Molecular biology and evolution最新文献_第2页

Deciphering Plant NLR Genomic Evolution: Synteny-Informed Classification Unveils Insights into TNL Gene Loss. 破译植物NLR基因组进化：Synteny-Informed分类揭示TNL基因丢失的见解。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf015

Bo-Cheng Guo, Yi-Rong Zhang, Zhi-Guang Liu, Xin-Chu Li, Ze Yu, Bo-Ya Ping, Ya-Qiang Sun, Harrold van den Burg, Feng-Wang Ma, Tao Zhao

{"title":"Deciphering Plant NLR Genomic Evolution: Synteny-Informed Classification Unveils Insights into TNL Gene Loss.","authors":"Bo-Cheng Guo, Yi-Rong Zhang, Zhi-Guang Liu, Xin-Chu Li, Ze Yu, Bo-Ya Ping, Ya-Qiang Sun, Harrold van den Burg, Feng-Wang Ma, Tao Zhao","doi":"10.1093/molbev/msaf015","DOIUrl":"10.1093/molbev/msaf015","url":null,"abstract":"Nucleotide-binding leucine-rich repeat receptor (NLR) genes encode a pivotal class of plant immune receptors. However, their rampant duplication and loss have made inferring their genomic evolutionary trajectory difficult, exemplified by the loss of TNL family genes in monocots. In this study, we introduce a novel classification system for angiosperm NLR genes, grounded in network analysis of microsynteny information. This refined classification categorizes these genes into five classes: CNL_A, CNL_B, CNL_C, TNL, and RNL. Compared to the previous classification, we further subdivided CNLs into three subclasses. The credibility of this classification is supported by phylogenetic analysis and examination of protein domain structures. Importantly, this classification enabled a model to explain the extinction of TNL genes in monocots. Compelling microsynteny evidence underscores this revelation, indicating a clear synteny correspondence between the non-TNLs in monocots and the extinct TNL subclass. Our study provides crucial insights into the genomic origin and divergence of plant NLR subfamilies, unveiling the malleability-driven journey that has shaped the functionality and diversity of plant NLR 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/PMC11789945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008410","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 convergent evolution of hummingbird pollination results in repeated floral scent loss through gene downregulation.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf027

Kathy Darragh, Kathleen M Kay, Santiago R Ramírez

{"title":"The convergent evolution of hummingbird pollination results in repeated floral scent loss through gene downregulation.","authors":"Kathy Darragh, Kathleen M Kay, Santiago R Ramírez","doi":"10.1093/molbev/msaf027","DOIUrl":"https://doi.org/10.1093/molbev/msaf027","url":null,"abstract":"The repeated evolution of the same trait in different lineages provides powerful natural experiments to study the phenotypic and genotypic predictability of trait gain and loss. A fascinating example is the repeated evolution of hummingbird pollination in plant lineages in the Americas, a widespread and often unidirectional phenomenon. The spiral gingers in the genus Costus are ancestrally bee-pollinated, and hummingbird pollination has evolved multiple times independently in the tropical Americas. These pollinator transitions are accompanied by predictable morphological and color changes, but the changes in floral scent have not been described. In this study, we describe the floral scent composition of 30 species of Costus sampled across the phylogeny to understand how floral scent has evolved across the genus with respect to pollinator transitions. We then combine transcriptomics and genomics to identify genetic expression differences and gene family evolution associated with pollinator transitions. We show that hummingbird-pollinated species have mostly lost their floral scent, whereas bee-pollinated species exhibit either floral scent maintenance or in some cases, gains of more diverse scent profiles. We find the floral scent loss appears to be due to gene downregulation rather than pseudogenization. The remarkable consistency of scent loss in hummingbird-pollinated species highlights the shared strong selection pressures experienced by these lineages. Even species with more recent transitions from bee to hummingbird pollination exhibit scent loss, highlighting the rapid breakdown of scent emission following pollinator transitions. This research highlights the capacity for rapid changes when selection pressures are strong through downregulation of floral scent 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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080480","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

Population Genomics of Premature Termination Codons in Cavefish With Substantial Trait Loss. 具有大量性状丧失的穴居鱼过早终止密码子的种群基因组学研究。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf012

Emma Y Roback, Estephany Ferrufino, Rachel L Moran, Devin Shennard, Charlotte Mulliniks, Josh Gallop, James Weagley, Jeffrey Miller, Yaouen Fily, Claudia Patricia Ornelas-García, Nicolas Rohner, Johanna E Kowalko, Suzanne E McGaugh

{"title":"Population Genomics of Premature Termination Codons in Cavefish With Substantial Trait Loss.","authors":"Emma Y Roback, Estephany Ferrufino, Rachel L Moran, Devin Shennard, Charlotte Mulliniks, Josh Gallop, James Weagley, Jeffrey Miller, Yaouen Fily, Claudia Patricia Ornelas-García, Nicolas Rohner, Johanna E Kowalko, Suzanne E McGaugh","doi":"10.1093/molbev/msaf012","DOIUrl":"10.1093/molbev/msaf012","url":null,"abstract":"Loss-of-function alleles are a pertinent source of genetic variation with the potential to contribute to adaptation. Cave-adapted organisms exhibit striking loss of ancestral traits such as eyes and pigment, suggesting that loss-of-function alleles may play an outsized role in these systems. