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Rapid Loss of Nutritional Symbionts in an Endemic Hawaiian Herbivore Radiation Is Associated with Plant Galling Habit. 夏威夷特有食草动物辐射中营养共生体的快速丧失与植物啃咬习性有关。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-09-04 DOI: 10.1093/molbev/msae190
Allison K Hansen, Jacob A Argondona, Sen Miao, Diana M Percy, Patrick H Degnan
{"title":"Rapid Loss of Nutritional Symbionts in an Endemic Hawaiian Herbivore Radiation Is Associated with Plant Galling Habit.","authors":"Allison K Hansen, Jacob A Argondona, Sen Miao, Diana M Percy, Patrick H Degnan","doi":"10.1093/molbev/msae190","DOIUrl":"10.1093/molbev/msae190","url":null,"abstract":"<p><p>Insect herbivores frequently cospeciate with symbionts that enable them to survive on nutritionally unbalanced diets. While ancient symbiont gain and loss events have been pivotal for insect diversification and feeding niche specialization, evidence of recent events is scarce. We examine the recent loss of nutritional symbionts (in as little as 1 MY) in sap-feeding Pariaconus, an endemic Hawaiian insect genus that has undergone adaptive radiation, evolving various galling and free-living ecologies on a single host-plant species, Metrosideros polymorpha within the last ∼5 MY. Using 16S rRNA sequencing, we investigated the bacterial microbiomes of 19 Pariaconus species and identified distinct symbiont profiles associated with specific host-plant ecologies. Phylogenetic analyses and metagenomic reconstructions revealed significant differences in microbial diversity and functions among psyllids with different host-plant ecologies. Within a few millions of years, Pariaconus species convergently evolved the closed-gall habit twice. This shift to enclosed galls coincided with the loss of the Morganella-like symbiont that provides the essential amino acid arginine to free-living and open-gall sister species. After the Pariaconus lineage left Kauai and colonized younger islands, both open- and closed-gall species lost the Dickeya-like symbiont. This symbiont is crucial for synthesizing essential amino acids (phenylalanine, tyrosine, and lysine) as well as B vitamins in free-living species. The recurrent loss of these symbionts in galling species reinforces evidence that galls are nutrient sinks and, combined with the rapidity of the evolutionary timeline, highlights the dynamic role of insect-symbiont relationships during the diversification of feeding ecologies. We propose new Candidatus names for the novel Morganella-like and Dickeya-like symbionts.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11425488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142140563","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
Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications. 吲哚:计算方法、进化动力学和生物应用。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-09-04 DOI: 10.1093/molbev/msae177
Benjamin D Redelings, Ian Holmes, Gerton Lunter, Tal Pupko, Maria Anisimova
{"title":"Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.","authors":"Benjamin D Redelings, Ian Holmes, Gerton Lunter, Tal Pupko, Maria Anisimova","doi":"10.1093/molbev/msae177","DOIUrl":"10.1093/molbev/msae177","url":null,"abstract":"<p><p>Insertions and deletions constitute the second most important source of natural genomic variation. Insertions and deletions make up to 25% of genomic variants in humans and are involved in complex evolutionary processes including genomic rearrangements, adaptation, and speciation. Recent advances in long-read sequencing technologies allow detailed inference of insertions and deletion variation in species and populations. Yet, despite their importance, evolutionary studies have traditionally ignored or mishandled insertions and deletions due to a lack of comprehensive methodologies and statistical models of insertions and deletion dynamics. Here, we discuss methods for describing insertions and deletion variation and modeling insertions and deletions over evolutionary time. We provide practical advice for tackling insertions and deletions in genomic sequences and illustrate our discussion with examples of insertions and deletion-induced effects in human and other natural populations and their contribution to evolutionary processes. We outline promising directions for future developments in statistical methodologies that would allow researchers to analyze insertions and deletion variation and their effects in large genomic data sets and to incorporate insertions and deletions in evolutionary inference.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11385596/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036386","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
