Genome Biology and Evolution最新文献_第2页

Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli. 实验室进化揭示了大肠杆菌热适应的转录机制。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2025-09-30 DOI: 10.1093/gbe/evaf171

Kevin Rychel, Ke Chen, Edward A Catoiu, Elina Olson, Troy E Sandberg, Ye Gao, Sibei Xu, Ying Hefner, Richard Szubin, Arjun Patel, Adam M Feist, Bernhard O Palsson

{"title":"Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.","authors":"Kevin Rychel, Ke Chen, Edward A Catoiu, Elina Olson, Troy E Sandberg, Ye Gao, Sibei Xu, Ying Hefner, Richard Szubin, Arjun Patel, Adam M Feist, Bernhard O Palsson","doi":"10.1093/gbe/evaf171","DOIUrl":"10.1093/gbe/evaf171","url":null,"abstract":"Adaptive laboratory evolution is able to generate microbial strains, which exhibit extreme phenotypes, revealing fundamental biological adaptation mechanisms. Here, we use adaptive laboratory evolution to evolve Escherichia coli strains that grow at temperatures as high as 45.3 °C, a temperature lethal to wild-type cells. The strains adopted a hypermutator phenotype and employed multiple systems-level adaptations that made global analysis of the DNA mutations difficult. Given the challenge at the genomic level, we were motivated to uncover high-temperature tolerance adaptation mechanisms at the transcriptomic level. We employed independently modulated gene set (iModulon) analysis to reveal five transcriptional mechanisms underlying growth at high temperatures. These mechanisms were connected to acquired mutations, changes in transcriptome composition, sensory inputs, phenotypes, and protein structures. They are as follows: (i) downregulation of general stress responses while upregulating the specific heat stress responses, (ii) upregulation of flagellar basal bodies without upregulating motility and upregulation fimbriae, (iii) shift toward anaerobic metabolism, (iv) shift in regulation of iron uptake away from siderophore production, and (v) upregulation of yjfIJKL, a novel heat tolerance operon whose structures we predicted with AlphaFold. iModulons associated with these five mechanisms explain nearly half of all variance in the gene expression in the adapted strains. These thermotolerance strategies reveal that optimal coordination of known stress responses and metabolism can be achieved with a small number of regulatory mutations and may suggest a new role for large protein export systems. Adaptive laboratory evolution with transcriptomic characterization is a productive approach for elucidating and interpreting adaptation to otherwise lethal stresses.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 10","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492005/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212504","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

Temporal Genomics Reveal a Century of Genomic Diversity Shifts Across a Biodiversity Hotspot Avian Assemblage. 时间基因组学揭示了一个世纪以来基因组多样性在生物多样性热点鸟类组合中的变化。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2025-09-30 DOI: 10.1093/gbe/evaf163

Joseph D Manthey, Amie E Settlecowski, Yonas Meheretu, Garrett J Behrends, Yann Bourgeois, Luke C Campillo, Stéphane Boissinot, Ben D Marks

{"title":"Temporal Genomics Reveal a Century of Genomic Diversity Shifts Across a Biodiversity Hotspot Avian Assemblage.","authors":"Joseph D Manthey, Amie E Settlecowski, Yonas Meheretu, Garrett J Behrends, Yann Bourgeois, Luke C Campillo, Stéphane Boissinot, Ben D Marks","doi":"10.1093/gbe/evaf163","DOIUrl":"10.1093/gbe/evaf163","url":null,"abstract":"Biodiversity has experienced tremendous shifts in community, species, and genetic diversity during the Anthropocene. Understanding temporal diversity shifts is especially critical in biodiversity hotspots, i.e., regions that are exceptionally biodiverse and threatened. Here, we use museomics and temporal genomics approaches to quantify temporal shifts in genomic diversity in an assemblage of eight generalist highland bird species from the Ethiopian Highlands (part of the Eastern Afromontane Biodiversity Hotspot). With genomic data from contemporary and historical samples, we demonstrate an assemblage-wide trend of increased genomic diversity through time, potentially due to improved habitat connectivity within highland regions. Genomic diversity shifts in these generalist species contrast with general trends of genomic diversity declines in specialist or imperiled species. In addition to genetic diversity shifts, we found an assemblage-wide trend of decreased realized mutational load, indicative of overall trends for potentially deleterious variation to be masked or selectively purged. Across this avian assemblage, we also show that shifts in population genomic structure are idiosyncratic, with species-specific trends. These results are in contrast with other charismatic and imperiled African taxa that have largely shown strong increases in population genetic structure over the recent past. This study highlights that not all taxa respond the same to environmental change, and generalists, in some cases, may even respond positively. Future comparative conservation genomics assessments on species groups or assemblages with varied natural history characteristics would help us better understand how diverse taxa respond to anthropogenic landscape changes.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12497481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144882793","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

