Molecular biology and evolution最新文献_第2页

Genetic Mechanisms and Adaptive Benefits of Anthocyanin Red Stigmas in a Wind-Pollinated Tree.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-03-05 DOI: 10.1093/molbev/msaf040

Wei-Hao Wang, Susanne S Renner, Hao-Sheng Liu, Liu-Feng Dai, Cai-Jin Chen, Yi Zhang, Bo-Wen Zhang, Da-Yong Zhang, Wei-Ning Bai

{"title":"Genetic Mechanisms and Adaptive Benefits of Anthocyanin Red Stigmas in a Wind-Pollinated Tree.","authors":"Wei-Hao Wang, Susanne S Renner, Hao-Sheng Liu, Liu-Feng Dai, Cai-Jin Chen, Yi Zhang, Bo-Wen Zhang, Da-Yong Zhang, Wei-Ning Bai","doi":"10.1093/molbev/msaf040","DOIUrl":"10.1093/molbev/msaf040","url":null,"abstract":"Anthocyanin accumulation in leaves or flowers mitigates photooxidation damage from reactive oxygen species (ROS) and functions in plant/animal interactions. Among the most conspicuously anthocyanin-accumulating tissues are stigmas, especially in wind-pollinated trees. In the walnut genus (Juglans), yellow stigmas are ancestral, but a few species have dark red stigmas. We have used a natural F1 hybrid resulting from crosses between yellow stigma and red stigma species to investigate the genetic basis of the red stigmas. We found that a Copia transposable element (TE) insertion in the ubiquitin-protein ligase gene MIEL1 suppresses its expression in stigmas through RNA-directed DNA methylation and has gone to fixation in red stigma species. A younger Gypsy TE insertion fully inhibits MIEL1 expression, but is not fixed, explaining the color segregation in hybrid populations. Based on reference genomes and whole-genome sequencing data representing 20 of the 22 species of Juglans, we traced the evolution of MIEL1, finding the insertions in all consistently red stigma species. Red stigmas had lower levels of ROS than yellow stigmas, and population genetic data reveal strong positive selection on the TE-bearing MIEL1 allele. In combination, these results suggest that anthocyanin-accumulating stigma tissues support pollen germination and growth by protecting cells from ROS.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382951","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 comparative assessment of self-limiting genetic control strategies for population suppression.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-28 DOI: 10.1093/molbev/msaf048

Yue Han, Jackson Champer

{"title":"A comparative assessment of self-limiting genetic control strategies for population suppression.","authors":"Yue Han, Jackson Champer","doi":"10.1093/molbev/msaf048","DOIUrl":"https://doi.org/10.1093/molbev/msaf048","url":null,"abstract":"Genetic control strategies are promising solutions for control of pest populations and invasive species. Methods utilizing repeated releases of males such as Sterile Insect Technique (SIT), Release of Insects carrying a Dominant Lethal (RIDL), self-limiting gene drives, and gene disruptors are highly controllable methods, ensuring biosafety. Although models of these strategies have been built, detailed comparisons are lacking, particularly for some of the newer strategies. Here, we conducted a thorough comparative assessment of self-limiting genetic control strategies by individual-based simulation models. Specifically, we find that repeated releases greatly enhance suppression power of weak and self-limiting gene drives, enabling population elimination with even low efficiency and high fitness costs. Moreover, dominant female sterility further strengthens self-limiting systems that can either use gene drive or disruptors that target genes without a mechanism to bias their own inheritance. Some of these strategies are highly persistent, resulting in relatively low release ratios even when released males suffer high fitness costs. To quantitively evaluate different strategies independent from ecological impact, we proposed constant-population genetic load, which achieves over 95% accuracy in predicting simulation outcomes for most strategies, though it is not as precise in a few frequency-dependent systems. Our results suggest that many new self-limiting strategies are safe, flexible, and more cost-effective than traditional SIT and RIDL, and thus have great potential for population suppression of insects and other pests.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Treasurer's Report for Financial Year (FY) 2023.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-27 DOI: 10.1093/molbev/msaf046

