Genome Biology and Evolution最新文献_第3页

Convergent Evolution Associated with the Loss of Developmental Diapause May Promote Extended Lifespan in Bees. 与失去发育休眠期有关的趋同进化可能会延长蜜蜂的寿命。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae255

Priscila K F Santos, Karen M Kapheim

{"title":"Convergent Evolution Associated with the Loss of Developmental Diapause May Promote Extended Lifespan in Bees.","authors":"Priscila K F Santos, Karen M Kapheim","doi":"10.1093/gbe/evae255","DOIUrl":"10.1093/gbe/evae255","url":null,"abstract":"Diapause has long been proposed to play a significant role in the evolution of eusociality in Hymenoptera. Recent studies have shown that shifts in the diapause stage precede social evolution in wasps and bees; however, the genomic basis remains unknown. Given the overlap in molecular pathways that regulate diapause and lifespan, we hypothesized that the evolutionary loss of developmental diapause may lead to extended lifespan among adults, which is a prerequisite for the evolution of eusociality. To test whether the loss of prepupal diapause is followed by genomic changes associated with lifespan extension, we compared 27 bee genomes with or without prepupal diapause. Our results point to several potential mechanisms for lifespan extension in species lacking prepupal diapause, including the loss of the growth hormone PTTH and its receptor TORSO, along with convergent selection in genes known to regulate lifespan in animals. Specifically, we observed purifying selection of prolongevity genes and relaxed selection of antilongevity genes within the IIS/TOR pathway in species that have lost prepupal diapause. Changes in selection pressures on this pathway may lead to the evolution of new phenotypes, such as lifespan extension and altered responses to nutritional signals that are crucial for social evolution.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695471","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

Genome Streamlining: Effect of Mutation Rate and Population Size on Genome Size Reduction. 基因组精简：突变率和种群规模对缩小基因组规模的影响。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae250

Juliette Luiselli, Jonathan Rouzaud-Cornabas, Nicolas Lartillot, Guillaume Beslon

{"title":"Genome Streamlining: Effect of Mutation Rate and Population Size on Genome Size Reduction.","authors":"Juliette Luiselli, Jonathan Rouzaud-Cornabas, Nicolas Lartillot, Guillaume Beslon","doi":"10.1093/gbe/evae250","DOIUrl":"10.1093/gbe/evae250","url":null,"abstract":"Genome streamlining, i.e. genome size reduction, is observed in bacteria with very different life traits, including endosymbiotic bacteria and several marine bacteria, raising the question of its evolutionary origin. None of the hypotheses proposed in the literature is firmly established, mainly due to the many confounding factors related to the diverse habitats of species with streamlined genomes. Computational models may help overcome these difficulties and rigorously test hypotheses. In this work, we used Aevol, a platform designed to study the evolution of genome architecture, to test 2 main hypotheses: that an increase in population size (N) or mutation rate (μ) could cause genome reduction. In our experiments, both conditions lead to streamlining but have very different resulting genome structures. Under increased population sizes, genomes lose a significant fraction of noncoding sequences but maintain their coding size, resulting in densely packed genomes (akin to streamlined marine bacteria genomes). By contrast, under an increased mutation rate, genomes lose both coding and noncoding sequences (akin to endosymbiotic bacteria genomes). Hence, both factors lead to an overall reduction in genome size, but the coding density of the genome appears to be determined by N×μ. Thus, a broad range of genome size and density can be achieved by different combinations of N and μ. Our results suggest that genome size and coding density are determined by the interplay between selection for phenotypic adaptation and selection for robustness.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11666309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681680","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 Basis of Eusocial Complexity: The Case of Worker Reproductivity in Bees.