Phylogenetic Methods Meet Deep Learning. 系统发育方法满足深度学习。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2025-09-30 DOI: 10.1093/gbe/evaf177

Svitlana Braichenko, Rui Borges, Carolin Kosiol

{"title":"Phylogenetic Methods Meet Deep Learning.","authors":"Svitlana Braichenko, Rui Borges, Carolin Kosiol","doi":"10.1093/gbe/evaf177","DOIUrl":"10.1093/gbe/evaf177","url":null,"abstract":"Deep learning (DL) has been widely used in various scientific fields, but its integration into phylogenetics has been slower, primarily due to the complex nature of phylogenetic data. The studies that apply DL to sequencing data often limit analyses to four-taxon trees. Many of these studies serve as \"proof of principle\" and perform similarly to traditional phylogeny reconstruction methods. New ways of using training data, such as encoding with compact bijective ladderized vectors or transformers, enable the handling of much larger trees and genomic data sets. This short perspective focuses on the application of DL in phylogenetics, introducing prevalent DL architectures. We highlight potential problems in the field by discussing the risks of using simulation-based training data and emphasize the importance of reproducibility and robustness in computational estimates. Finally, we explore promising research areas, including the combination of phylogenetics and population genetics in DL, the analysis of neighbor dependencies, and the potential to significantly reduce computational cost compared to traditional methods. This perspective illustrates the potential of DL in complementing traditional phylogeny reconstruction methods and aiding the advancement of phylogenetic analysis, especially in performing computationally demanding tasks such as model selection or estimating branch support values.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12514720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091380","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

Evolutionary Diversification and Functions of the Candidate Male Killing Gene wmk. 候选雄性杀伤基因wmk的进化多样化及其功能。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2025-09-30 DOI: 10.1093/gbe/evaf179

Emilie Lefoulon, Sarah R Bordenstein, Leah R Carpenter, Jessica L Buchser, Caroline J Nowicki, Anastasiya A Yakhnina, Jeremy B Gutierrez, Rupinder Kaur, Madangchanok Imchen, Seth R Bordenstein

{"title":"Evolutionary Diversification and Functions of the Candidate Male Killing Gene wmk.","authors":"Emilie Lefoulon, Sarah R Bordenstein, Leah R Carpenter, Jessica L Buchser, Caroline J Nowicki, Anastasiya A Yakhnina, Jeremy B Gutierrez, Rupinder Kaur, Madangchanok Imchen, Seth R Bordenstein","doi":"10.1093/gbe/evaf179","DOIUrl":"10.1093/gbe/evaf179","url":null,"abstract":"Symbiont-mediated male killing (MK) is a mechanism that selectively eliminates male offspring, often by disrupting sex-specific developmental processes. In Drosophila melanogaster, the WO-mediated killing gene wmk from Wolbachia prophage WO transgenically reproduces the MK phenotype, yet how the gene evolves and functions across diverse Wolbachia has not been systematically investigated. We analyzed 32 Wolbachia genomes available in the NCBI database to study wmk homologs across different arthropod hosts, reproductive parasitism functions, and Wolbachia supergroups. First, we report at least five distinct wmk phylogenetic clusters (Types I to V), often organized in multigenic dyads or triads. Second, among MK Wolbachia, there is a significantly higher number of wmk genes and diversity in Lepidoptera strains than in Drosophila strains, which exclusively harbor wmk Types I and III. Third, there are three patterns of wmk sequence and genomic organizational changes in Drosophila MK strains that associate with different evolutionary trajectories underpinning the MK phenotype. Fourth, single and combinatory transgenic expression of Types I and III in D. melanogaster uncovers male-biased lethality associated with Type I; however, dual expression of the Types together elicits a major reduction in offspring number. Fifth, wmk genes have low expression level across D. melanogaster developmental stages relative to the cifA and cifB genes, which could explain why cytoplasmic incompatibility is expressed in this system. These findings establish a complex and phylogenetically informed genetic basis of wmk-induced lethality, highlighting the role of gene copy number and expression, wmk Types, and host background in shaping the phenotype.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12504857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091197","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

