traced their evolutionary trajectories. Our analyses revealed that an initial X-to-Y translocation of a sequence containing the boundary-associated segmental duplication in a common ancestor of Tokudaia marked the beginning of their unique sex chromosome evolution. The boundary-associated segmental duplication, uniquely multi-copied in Tokudaia, facilitated further rearrangements through nonallelic homologous recombination and duplications. These processes culminated in subsequent Y-to-X translocations and duplications, leading to the complete loss of the Y chromosome as a distinct entity while preserving Y-linked genes in a multicopy state on the X chromosome. These findings highlight Tokudaia's rapid sex chromosome evolution within 3 million years and provide insights into the mechanisms underlying Y chromosome loss, contributing to a broader understanding of sex chromosome evolution in rodents.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12104558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033715","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

ERCnet: Phylogenomic Prediction of Interaction Networks in the Presence of Gene Duplication. ERCnet：基因重复存在下相互作用网络的系统基因组预测。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf089

Evan S Forsythe, Tony C Gatts, Linnea E Lane, Chris deRoux, Monica J Berggren, Elizabeth A Rehmann, Emily N Zak, Trinity Bartel, Luna A L'Argent, Daniel B Sloan

{"title":"ERCnet: Phylogenomic Prediction of Interaction Networks in the Presence of Gene Duplication.","authors":"Evan S Forsythe, Tony C Gatts, Linnea E Lane, Chris deRoux, Monica J Berggren, Elizabeth A Rehmann, Emily N Zak, Trinity Bartel, Luna A L'Argent, Daniel B Sloan","doi":"10.1093/molbev/msaf089","DOIUrl":"https://doi.org/10.1093/molbev/msaf089","url":null,"abstract":"Assigning gene function from genome sequences is a rate-limiting step in molecular biology research. A protein's position within an interaction network can potentially provide insights into its molecular mechanisms. Phylogenetic analysis of evolutionary rate covariation (ERC) in protein sequence has been shown to be effective for large-scale prediction of functional relationships and interactions. However, gene duplication, gene loss, and other sources of phylogenetic incongruence are barriers for analyzing ERC on a genome-wide basis. Here, we developed ERCnet, a bioinformatic program designed to overcome these challenges, facilitating efficient all-versus-all ERC analyses for large protein sequence datasets. We simulated proteome datasets and found that ERCnet achieves combined false positive and negative error rates well below 10% and that our novel \"branch-by-branch\" length measurements outperforms \"root-to-tip\" approaches in most cases, offering a valuable new strategy for performing ERC. We also compiled a sample set of 35 angiosperm genomes to test the performance of ERCnet on empirical data, including its sensitivity to user-defined analysis parameters such as input dataset size and branch-length measurement strategy. We investigated the overlap between ERCnet runs with different species samples to understand how species number and composition affect predicted interactions and to identify the protein sets that consistently exhibit ERC across angiosperms. Our systematic exploration of the performance of ERCnet provides a roadmap for design of future ERC analyses to predict functional interactions in a wide array of genomic datasets. ERCnet code is freely available at https://github.com/EvanForsythe/ERCnet.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 5","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12062884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028352","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

Genetic Differentiation is Constrained to Chromosomal Inversions and Putative Centromeres in Locally Adapted Populations With Higher Gene Flow. 在具有较高基因流的局部适应群体中，遗传分化仅限于染色体倒位和假定的着丝粒。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf092

Maria Akopyan, Anna Tigano, Arne Jacobs, Aryn P Wilder, Nina O Therkildsen

{"title":"Genetic Differentiation is Constrained to Chromosomal Inversions and Putative Centromeres in Locally Adapted Populations With Higher Gene Flow.","authors":"Maria Akopyan, Anna Tigano, Arne Jacobs, Aryn P Wilder, Nina O Therkildsen","doi":"10.1093/molbev/msaf092","DOIUrl":"https://doi.org/10.1093/molbev/msaf092","url":null,"abstract":"The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and recombination landscapes in shaping genetic diversity across genomes and among populations. This is particularly relevant when local adaptation occurs despite gene flow, where clustering of differentiated loci can maintain locally adapted variants by reducing recombination between them. However, the limited genomic resources for nonmodel species, including reference genomes and recombination maps, have constrained our understanding of these patterns. In this study, we leverage the Atlantic silverside-a nonmodel fish with extensive local adaptation across a steep latitudinal gradient-as an ideal system to explore how genome structure influences adaptation under varying levels of gene flow, using a newly available reference genome and multiple recombination maps. Analyzing 168 genomes from four populations, we found a continuum of genome-wide differentiation increasing from south to north, reflecting higher connectivity among southern populations and reduced gene flow at northern latitudes. With increasing gene flow, the number and clustering of FST outlier loci also increased, with differentiated loci found exclusively within large haploblocks harboring inversions and smaller peaks overlapping putative centromeric regions. Notably, sequence divergence was only evident in inversions, supporting their role in adaptive divergence with gene flow, whereas centromeric regions appeared differentiated because of low recombination and diversity, with no indication of elevated divergence. Our results support the hypothesis that clustered genomic architectures evolve with high gene flow and enhance our understanding of how inversions and centromeres are linked to different evolutionary processes.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 5","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12046131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144044402","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

Quantifying Transcriptome Turnover on Phylogenies by Modeling Gene Expression as a Binary Trait. 通过将基因表达建模为二元性状来量化系统发育中的转录组转换。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf106

Ammon Thompson, Michael R May, Ben R Hopkins, Nerisa Riedl, Olga Barmina, Benjamin J Liebeskind, Li Zhao, David Begun, Artyom Kopp

{"title":"Quantifying Transcriptome Turnover on Phylogenies by Modeling Gene Expression as a Binary Trait.","authors":"Ammon Thompson, Michael R May, Ben R Hopkins, Nerisa Riedl, Olga Barmina, Benjamin J Liebeskind, Li Zhao, David Begun, Artyom Kopp","doi":"10.1093/molbev/msaf106","DOIUrl":"10.1093/molbev/msaf106","url":null,"abstract":"Changes in gene expression are a key driver of phenotypic evolution, leading to a persistent interest in the evolution of transcriptomes. Traditionally, gene expression is modeled as a continuous trait, leaving qualitative transitions largely unexplored. In this paper, we detail the development of new Bayesian inference techniques to study the evolutionary turnover of organ-specific transcriptomes, which we define as instances where orthologous genes gain or lose expression in a particular organ. To test these techniques, we analyze the transcriptomes of 2 male reproductive organs, testes and accessory glands, across 11 species of the Drosophila melanogaster species group. We first discretize gene expression states by estimating the probability that each gene is expressed in each organ and species. We then define a phylogenetic model of correlated transcriptome evolution in 2 or more organs and fit it to the expression state data. Inferences under this model imply that many genes have gained and lost expression in each organ, and that the 2 organs experienced accelerated transcriptome turnover on different branches of the Drosophila phylogeny.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 5","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151205","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

Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates. 比较系统遗传学揭示了脊椎动物重组率进化的分支特异性驱动因素。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf100

Taylor Szasz-Green, Katherynne Shores, Vineel Vanga, Luke Zacharias, Andrew K Lawton, Amy L Dapper

{"title":"Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates.","authors":"Taylor Szasz-Green, Katherynne Shores, Vineel Vanga, Luke Zacharias, Andrew K Lawton, Amy L Dapper","doi":"10.1093/molbev/msaf100","DOIUrl":"10.1093/molbev/msaf100","url":null,"abstract":"Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143982358","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

Correction to: Deleterious and Adaptive Mutations in Plant Germplasm Conserved Ex Situ. 修正：非原位保存的植物种质中的有害和适应性突变。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf098

引用次数: 0

Divergent Cardiovascular Adaptations and Gene Regulation in High-Elevation Natives and Recent Colonizers of the Qinghai-Tibetan Plateau. 青藏高原高海拔原住民和新移民的心血管适应和基因调控差异

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf103

Huishang She, Graham R Scott, Yun Fang, Qingshuo Zhao, Fanwei Meng, Yanhua Qu

{"title":"Divergent Cardiovascular Adaptations and Gene Regulation in High-Elevation Natives and Recent Colonizers of the Qinghai-Tibetan Plateau.","authors":"Huishang She, Graham R Scott, Yun Fang, Qingshuo Zhao, Fanwei Meng, Yanhua Qu","doi":"10.1093/molbev/msaf103","DOIUrl":"10.1093/molbev/msaf103","url":null,"abstract":"High elevation imposes unrelenting and unavoidable hypoxia on species inhabiting these environments, providing an excellent natural setting for studying convergent or divergent evolution. By integrating measures of phenotypic variation, gene regulation, and functional performance, our study demonstrates that recent colonizers of high-elevation environments exhibit fundamentally different cardiovascular changes compared to long-term natives of these environments. Through the studying of heart morphological phenotypes, we showed that recent colonizers exhibit signs of cardiac hypertrophy, reflected by increased relative heart mass (heart mass/body mass) and cardiomyocyte size compared to their low-elevation relatives. In contrast, native species show no signs of cardiac hypertrophy and instead have 3-fold higher capillary densities than the colonizers, a change that likely enhances tissue oxygen diffusing capacity in the former. Using phylogenetic principal component analysis to quantify multivariate trait divergence, we show that native species are similar in cardiovascular phenotype and underlying gene expression, but differ appreciably from recent colonizers. We further demonstrate, using a functional assay, that differential expression of two genes (IRS2 and AKT1) in a conserved regulatory pathway mediates cardiomyocyte hypertrophy, which could explain the observed variation in cardiomyocyte size between native species and recent colonizers. This regulatory basis of variation in cardiac phenotype involves the differential expression of genes in a cardiomyocyte hypertrophy pathway that is conserved across birds, humans and other mammals. Collectively, our study highlights that evolutionary history is a critical determinant of cardiovascular variation in high-elevation environments.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12103977/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144008311","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

Chromatin Landscape Is Associated With Sex-Biased Expression and Drosophila-Like Dosage Compensation of the Z Chromosome in Artemia franciscana. 染色质景观与法氏鲟的性别表达和果蝇类剂量补偿有关

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf085

Vincent Kiplangat Bett, Minerva Susana Trejo-Arellano, Beatriz Vicoso

{"title":"Chromatin Landscape Is Associated With Sex-Biased Expression and Drosophila-Like Dosage Compensation of the Z Chromosome in Artemia franciscana.","authors":"Vincent Kiplangat Bett, Minerva Susana Trejo-Arellano, Beatriz Vicoso","doi":"10.1093/molbev/msaf085","DOIUrl":"10.1093/molbev/msaf085","url":null,"abstract":"The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12060005/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811728","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

Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes. 远亲硬骨鱼之间免疫基因的多重水平转移。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf107

Maxime Policarpo, Walter Salzburger, Florian Maumus, Clément Gilbert

{"title":"Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes.","authors":"Maxime Policarpo, Walter Salzburger, Florian Maumus, Clément Gilbert","doi":"10.1093/molbev/msaf107","DOIUrl":"10.1093/molbev/msaf107","url":null,"abstract":"Horizontal gene transfer (HGT) is less frequent in eukaryotes than in prokaryotes, yet can have strong functional implications and was proposed as a causal factor for major adaptations in several eukaryotic lineages. Most cases of eukaryote HGT reported to date are inter-domain transfers, and few studies have investigated eukaryote-to-eukaryote HGTs. Here, we performed a large-scale survey of HGT among 242 species of ray-finned fishes. We found multiple lines of evidence supporting 19 teleost-to-teleost HGT events that involve 17 different genes in 11 teleost fish orders. The genes involved in these transfers show lower synonymous divergence than expected under vertical transmission, their phylogeny is inconsistent with that of teleost fishes, and they occur at non-syntenic positions in donor and recipient lineages. The distribution of HGT events in the teleost tree is heterogenous, with 8 of the 19 transfers occurring between the same two orders (Osmeriformes and Clupeiformes). Though we favor a scenario involving multiple HGT events, future work should evaluate whether hybridization between species belonging to different teleost orders may generate HGT-like patterns. Besides the previously reported transfer of an antifreeze protein, most transferred genes play roles in immunity or are pore-forming proteins, suggesting that such genes may be more likely than others to confer a strong selective advantage to the recipient species. Overall, our work shows that teleost-to-teleost HGT has occurred on multiple occasions, and it will be worth further quantifying these transfers and evaluating their impact on teleost evolution as more genomes are sequenced.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078738","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

Functional Characterization of Luciferase in a Brittle Star Indicates Parallel Evolution Influenced by Genomic Availability of Haloalkane Dehalogenase. 海蛇尾荧光素酶的功能表征表明，卤代烷烃脱卤酶的基因组可用性影响了平行进化。

IF 5.3 1区生物学

Molecular biology and evolution Pub Date : 2025-04-30 DOI: 10.1093/molbev/msaf081

Emily S Lau, Marika Majerova, Nicholai M Hensley, Arnab Mukherjee, Michal Vasina, Daniel Pluskal, Jiri Damborsky, Zbynek Prokop, Jérôme Delroisse, Wendy-Shirley Bayaert, Elise Parey, Paola Oliveri, Ferdinand Marlétaz, Martin Marek, Todd H Oakley

{"title":"Functional Characterization of Luciferase in a Brittle Star Indicates Parallel Evolution Influenced by Genomic Availability of Haloalkane Dehalogenase.","authors":"Emily S Lau, Marika Majerova, Nicholai M Hensley, Arnab Mukherjee, Michal Vasina, Daniel Pluskal, Jiri Damborsky, Zbynek Prokop, Jérôme Delroisse, Wendy-Shirley Bayaert, Elise Parey, Paola Oliveri, Ferdinand Marlétaz, Martin Marek, Todd H Oakley","doi":"10.1093/molbev/msaf081","DOIUrl":"10.1093/molbev/msaf081","url":null,"abstract":"Determining why convergent traits use distinct versus shared genetic components is crucial for understanding how evolutionary processes generate and sustain biodiversity. However, the factors dictating the genetic underpinnings of convergent traits remain incompletely understood. Here, we use heterologous protein expression, biochemical assays, and phylogenetic analyses to confirm the origin of a luciferase gene from haloalkane dehalogenases in the brittle star Amphiura filiformis. Through database searches and gene tree analyses, we also show a complex pattern of the presence and absence of haloalkane dehalogenases across organismal genomes. These results first confirm parallel evolution across a vast phylogenetic distance, because octocorals like Renilla also use luciferase derived from haloalkane dehalogenases. This parallel evolution is surprising, even though previously hypothesized, because many organisms that also use coelenterazine as the bioluminescence substrate evolved completely distinct luciferases. The inability to detect haloalkane dehalogenases in the genomes of several bioluminescent groups suggests that the distribution of this gene family influences its recruitment as a luciferase. Together, our findings highlight how biochemical function and genomic availability help determine whether distinct or shared genetic components are used during the convergent evolution of traits like bioluminescence.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":5.3,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12059646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143779734","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