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae269

David C Prince, Anders Wirén, Timothy J Huggins, David H Collins, Tamas Dalmay, Andrew F G Bourke

{"title":"Molecular Basis of Eusocial Complexity: The Case of Worker Reproductivity in Bees.","authors":"David C Prince, Anders Wirén, Timothy J Huggins, David H Collins, Tamas Dalmay, Andrew F G Bourke","doi":"10.1093/gbe/evae269","DOIUrl":"10.1093/gbe/evae269","url":null,"abstract":"In eusocial insects, the molecular basis of worker reproductivity, including how it changes with eusocial complexity, remains relatively poorly understood. To address this, we used mRNA-seq to isolate genes differentially expressed between ovary-active and ovary-inactive workers in the intermediately eusocial bumblebee Bombus terrestris. By comparisons with data from the advanced eusocial honeybee Apis mellifera, which shows reduced worker reproductivity, we characterized gene expression differences associated with change in worker reproductivity as a function of eusocial complexity. By comparisons with genes associated with queen-worker caste development in B. terrestris larvae, we tested the behavioral-morphological caste homology hypothesis, which proposes co-option of genes influencing reproductive division of labor in adults in morphological caste evolution. We conducted comparisons having isolated genes expressed in B. terrestris worker-laid eggs to remove the potential confound caused by gene expression in eggs. Gene expression differences between the B. terrestris worker phenotypes were mainly in fat body and ovary, not brain. Many genes (86%) more highly expressed in ovary of ovary-active workers were also expressed in worker-laid eggs, confirming egg-expressed genes were potentially confounding. Comparisons across B. terrestris and A. mellifera, and with B. terrestris larvae, returned significant percentage overlaps in differentially expressed genes and/or enriched Gene Ontology terms, suggesting conserved gene functions underpin worker reproductivity as it declines with increasing eusocial complexity and providing support for the behavioral-morphological caste homology hypothesis. Therefore, within bees, both a degree of conserved gene use and gene co-option appear to underlie the molecular basis of worker reproductivity and morphological caste evolution.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11670783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142812736","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

Chromosome-scale Reference Genome and RAD-based Genetic Map of Yellow Starthistle (Centaurea solstitialis) Reveal Putative Structural Variation and QTL Associated With Invader Traits. 基于染色体尺度的黄星蓟（Centaurea solstitialis）参考基因组和 RAD 遗传图谱揭示了与入侵者性状相关的假定结构变异和 QTL。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae243

Bryan Reatini, Jessie A Pelosi, F Alice Cang, Qiuyu Jiang, Michael T W McKibben, Michael S Barker, Loren H Rieseberg, Katrina M Dlugosch

{"title":"Chromosome-scale Reference Genome and RAD-based Genetic Map of Yellow Starthistle (Centaurea solstitialis) Reveal Putative Structural Variation and QTL Associated With Invader Traits.","authors":"Bryan Reatini, Jessie A Pelosi, F Alice Cang, Qiuyu Jiang, Michael T W McKibben, Michael S Barker, Loren H Rieseberg, Katrina M Dlugosch","doi":"10.1093/gbe/evae243","DOIUrl":"10.1093/gbe/evae243","url":null,"abstract":"Invasive species offer outstanding opportunities to identify the genomic sources of variation that contribute to rapid adaptation, as well as the genetic mechanisms facilitating invasions. The Eurasian plant yellow starthistle (Centaurea solstitialis) is highly invasive in North and South American grasslands and known to have evolved increased growth and reproduction during invasion. Here, we develop new genomic resources for C. solstitialis and map the genetic basis of invasiveness traits. We present a chromosome-scale (1N = 8) reference genome using PacBio CLR and Dovetail Omni-C technologies, and functional gene annotation using RNAseq. We find repeat structure typical of the family Asteraceae, with over 25% of gene content derived from ancestral whole-genome duplications (paleologs). Using an F2 mapping population derived from a cross between native and invading parents, with a restriction site-associated DNA (RAD)-based genetic map, we validate the assembly and identify 13 quantitative trait loci underpinning size traits that have evolved during invasion. We find evidence that large effects of quantitative trait loci may be associated with structural variants between native and invading genotypes, including a variant with an overdominant and pleiotropic effect on key invader traits. We also find evidence of significant paleolog enrichment under two quantitative trait loci. Our results add to growing evidence of the importance of structural variants in evolution, and to understanding of the rapid evolution of invaders.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142727982","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

Multiple Displacement Amplification Facilitates SMRT Sequencing of Microscopic Animals and the Genome of the Gastrotrich Lepidodermella squamata (Dujardin 1841). 多重置换扩增技术促进了微小动物 SMRT 测序和鱿鱼胃肠动物 Lepidodermella squamata（Dujardin，1841 年）基因组的测序。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae254

Nickellaus G Roberts, Michael J Gilmore, Torsten H Struck, Kevin M Kocot

{"title":"Multiple Displacement Amplification Facilitates SMRT Sequencing of Microscopic Animals and the Genome of the Gastrotrich Lepidodermella squamata (Dujardin 1841).","authors":"Nickellaus G Roberts, Michael J Gilmore, Torsten H Struck, Kevin M Kocot","doi":"10.1093/gbe/evae254","DOIUrl":"10.1093/gbe/evae254","url":null,"abstract":"Obtaining adequate DNA for long-read genome sequencing remains a roadblock to producing contiguous genomes from small-bodied organisms, hindering understanding of phylogenetic relationships and genome evolution. Multiple displacement amplification leverages Phi29 DNA polymerase to produce micrograms of DNA from picograms of input. However, multiple displacement amplification's inherent biases in amplification related to guanine and cytosine (GC) content, repeat content and chimera production are a problem for long-read genome assembly, which has been little investigated. We explored the utility of multiple displacement amplification for generating template DNA for High Fidelity (HiFi) sequencing directly from living cells of Caenorhabditis elegans (Nematoda) and Lepidodermella squamata (Gastrotricha) containing one order of magnitude less DNA than required for the PacBio Ultra-Low DNA Input Workflow. High Fidelity sequencing of libraries prepared from multiple displacement amplification products resulted in highly contiguous and complete genomes for both C. elegans (102 Mbp assembly; 336 contigs; N50 = 868 kbp; L50 = 39; BUSCO_nematoda_nucleotide: S:96.1%, D:2.8%) and L. squamata (122 Mbp assembly; 157 contigs; N50 = 3.9 Mbp; L50 = 13; BUSCO_metazoa_nucleotide: S:80.8%, D:2.8%). Coverage uniformity for reads from multiple displacement amplification DNA (Gini Index: 0.14, normalized mean across all 100 kbp blocks: 0.49) and reads from pooled nematode DNA (Gini Index: 0.16, normalized mean across all 100 kbp blocks: 0.49) proved similar. Using this approach, we sequenced the genome of the microscopic invertebrate L. squamata (Gastrotricha), the first of its phylum. Using the newly sequenced genome, we infer Gastrotricha's long-debated phylogenetic position as the sister taxon of Platyhelminthes and conduct a comparative analysis of the Hox cluster.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11660948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142727999","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

TIdeS: A Comprehensive Framework for Accurate Open Reading Frame Identification and Classification in Eukaryotic Transcriptomes. TIdeS：真核生物转录组中开放阅读框准确识别和分类的综合框架。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae252

Xyrus X Maurer-Alcalá, Eunsoo Kim

{"title":"TIdeS: A Comprehensive Framework for Accurate Open Reading Frame Identification and Classification in Eukaryotic Transcriptomes.","authors":"Xyrus X Maurer-Alcalá, Eunsoo Kim","doi":"10.1093/gbe/evae252","DOIUrl":"10.1093/gbe/evae252","url":null,"abstract":"Studying fundamental aspects of eukaryotic biology through genetic information can face numerous challenges, including contamination and intricate biotic interactions, which are particularly pronounced when working with uncultured eukaryotes. However, existing tools for predicting open reading frames (ORFs) from transcriptomes are limited in these scenarios. Here we introduce Transcript Identification and Selection (TIdeS), a framework designed to address these nontrivial challenges associated with current 'omics approaches. Using transcriptomes from 32 taxa, representing the breadth of eukaryotic diversity, TIdeS outperforms most conventional ORF-prediction methods (i.e. TransDecoder), identifying a greater proportion of complete and in-frame ORFs. Additionally, TIdeS accurately classifies ORFs using minimal input data, even in the presence of \"heavy contamination\". This built-in flexibility extends to previously unexplored biological interactions, offering a robust single-stop solution for precise ORF predictions and subsequent decontamination. Beyond applications in phylogenomic-based studies, TIdeS provides a robust means to explore biotic interactions in eukaryotes (e.g. host-symbiont, prey-predator) and for reproducible dataset curation from transcriptomes and genomes.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686861","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

Transcriptomic Sexual Conflict at Two Evolutionary Timescales Revealed by Experimental Evolution in Caenorhabditis elegans. 通过实验性进化揭示了草履虫在两个进化时间尺度上的转录组性冲突。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae256

Katja R Kasimatis, John H Willis, Christine A Sedore, Patrick C Phillips

{"title":"Transcriptomic Sexual Conflict at Two Evolutionary Timescales Revealed by Experimental Evolution in Caenorhabditis elegans.","authors":"Katja R Kasimatis, John H Willis, Christine A Sedore, Patrick C Phillips","doi":"10.1093/gbe/evae256","DOIUrl":"10.1093/gbe/evae256","url":null,"abstract":"Sex-specific regulation of gene expression is the most plausible way for generating sexually differentiated phenotypes from an essentially shared genome. However, since genetic material is shared, sex-specific selection in one sex can have an indirect response in the other sex. From a gene expression perspective, this tethered response can move one sex away from their wild-type expression state and potentially impact many gene regulatory networks. Here, using experimental evolution in the model nematode Caenorhabditis elegans, we explore the coupling of direct sexual selection on males with the transcriptomic response in males and females over microevolutionary timescales to uncover the extent to which postinsemination reproductive traits share a genetic basis between the sexes. We find that differential gene expression evolved in a sex-specific manner in males, while in females, indirect selection causes an evolved response. Almost all differentially expressed genes were downregulated in both evolved males and females. Moreover, 97% of significantly differentially expressed genes in males and 69% of significantly differentially expressed genes in females have wild-type female-biased expression profile. Changes in gene expression profiles were likely driven through trans-acting pathways that are shared between the sexes. We found no evidence that the core dosage compensation machinery was impacted by experimental evolution. Together, these data suggest a defeminization of the male transcriptome and masculinization of the female transcriptome driven by direct selection on male sperm competitive ability. Our results indicate that on short evolutionary timescales, sexual selection can generate putative sexual conflict in expression space.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11687035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686871","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

Paralogous Gene Recruitment in Multiple Families Constitutes Genetic Architecture and Robustness of Pod Dehiscence in Legumes.

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae267

Bin Yong, Jana Balarynová, Bingbing Li, Denisa Konečná, Jorge Rencoret, José C Del Río, Petr Smýkal, Chaoying He

{"title":"Paralogous Gene Recruitment in Multiple Families Constitutes Genetic Architecture and Robustness of Pod Dehiscence in Legumes.","authors":"Bin Yong, Jana Balarynová, Bingbing Li, Denisa Konečná, Jorge Rencoret, José C Del Río, Petr Smýkal, Chaoying He","doi":"10.1093/gbe/evae267","DOIUrl":"10.1093/gbe/evae267","url":null,"abstract":"Pod dehiscence facilitates seed dispersal in wild legumes while indehiscence is a key domestication trait in cultivated ones. However, the evolutionary genetic mechanisms underlying its diversity are largely unclear. In this study, we compared transcriptomes of two warm-season (Glycine spp. and Phaseolus spp.) and two cool-season (Pisum spp. and Medicago ruthenica) legumes in analysis of dehiscent and indehiscent pod genotypes. Differentially expressed genes in AP2/ERF-like transcription factors and seven structural gene families, including lactoperoxidase, laccase, and cellulose synthase-interactive proteins, which are involved in secondary cell wall component accumulation, were identified to exert key roles in pod dehiscence variation. In accordance with this, higher lignin and cellulose contents were observed in pod secondary cell wall of dehiscent accessions of soybean and pea; however, the variation patterns of lignin polymers in soybean (accumulation) and pea (proportion) differed between dehiscent and indehiscent pods. Moreover, genome-wide comparative analysis revealed that orthogroups represented <1% of all identified differentially expressed genes could be traced among the four genera of legumes, while recruiting paralogous members may constitute the genetic robustness of legume pod dehiscence. This study compared the genetic mechanism among several legumes in pod dehiscence formation and revealed a compensating role of paralogous redundancy of involved gene families in seed dispersal, which can guide crop breeding.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11652722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806819","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

Coevolution and Adaptation of Transition Nuclear Proteins and Protamines in Naturally Ascrotal Mammals Support the Black Queen Hypothesis.