Aline Muyle

引用次数: 0

Genetic and anatomical determinants of olfaction in dogs and wild canids.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-14 DOI: 10.1093/molbev/msaf035

Alice Mouton, Deborah Bird, Gang Li, Brent A Craven, Jonathan M Levine, Marco Morselli, Matteo Pellegrini, Blaire Van Valkenburgh, Robert K Wayne, William J Murphy

{"title":"Genetic and anatomical determinants of olfaction in dogs and wild canids.","authors":"Alice Mouton, Deborah Bird, Gang Li, Brent A Craven, Jonathan M Levine, Marco Morselli, Matteo Pellegrini, Blaire Van Valkenburgh, Robert K Wayne, William J Murphy","doi":"10.1093/molbev/msaf035","DOIUrl":"https://doi.org/10.1093/molbev/msaf035","url":null,"abstract":"Understanding the anatomical and genetic basis of complex phenotypic traits has long been a challenge for biological research. Domestic dogs offer a compelling model as they demonstrate more phenotypic variation than any other vertebrate species. Dogs have been intensely selected for specific traits and abilities, directly or indirectly, over the past 15,000 years since their initial domestication from the gray wolf. Because olfaction plays a central role in critical tasks, such as the detection of drugs, diseases, and explosives, as well as human rescue, we compared relative olfactory capacity across dog breeds and assessed changes to the canine olfactory system to their direct ancestors, wolves and coyotes. We conducted a cross-disciplinary survey of olfactory anatomy, olfactory receptor (OR) gene variation, and OR gene expression in domestic dogs. Through comparisons to their closest wild canid relatives, the gray wolf and coyote, we show that domestic dogs might have lost functional OR genes commensurate with a documented reduction in nasal morphology as an outcome of the domestication process prior to breed formation. Critically, within domestic dogs alone, we found no genetic or morphological profile shared among functional or genealogical breed groupings, such as scent hounds, that might indicate evidence of any human-directed selection for enhanced olfaction. Instead, our results suggest that superior scent detection dogs likely owe their success to advantageous behavioral traits and training rather than an \"olfactory edge\" provided by morphology or genes.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Drosophila CG11700 may not affect male fecundity-lifespan tradeoff as previously reported. 果蝇CG11700可能不会像之前报道的那样影响雄性生殖力-寿命权衡。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf003

Dashuang Zuo, Weiwei Liu, Ruoping Zhao, Kesen Zhu, Wen Wang, Hui Xiang

{"title":"Drosophila CG11700 may not affect male fecundity-lifespan tradeoff as previously reported.","authors":"Dashuang Zuo, Weiwei Liu, Ruoping Zhao, Kesen Zhu, Wen Wang, Hui Xiang","doi":"10.1093/molbev/msaf003","DOIUrl":"10.1093/molbev/msaf003","url":null,"abstract":"Our recent investigations on the function of Drosophila CG11700 and CG32744 (Ubi-p5E) genes using CRISPR/Cas9 deletion technology could not repeat or confirm the results on CG11700 shown in our previous study, which was based on P-element excision assay (Zhan Z, Ding Y, Zhao R, Zhang Y, Yu H, Zhou Q, Yang S, Xiang H, Wang W. Rapid functional divergence of a newly evolved polyubiquitin gene in Drosophila and its role in the trade-off between male fecundity and lifespan. Mol Biol Evol. 2012:29(5):1407-1416. doi:10.1093/molbev/msr299). Here, by CRISPR/Cas9 editing, we generated mutants of CG32744 with the whole gene body fully deleted from the genome, and truncated mutants of CG11700 with N-terminal 103 aa deleted out of its total 301 aa peptide sequence. We carefully conducted the male fecundity assay and found that offsprings of the CG11700 mutant were not significantly more than the wild type, inconsistent with our previous report (Zhan et al. 2012). Meanwhile, we repeated the lifespan assay and did not find that the lifespan of the CG11700 mutant was significantly shorter than the wild type as reported (2012). The new results suggest that the CG11700 gene may not affect male fecundity-lifespan tradeoff as previously reported (Zhan et al. 2012). The new results are thus worthy of reporting to avoid possible misleading by the previous results to the scientific community.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008413","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

Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History. 人类历史进程中人类肠道共生菌群的人口历史和选择效应的推断。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf010

Jonathan C Mah, Kirk E Lohmueller, Nandita R Garud

引用次数: 0

Fungal-Derived tRNAs Are Expressed and Aminoacylated in Orchid Mitochondria.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf025

Jessica M Warren, Luis F Ceriotti, M Virginia Sanchez-Puerta, Daniel B Sloan

{"title":"Fungal-Derived tRNAs Are Expressed and Aminoacylated in Orchid Mitochondria.","authors":"Jessica M Warren, Luis F Ceriotti, M Virginia Sanchez-Puerta, Daniel B Sloan","doi":"10.1093/molbev/msaf025","DOIUrl":"10.1093/molbev/msaf025","url":null,"abstract":"Plant mitochondrial genomes (mitogenomes) experience remarkable levels of horizontal gene transfer, including the recent discovery that orchids anciently acquired DNA from fungal mitogenomes. Thus far, however, there is no evidence that any of the genes from this interkingdom horizontal gene transfer are functional in orchid mitogenomes. Here, we applied a specialized sequencing approach to the orchid Corallorhiza maculata and found that some fungal-derived tRNA genes in the transferred region are transcribed, post-transcriptionally modified, and aminoacylated. In contrast, all the transferred protein-coding sequences appear to be pseudogenes. These findings show that fungal horizontal gene transfer has altered the composition of the orchid mitochondrial tRNA pool and suggest that these foreign tRNAs function in translation. The exceptional capacity of tRNAs for horizontal gene transfer and functional replacement is further illustrated by the diversity of tRNA genes in the C. maculata mitogenome, which also include genes of plastid and bacterial origin in addition to their native mitochondrial counterparts.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11827590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066550","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

Genomic Signatures of Adaptation to Stress Reveal Shared Evolutionary Trends Between Tetrahymena utriculariae and Its Algal Endosymbiont, Micractinium tetrahymenae.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf030

Joseph B Kelly, David E Carlson, Manuela Reuter, Annette Sommershof, Lubomír Adamec, Lutz Becks

{"title":"Genomic Signatures of Adaptation to Stress Reveal Shared Evolutionary Trends Between Tetrahymena utriculariae and Its Algal Endosymbiont, Micractinium tetrahymenae.","authors":"Joseph B Kelly, David E Carlson, Manuela Reuter, Annette Sommershof, Lubomír Adamec, Lutz Becks","doi":"10.1093/molbev/msaf030","DOIUrl":"10.1093/molbev/msaf030","url":null,"abstract":"The evolution of intracellular endosymbiosis marks a major transition in the biology of the host and endosymbiont. Yet, how adaptation manifests in the genomes of the participants remains relatively understudied. We investigated this question by sequencing the genomes of Tetrahymena utriculariae, a commensal of the aquatic carnivorous bladderwort Utricularia reflexa, and its intracellular algae, Micractinium tetrahymenae. We discovered an expansion in copy number and negative selection in a TLD domain-bearing gene family in the genome of T. utriculariae, identifying it as a candidate for being an adaptive response to oxidative stress resulting from the physiology of its endosymbionts. We found that the M. tetrahymenae genome is larger than those of other Micractinium and Chlorella and contains a greater number of rapidly expanding orthogroups. These were enriched for Gene Ontology terms relevant to the regulation of intracellular signal transduction and cellular responses to stress and stimulus. Single-exon tandem repeats were overrepresented in paralogs belonging to these rapidly expanding orthogroups, which implicates long terminal repeat retrotransposons (LTRs) as potential agents of adaptation. We additionally performed a comparative transcriptomic analysis of M. tetrahymenae in a free-living state and in endosymbiosis with T. utriculariae and discovered that the genes that are differentially expressed were enriched for pathways that evidence shifts in energy generation and storage and in cellular protection strategies. Together, our results elucidate the axes along which the participants must adapt in this young endosymbiosis and highlight evolutionary responses to stress as a shared trend.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080479","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