Mitochondrial Impostors: Prevalence and Impacts of NUMTs on Genetic and Evolutionary Studies in Carnivora. 线粒体冒充者：numt在食肉动物遗传和进化研究中的流行和影响。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2025-09-30 DOI: 10.1093/gbe/evaf174

Huiwen Liu, Yixin Liu, Yibo Hu

{"title":"Mitochondrial Impostors: Prevalence and Impacts of NUMTs on Genetic and Evolutionary Studies in Carnivora.","authors":"Huiwen Liu, Yixin Liu, Yibo Hu","doi":"10.1093/gbe/evaf174","DOIUrl":"10.1093/gbe/evaf174","url":null,"abstract":"Nuclear mitochondrial pseudogenes are mitochondria-derived DNA sequences integrated into the nuclear genome, which can introduce errors in species identification, phylogenetic inference, and population genetics. Although nuclear mitochondrial pseudogene contamination has been reported in some Carnivora species, a systematic investigation into the prevalence and impacts of nuclear mitochondrial pseudogenes across an order is still lacking. In this study, 22,102 mitochondrial DNA sequences of 80 Carnivora species from 14 families and 54 genera were retrieved from the public National Center for Biotechnology Information database and further analyzed. Using alignment-based methods, 158 problematic sequences/sequence groups were identified and categorized into four types: nuclear mitochondrial pseudogenes, species misidentification or mislabeling, sequence errors, and anomalous sites. Among families, Felidae exhibited the highest rate of nuclear mitochondrial pseudogene contamination, particularly in species of the genus Panthera. In contrast, no nuclear mitochondrial pseudogene contamination was detected in members of Ursidae and Ailuridae. Phylogenetic analysis revealed multiple independent origins of nuclear mitochondrial pseudogene, with some tracing back to the common ancestor of Carnivora. To mitigate nuclear mitochondrial pseudogene-related errors, rigorous sequence verification strategies, such as sequence alignment and phylogenetic validation, should be implemented. In conclusion, our findings highlight the necessity of nuclear mitochondrial pseudogene awareness in genetic and evolutionary studies of Carnivora and other taxa.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12491944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091346","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-Level Assembly and Annotation of the Grey Reef Shark (Carcharhinus amblyrhynchos) Genome. 灰礁鲨（Carcharhinus amblyrhynchos）基因组的染色体水平组装与注释。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2025-09-30 DOI: 10.1093/gbe/evaf176

Carolin Dahms, Laurent Vigliola, Leni Hiu Tong Cheung, Jerome Ho Lam Hui, Paolo Momigliano

{"title":"Chromosome-Level Assembly and Annotation of the Grey Reef Shark (Carcharhinus amblyrhynchos) Genome.","authors":"Carolin Dahms, Laurent Vigliola, Leni Hiu Tong Cheung, Jerome Ho Lam Hui, Paolo Momigliano","doi":"10.1093/gbe/evaf176","DOIUrl":"10.1093/gbe/evaf176","url":null,"abstract":"To date less than 5% of shark species have nuclear reference genomes, despite next-generation sequencing advances. Particularly for threatened shark species, there is a lack of reliable genomes which are crucial in facilitating research and conservation applications. We assembled the first nuclear reference genome of the endangered grey reef shark (Carcharhinus amblyrhynchos) using long-read PacBio HiFi and Omni-C sequencing to reach chromosome-level contiguity (36 pseudochromosomes; 2.9 Gbp) and high completeness (94% complete BUSCOs). BRAKER3 annotated 16,505 protein-coding genes after masking repetitive elements which accounted for 59% of the genome. We identified potential X and Y sex chromosomes on pseudochromosomes 36 and 57, respectively. The quality and completeness of the draft genome of C. amblyrhynchos will enable researchers to investigate genetic variations and adaptations specific to this species as well as across other Carcharhinus spp., opening new venues for comparative genomics and advancing conservation genetic applications.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12498223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091639","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

Loss and Gain of Aqp10 Paralogs With Broad Solute Selectivity in Anguillid Eels. 具有广泛溶质选择性的Aqp10亲缘物在鳗鲡中的损失和增益。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2025-09-30 DOI: 10.1093/gbe/evaf169

Ayumi Nagashima, Shinichiro Hidaka, Chihiro Ota, Daisuke Yamanaka, Koichi Ito, Tsutomu Nakada, Tadaomi Furuta, Akira Kato

{"title":"Loss and Gain of Aqp10 Paralogs With Broad Solute Selectivity in Anguillid Eels.","authors":"Ayumi Nagashima, Shinichiro Hidaka, Chihiro Ota, Daisuke Yamanaka, Koichi Ito, Tsutomu Nakada, Tadaomi Furuta, Akira Kato","doi":"10.1093/gbe/evaf169","DOIUrl":"10.1093/gbe/evaf169","url":null,"abstract":"Aquaporin (Aqp) 10 is a member of the aquaglyceriporin family, which transports small, uncharged solutes in addition to water. Although the solute selectivity of aquaglyceroporins varies, the mechanism of solute selectivity has not yet been fully elucidated. The common ancestor of ray-finned fish possessed two paralogous genes for aquaporin 10, aqp10.1 and aqp10.2, which produce Aqps with different solute selectivities. Most teleosts possess one or more ohnologs derived from aqp10.1 and aqp10.2; however, the common ancestor of Anguilliformes species lost all aqp10.1-derived ohnologs. Anguilliformes species, except Anguilla species, have one aqp10.2b, but recent tandem duplications in the European eel have generated three aqp10.2b paralogs (aqp10.2b1-aqp10.2b3), whose activities remain ambiguous. In this study, we found that the four sites forming the aromatic/arginine (ar/R) selectivity filter in European eel Aqp10.2b1 were identical to those in Aqp10.2b of other species. However, the Y residue at position 3 was replaced with G in the ar/R selectivity filter of Aqp10.2b2 and b3. When expressed in Xenopus oocytes, Aqp10.2b2 and b3 showed higher permeability to urea and boric acid than Aqp10.2b1, indicating that Aqp10.2b2 and b3 acquired broad solute selectivity similar to that of Aqp10.1, which was lost in the ancestral Anguilliformes species. Urea and boric acid permeabilities of Aqp10.2b1 increased when the Y residue at position 3 of the ar/R selectivity filter was replaced with G. Overall, our results outline the history of the loss and gain of Aqp10 paralogs with broad solute selectivity in anguillid eels.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086024","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

De novo genome sequence assembly of the RNAi-tractable Paramecium bursaria 186b an endosymbiotic model system. rnai易感滑囊草履虫186b内共生模型系统的从头基因组序列组装。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2025-09-25 DOI: 10.1093/gbe/evaf183

Guy Leonard, Benjamin H Jenkins, Fiona R Savory, Estelle S Kilias, Finlay Maguire, David S Milner, Thomas A Richards

{"title":"De novo genome sequence assembly of the RNAi-tractable Paramecium bursaria 186b an endosymbiotic model system.","authors":"Guy Leonard, Benjamin H Jenkins, Fiona R Savory, Estelle S Kilias, Finlay Maguire, David S Milner, Thomas A Richards","doi":"10.1093/gbe/evaf183","DOIUrl":"https://doi.org/10.1093/gbe/evaf183","url":null,"abstract":"How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a useful approach to understand how endosymbiotic functions can arise. The ciliate protist Paramecium bursaria hosts green algae of the order Chlorellales in a facultative photo-endosymbiosis. We have recently reported RNAi as a tool for understanding gene function in Paramecium bursaria 186b (CCAP strain 1660/18). To complement this work, here we report a near complete host genome and transcriptome sequence dataset, using both Illumina and PacBio sequencing methods, in order to aid genome analysis and to enable the design of RNAi experiments. Our analyses demonstrate Paramecium bursaria 186b, like other ciliates such as diverse species of Paramecia, possess numerous tiny introns. These data, combined with the alternative genetic code common to ciliates, makes gene identification and annotation challenging; as such we identify gene models using Iso-Seq methodologies. These data will aid the investigation of genome evolution in the Paramecia and provide additional source data for the exploration of endosymbiotic functions.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145148740","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

Hemoglobin-gene cluster deletions in Antarctic white-blooded icefishes facilitated by transposable elements. 转座因子促进南极白血鱼血红蛋白基因簇缺失。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2025-09-25 DOI: 10.1093/gbe/evaf184