The Genetic Architecture of Recombination Rates is Polygenic and Differs Between the Sexes in Wild House Sparrows (Passer domesticus). 在野生家雀(Passer domesticus)中,重组率的遗传结构是多基因的,并且在性别之间存在差异。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-09-04 DOI: 10.1093/molbev/msae179
John B McAuley, Bertrand Servin, Hamish A Burnett, Cathrine Brekke, Lucy Peters, Ingerid J Hagen, Alina K Niskanen, Thor Harald Ringsby, Arild Husby, Henrik Jensen, Susan E Johnston
{"title":"The Genetic Architecture of Recombination Rates is Polygenic and Differs Between the Sexes in Wild House Sparrows (Passer domesticus).","authors":"John B McAuley, Bertrand Servin, Hamish A Burnett, Cathrine Brekke, Lucy Peters, Ingerid J Hagen, Alina K Niskanen, Thor Harald Ringsby, Arild Husby, Henrik Jensen, Susan E Johnston","doi":"10.1093/molbev/msae179","DOIUrl":"10.1093/molbev/msae179","url":null,"abstract":"<p><p>Meiotic recombination through chromosomal crossing-over is a fundamental feature of sex and an important driver of genomic diversity. It ensures proper disjunction, allows increased selection responses, and prevents mutation accumulation; however, it is also mutagenic and can break up favorable haplotypes. This cost-benefit dynamic is likely to vary depending on mechanistic and evolutionary contexts, and indeed, recombination rates show huge variation in nature. Identifying the genetic architecture of this variation is key to understanding its causes and consequences. Here, we investigate individual recombination rate variation in wild house sparrows (Passer domesticus). We integrate genomic and pedigree data to identify autosomal crossover counts (ACCs) and intrachromosomal allelic shuffling (r¯intra) in 13,056 gametes transmitted from 2,653 individuals to their offspring. Females had 1.37 times higher ACC, and 1.55 times higher r¯intra than males. ACC and r¯intra were heritable in females and males (ACC h2 = 0.23 and 0.11; r¯intra  h2 = 0.12 and 0.14), but cross-sex additive genetic correlations were low (rA = 0.29 and 0.32 for ACC and r¯intra). Conditional bivariate analyses showed that all measures remained heritable after accounting for genetic values in the opposite sex, indicating that sex-specific ACC and r¯intra can evolve somewhat independently. Genome-wide models showed that ACC and r¯intra are polygenic and driven by many small-effect loci, many of which are likely to act in trans as global recombination modifiers. Our findings show that recombination rates of females and males can have different evolutionary potential in wild birds, providing a compelling mechanism for the evolution of sexual dimorphism in recombination.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11385585/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142056094","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
A Novel Expression Domain of extradenticle Underlies the Evolutionary Developmental Origin of the Chelicerate Patella. 髌骨外的新表达域是螯肢髌骨进化发展起源的基础。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-09-04 DOI: 10.1093/molbev/msae188
Benjamin C Klementz, Georg Brenneis, Isaac A Hinne, Ethan M Laumer, Sophie M Neu, Grace M Hareid, Guilherme Gainett, Emily V W Setton, Catalina Simian, David E Vrech, Isabella Joyce, Austen A Barnett, Nipam H Patel, Mark S Harvey, Alfredo V Peretti, Monika Gulia-Nuss, Prashant P Sharma
{"title":"A Novel Expression Domain of extradenticle Underlies the Evolutionary Developmental Origin of the Chelicerate Patella.","authors":"Benjamin C Klementz, Georg Brenneis, Isaac A Hinne, Ethan M Laumer, Sophie M Neu, Grace M Hareid, Guilherme Gainett, Emily V W Setton, Catalina Simian, David E Vrech, Isabella Joyce, Austen A Barnett, Nipam H Patel, Mark S Harvey, Alfredo V Peretti, Monika Gulia-Nuss, Prashant P Sharma","doi":"10.1093/molbev/msae188","DOIUrl":"10.1093/molbev/msae188","url":null,"abstract":"<p><p>Neofunctionalization of duplicated gene copies is thought to be an important process underlying the origin of evolutionary novelty and provides an elegant mechanism for the origin of new phenotypic traits. One putative case where a new gene copy has been linked to a novel morphological trait is the origin of the arachnid