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae260

Simin Chai, Jieqiong Kang, Tianzhen Wu, Yu Zheng, Xu Zhou, Shixia Xu, Wenhua Ren, Guang Yang

{"title":"Coevolution and Adaptation of Transition Nuclear Proteins and Protamines in Naturally Ascrotal Mammals Support the Black Queen Hypothesis.","authors":"Simin Chai, Jieqiong Kang, Tianzhen Wu, Yu Zheng, Xu Zhou, Shixia Xu, Wenhua Ren, Guang Yang","doi":"10.1093/gbe/evae260","DOIUrl":"10.1093/gbe/evae260","url":null,"abstract":"Protamines (PRMs) and transition nuclear proteins (TNPs) are two key classes of sperm nuclear basic proteins that regulate chromatin reorganization and condensation in the spermatozoon head, playing crucial roles in mammalian spermatogenesis. In scrotal mammals, such as humans, cryptorchidism, the failure of the testes to descend into the scrotal sac is generally associated with higher rates of defective spermatozoon quality and function. However, ascrotal mammals, such as cetaceans, with naturally undescended testes, produce normal spermatozoa similar to their scrotal counterparts. This study investigates the evolutionary pattern and functional changes in PRMs and TNPs to explore the potential molecular mechanisms underlying spermatogenesis in naturally ascrotal mammals. Although we found a conserved genomic arrangement for PRM and TNP genes across mammals, the coevolutionary loss of intact PRM2 and TNP2 was observed in several species, correlating significantly with diverse testicular positions. Notably, in cetaceans, which lack intact PRM2 and TNP2, we detected enhanced thermostability and DNA binding in PRM1, along with superior DNA repair capability in TNP1. These findings suggest that gene loss of PRM2 and TNP2, combined with functional enhancements in PRM1 and TNP1 proteins, evolved in response to physiological challenges posed by natural cryptorchidism in most ascrotal lineages. This evolutionary strategy enhances chromatin condensation efficiency and promotes DNA repair during spermatogenesis in natural cryptorchid mammals, supporting the Black Queen Hypothesis.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11652718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142835275","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

Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchin Heliocidaris erythrogramma. 单细胞转录组学揭示了海胆红海胆（Heliocidaris erythrogramma）胚胎细胞命运规范的进化重构。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-26 DOI: 10.1093/gbe/evae258

Abdull J Massri, Alejandro Berrio, Anton Afanassiev, Laura Greenstreet, Krista Pipho, Maria Byrne, Geoffrey Schiebinger, David R McClay, Gregory A Wray

{"title":"Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchin Heliocidaris erythrogramma.","authors":"Abdull J Massri, Alejandro Berrio, Anton Afanassiev, Laura Greenstreet, Krista Pipho, Maria Byrne, Geoffrey Schiebinger, David R McClay, Gregory A Wray","doi":"10.1093/gbe/evae258","DOIUrl":"10.1093/gbe/evae258","url":null,"abstract":"Altered regulatory interactions during development likely underlie a large fraction of phenotypic diversity within and between species, yet identifying specific evolutionary changes remains challenging. Analysis of single-cell developmental transcriptomes from multiple species provides a powerful framework for unbiased identification of evolutionary changes in developmental mechanisms. Here, we leverage a \"natural experiment\" in developmental evolution in sea urchins, where a major life history switch recently evolved in the lineage leading to Heliocidaris erythrogramma, precipitating extensive changes in early development. Comparative analyses of scRNA-seq developmental time courses from H. erythrogramma and Lytechinus variegatus (representing the derived and ancestral states respectively) reveals numerous evolutionary changes in embryonic patterning. The earliest cell fate specification events and the primary signaling center are co-localized in the ancestral dGRN; remarkably, in H. erythrogramma they are spatially and temporally separate. Fate specification and differentiation are delayed in most embryonic cell lineages, although in some cases, these processes are conserved or even accelerated. Comparative analysis of regulator-target gene co-expression is consistent with many specific interactions being preserved but delayed in H. erythrogramma, while some otherwise widely conserved interactions have likely been lost. Finally, specific patterning events are directly correlated with evolutionary changes in larval morphology, suggesting that they are directly tied to the life history shift. Together, these findings demonstrate that comparative scRNA-seq developmental time courses can reveal a diverse set of evolutionary changes in embryonic patterning and provide an efficient way to identify likely candidate regulatory interactions for subsequent experimental validation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142716071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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