Subcellular Enrichment Patterns of New Genes in Drosophila Evolution.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf038

Chuan Dong, Shengqian Xia, Li Zhang, Deanna Arsala, Chengchi Fang, Shengjun Tan, Andrew G Clark, Manyuan Long

{"title":"Subcellular Enrichment Patterns of New Genes in Drosophila Evolution.","authors":"Chuan Dong, Shengqian Xia, Li Zhang, Deanna Arsala, Chengchi Fang, Shengjun Tan, Andrew G Clark, Manyuan Long","doi":"10.1093/molbev/msaf038","DOIUrl":"10.1093/molbev/msaf038","url":null,"abstract":"The evolutionary patterns of proteins within subcellular compartments underlie the innovation and diversification foundation of the living eukaryotic organism. The location of proteins in subcellular compartments promotes the formation of network interaction modules, which in turn reshape the architecture of higher-level protein-protein interaction networks. Here, we conducted the most up-to-date gene age dating of Drosophila melanogaster by employing recently available long-read sequencing genomes as references. We found that an elevated gene fixation in the most recent common ancestor of Drosophila genus predated the divergence between two Drosophila subgenera, and a significant tendency of these genes in D. melanogaster encode proteins that localize to the extracellular matrix, accompanying the adaptive radiation of Drosophila species. Proteins encoded by genes located in the extracellular space exhibit higher sequence divergence, suggesting a rapid evolutionary process. We also observed that proteins encoded by genes originating from the same evolutionary branches tend to co-localize in the same subcellular compartments, and proteins in the same subcellular compartment tend to interact with each other. The proteins encoded by genes that have persisted through deeper branches exhibit broader localization across multiple subcellular compartments, enhancing the likelihood of their integration into various protein or gene regulatory networks, thereby increasing functional diversity. These evolutionary patterns not only contribute to understanding the evolution of subcellular localization in proteins encoded by genes originating from different branches, but also provide insights into the evolution of protein-protein networks driven by the emergence of new genes.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370879","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

Estimating Gene Conversion Tract Length and Rate From PacBio HiFi Data. 从 PacBio HiFi 数据估算基因转换链长度和速率

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf019

Anders Poulsen Charmouh, Peter Sørud Porsborg, Lasse Thorup Hansen, Søren Besenbacher, Sofia Boeg Winge, Kristian Almstrup, Asger Hobolth, Thomas Bataillon, Mikkel Heide Schierup

{"title":"Estimating Gene Conversion Tract Length and Rate From PacBio HiFi Data.","authors":"Anders Poulsen Charmouh, Peter Sørud Porsborg, Lasse Thorup Hansen, Søren Besenbacher, Sofia Boeg Winge, Kristian Almstrup, Asger Hobolth, Thomas Bataillon, Mikkel Heide Schierup","doi":"10.1093/molbev/msaf019","DOIUrl":"10.1093/molbev/msaf019","url":null,"abstract":"Gene conversions are broadly defined as the transfer of genetic material from a \"donor\" to an \"acceptor\" sequence and can happen both in meiosis and mitosis. They are a subset of noncrossover (NCO) events and, like crossover (CO) events, gene conversion can generate new combinations of alleles and counteract mutation load by reverting germline mutations through GC-biased gene conversion. Estimating gene conversion rate and the distribution of gene conversion tract lengths remains challenging. We present a new method for estimating tract length, rate, and detection probability of NCO events directly in HiFi PacBio long read data. The method can be used to make inference from sequencing of gametes from a single individual. The method is unbiased even under low single nucleotide variant (SNV) densities and does not necessitate any demographic or evolutionary assumptions. We test the accuracy and robustness of our method using simulated datasets where we vary length of tracts, number of tracts, the genomic SNV density, and levels of correlation between SNV density and NCO event position. Our simulations show that under low SNV densities, like those found in humans, only a minute fraction (∼2%) of NCO events are expected to become visible as gene conversions by moving at least 1 SNV. We finally illustrate our method by applying it to PacBio sequencing data from human sperm.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":"42 2","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472707","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