Thomas Desvignes, Angel G Rivera-Colón, John H Postlethwait

{"title":"Hemoglobin-gene cluster deletions in Antarctic white-blooded icefishes facilitated by transposable elements.","authors":"Thomas Desvignes, Angel G Rivera-Colón, John H Postlethwait","doi":"10.1093/gbe/evaf184","DOIUrl":"https://doi.org/10.1093/gbe/evaf184","url":null,"abstract":"Vertebrates transport oxygen throughout the body bound to hemoglobin packed in red blood cells. Antarctic icefishes are evolutionary oddities with transparent, white blood lacking hemoglobin. Previous work revealed that the icefish ancestor lost all hemoglobin genes, except for one exon of one alpha-globin gene. This peculiar condition has puzzled biologists for decades and is widely considered maladaptive because it is associated with numerous physiological and anatomical compensations. While we know that hemoglobin genes evolved episodically during cold adaptation in Antarctic notothenioid ancestors and that red-blooded sister species to icefishes have seemingly altered hemoglobin and lack multiple hemoglobin isoforms (hemoglobin multiplicity), we still do not know how the two hemoglobin gene clusters, the LA and MN clusters, shared by all other teleost fishes, were lost in the icefish ancestor. Here, we analyzed the two hemoglobin cluster regions in 10 red-blooded notothenioid species and their orthologous region in eight icefishes, and identified traces of molecular mechanisms that could have independently deleted each cluster. Adjacent to the LA cluster, an Antarctic notothenioid-specific massive amplification of tRNA genes associated with transposable elements likely deleted the hemoglobin cluster when tRNAs transposed into the second intron of the second alpha globin gene. Independently, extreme species-specific gene turnover characterized the evolution of the MN cluster in all notothenioids. Conserved transposable elements precisely located at the boundaries of the deleted MN hemoglobin gene cluster incriminate them in the cluster's deletion. Together, these results provide a deeper understanding of the evolution of the iconic icefishes and their unique phenotype.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145148776","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

High-quality draft genome for Armillaria mexicana, a recently described species in North America. 高质量的墨西哥蜜环菌基因组草图，一个最近在北美发现的物种。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2025-09-25 DOI: 10.1093/gbe/evaf185

Jane E Stewart, Mee-Sook Kim, Jorge R Ibarra Caballero, Patrick I Bennett, John W Hanna, Rubén D Elías-Román, Ned B Klopfenstein

{"title":"High-quality draft genome for Armillaria mexicana, a recently described species in North America.","authors":"Jane E Stewart, Mee-Sook Kim, Jorge R Ibarra Caballero, Patrick I Bennett, John W Hanna, Rubén D Elías-Román, Ned B Klopfenstein","doi":"10.1093/gbe/evaf185","DOIUrl":"https://doi.org/10.1093/gbe/evaf185","url":null,"abstract":"The genus Armillaria is a broad group of basidiomycete (Agaricales, Physalacriaceae) plant pathogens that can have detrimental effects on woody hosts in forested, urban, and horticultural landscapes. Several species are known as aggressive root pathogens on both conifers and deciduous woody plants. Armillaria species are considered white rot fungi due to their capacity to degrade both lignin and cellulose in woody tissues. Armillaria mexicana was recently described as a new species found in peach (Prunus persica) orchards of Coatepec Harinas, State of Mexico. However, a subsequent study identified A. mexicana on avocado (Persea americana) and pine (Pinus sp.), suggesting that A. mexicana may be able to infect diverse hosts that are planted in disturbed areas following deforestation. We assembled a reference genome for A. mexicana consisting of 38 contigs constructed using PacBio and Illumina sequencing reads. Genome annotation and comparison with A. mellea, a phylogenetic sister taxon revealed notable differences, including a larger number of interspersed repeats in A. mexicana and the absence of small RNAs, which were detected in A. mellea. While A. mexicana (49 Mb) has a roughly 30% smaller genome than A. mellea (70 Mb), it has a similar number of genes encoding pectinases and nonribosomal peptide synthetase (NRPS) and NPRS-like secondary metabolites, which may influence the pathogenicity of A. mexicana. This reference genome of A. mexicana allows future genomic comparisons that can help characterize the evolutionary history and enhance our understanding of the molecular mechanisms involved in pathogenicity and wood decomposition of Armillaria species.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145148752","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