patella, a taxonomically restricted leg segment. In spiders, the origin of this segment has been linked to the origin of the paralog dachshund-2, suggesting that a new gene facilitated the expression of a new trait. However, various arachnid groups that possess patellae do not have a copy of dachshund-2, disfavoring the direct link between gene origin and trait origin. We investigated the developmental genetic basis for patellar patterning in the harvestman Phalangium opilio, which lacks dachshund-2. Here, we show that the harvestman patella is established by a novel expression domain of the transcription factor extradenticle. Leveraging this definition of patellar identity, we surveyed targeted groups across chelicerate phylogeny to assess when this trait evolved. We show that a patellar homolog is present in Pycnogonida (sea spiders) and various arachnid orders, suggesting a single origin of the patella in the ancestor of Chelicerata. A potential loss of the patella is observed in Ixodida. Our results suggest that the modification of an ancient gene, rather than the neofunctionalization of a new gene copy, underlies the origin of the patella. Broadly, this work underscores the value of comparative data and broad taxonomic sampling when testing hypotheses in evolutionary developmental biology.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11422720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133203","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
Patterns of Fitness and Gene Expression Epistasis Generated by Beneficial Mutations in the rho and rpoB Genes of Escherichia coli during High-Temperature Adaptation. 高温适应过程中大肠杆菌 rho 和 rpoB 基因有益突变产生的适应性和基因表达表观模式。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-09-04 DOI: 10.1093/molbev/msae187
Andrea González-González, Tiffany N Batarseh, Alejandra Rodríguez-Verdugo, Brandon S Gaut
{"title":"Patterns of Fitness and Gene Expression Epistasis Generated by Beneficial Mutations in the rho and rpoB Genes of Escherichia coli during High-Temperature Adaptation.","authors":"Andrea González-González, Tiffany N Batarseh, Alejandra Rodríguez-Verdugo, Brandon S Gaut","doi":"10.1093/molbev/msae187","DOIUrl":"10.1093/molbev/msae187","url":null,"abstract":"<p><p>Epistasis is caused by genetic interactions among mutations that affect fitness. To characterize properties and potential mechanisms of epistasis, we engineered eight double mutants that combined mutations from the rho and rpoB genes of Escherichia coli. The two genes encode essential functions for transcription, and the mutations in each gene were chosen because they were beneficial for adaptation to thermal stress (42.2 °C). The double mutants exhibited patterns of fitness epistasis that included diminishing returns epistasis at 42.2 °C, stronger diminishing returns between mutations with larger beneficial effects and both negative and positive (sign) epistasis across environments (20.0 °C and 37.0 °C). By assessing gene expression between single and double mutants, we detected hundreds of genes with gene expression epistasis. Previous work postulated that highly connected hub genes in coexpression networks have low epistasis, but we found the opposite: hub genes had high epistasis values in both coexpression and protein-protein interaction networks. We hypothesized that elevated epistasis in hub genes reflected that they were enriched for targets of Rho termination but that was not the case. Altogether, gene expression and coexpression analyses revealed that thermal adaptation occurred in modules, through modulation of ribonucleotide biosynthetic processes and ribosome assembly, the attenuation of expression in genes related to heat shock and stress responses, and with an overall trend toward restoring gene expression toward the unstressed state.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11414761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133204","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
Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms. 进化生物学中的表观遗传学研究:关于时间尺度和机制的观点。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-09-03 DOI: 10.1093/molbev/msae170
Soojin V Yi
{"title":"Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms.","authors":"Soojin V Yi","doi":"10.1093/molbev/msae170","DOIUrl":"10.1093/molbev/msae170","url":null,"abstract":"<p><p>Epigenetics research in evolutionary biology encompasses a variety of research areas, from regulation of gene expression to inheritance of environmentally mediated phenotypes. Such divergent research foci can occasionally render the umbrella term \"epigenetics\" ambiguous. Here I discuss several areas of contemporary epigenetics research in the context of evolutionary biology, aiming to provide balanced views across timescales and molecular mechanisms. The importance of epigenetics in development is now being assessed in many nonmodel species. These studies not only confirm the importance of epigenetic marks in developmental processes, but also highlight the significant diversity in epigenetic regulatory mechanisms across taxa. Further, these comparative epigenomic studies have begun to show promise toward enhancing our understanding of how regulatory programs evolve. A key property of epigenetic marks is that they can be inherited along mitotic cell lineages, and epigenetic differences that occur during early development can have lasting consequences on the organismal phenotypes. Thus, epigenetic marks may play roles in short-term (within an organism's lifetime or to the next generation) adaptation and phenotypic plasticity. However, the extent to which observed epigenetic variation occurs independently of genetic influences remains uncertain, due to the widespread impact of genetics on epigenetic variation and the limited availability of comprehensive (epi)genomic resources from most species. While epigenetic marks can be inherited independently of genetic sequences in some species, there is little evidence that such \"transgenerational inheritance\" is a general phenomenon. Rather, molecular mechanisms of epigenetic inheritance are highly variable between species.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"41 9","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11376073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133205","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
Invasion and Amplification of Endogenous Retroviruses in Dasyuridae Marsupial Genomes. 有袋动物基因组中内源性逆转录病毒的入侵和扩增。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-08-02 DOI: 10.1093/molbev/msae160
Emma F Harding, Lewis K Mercer, Grace J H Yan, Paul D Waters, Peter A White
{"title":"Invasion and Amplification of Endogenous Retroviruses in Dasyuridae Marsupial Genomes.","authors":"Emma F Harding, Lewis K Mercer, Grace J H Yan, Paul D Waters, Peter A White","doi":"10.1093/molbev/msae160","DOIUrl":"10.1093/molbev/msae160","url":null,"abstract":"<p><p>Retroviruses are an ancient viral family that have globally coevolved with vertebrates and impacted their evolution. In Australia, a continent that has been geographically isolated for millions of years, little is known about retroviruses in wildlife, despite the devastating impacts of a retrovirus on endangered koala populations. We therefore sought to identify and characterize Australian retroviruses through reconstruction of endogenous retroviruses from marsupial genomes, in particular the Tasmanian devil due to its high cancer incidence. We screened 19 marsupial genomes and identified over 80,000 endogenous retrovirus fragments which we classified into eight retrovirus clades. The retroviruses were similar to either Betaretrovirus (5/8) or Gammaretrovirus (3/8) retroviruses, but formed distinct phylogenetic clades compared to extant retroviruses. One of the clades (MEBrv 3) lost an envelope but retained retrotranspositional activity, subsequently amplifying throughout all Dasyuridae genomes. Overall, we provide insights into Australian retrovirus evolution and identify a highly active endogenous retrovirus within Dasyuridae genomes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141889758","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
Evolution of Virus-like Features and Intrinsically Disordered Regions in Retrotransposon-derived Mammalian Genes. 逆转录转座子衍生哺乳动物基因中病毒样特征和内在紊乱区的进化
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-08-02 DOI: 10.1093/molbev/msae154
Rachele Cagliani, Diego Forni, Alessandra Mozzi, Rotem Fuchs, Dafna Tussia-Cohen, Federica Arrigoni, Uberto Pozzoli, Luca De Gioia, Tzachi Hagai, Manuela Sironi
{"title":"Evolution of Virus-like Features and Intrinsically Disordered Regions in Retrotransposon-derived Mammalian Genes.","authors":"Rachele Cagliani, Diego Forni, Alessandra Mozzi, Rotem Fuchs, Dafna Tussia-Cohen, Federica Arrigoni, Uberto Pozzoli, Luca De Gioia, Tzachi Hagai, Manuela Sironi","doi":"10.1093/molbev/msae154","DOIUrl":"10.1093/molbev/msae154","url":null,"abstract":"<p><p>Several mammalian genes have originated from the domestication of retrotransposons, selfish mobile elements related to retroviruses. Some of the proteins encoded by these genes have maintained virus-like features; including self-processing, capsid structure formation, and the generation of different isoforms through -1 programmed ribosomal frameshifting. Using quantitative approaches in molecular evolution and biophysical analyses, we studied 28 retrotransposon-derived genes, with a focus on the evolution of virus-like features. By analyzing the rate of synonymous substitutions, we show that the -1 programmed ribosomal frameshifting mechanism in three of these genes (PEG10, PNMA3, and PNMA5) is conserved across mammals and originates alternative proteins. These genes were targets of positive selection in primates, and one of the positively selected sites affects a B-cell epitope on the spike domain of the PNMA5 capsid, a finding reminiscent of observations in infectious viruses. More generally, we found that retrotransposon-derived proteins vary in their intrinsically disordered region content and this is directly associated with their evolutionary rates. Most positively selected sites in these proteins are located in intrinsically disordered regions and some of them impact protein posttranslational modifications, such as autocleavage and phosphorylation. Detailed analyses of the biophysical properties of intrinsically disordered regions showed that positive selection preferentially targeted regions with lower conformational entropy. Furthermore, positive selection introduces variation in binary sequence patterns across orthologues, as well as in chain compaction. Our results shed light on the evolutionary trajectories of a unique class of mammalian genes and suggest a novel approach to study how intrinsically disordered region biophysical characteristics are affected by evolution.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"41 8","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141889761","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
phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases. phyloBARCODER:利用定制参考数据库对真核生物代谢条进行系统发育分类的网络工具。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-08-02 DOI: 10.1093/molbev/msae111
Jun Inoue, Chuya Shinzato, Junya Hirai, Sachihiko Itoh, Yuki Minegishi, Shin-Ichi Ito, Susumu Hyodo
{"title":"phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases.","authors":"Jun Inoue, Chuya Shinzato, Junya Hirai, Sachihiko Itoh, Yuki Minegishi, Shin-Ichi Ito, Susumu Hyodo","doi":"10.1093/molbev/msae111","DOIUrl":"10.1093/molbev/msae111","url":null,"abstract":"<p><p>We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on the uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (i) species or classification of query sequences and (ii) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of nonmitochondrial genes, e.g. ITS or rbcL.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11297486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141293566","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
Exploring the Origins and Evolution of Oxygenic and Anoxygenic Photosynthesis in Deeply Branched Cyanobacteriota. 探索深枝蓝细菌含氧和缺氧光合作用的起源和进化。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-08-02 DOI: 10.1093/molbev/msae151
Sha Tan, Lan Liu, Jian-Yu Jiao, Meng-Meng Li, Chao-Jian Hu, Ai-Ping Lv, Yan-Ling Qi, Yu-Xian Li, Yang-Zhi Rao, Yan-Ni Qu, Hong-Chen Jiang, Rochelle M Soo, Paul N Evans, Zheng-Shuang Hua, Wen-Jun Li
{"title":"Exploring the Origins and Evolution of Oxygenic and Anoxygenic Photosynthesis in Deeply Branched Cyanobacteriota.","authors":"Sha Tan, Lan Liu, Jian-Yu Jiao, Meng-Meng Li, Chao-Jian Hu, Ai-Ping Lv, Yan-Ling Qi, Yu-Xian Li, Yang-Zhi Rao, Yan-Ni Qu, Hong-Chen Jiang, Rochelle M Soo, Paul N Evans, Zheng-Shuang Hua, Wen-Jun Li","doi":"10.1093/molbev/msae151","DOIUrl":"10.1093/molbev/msae151","url":null,"abstract":"<p><p>Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, vesicle-inducing protein in plastids 1 (Vipp1). Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven AnoxyP by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11304991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141748581","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
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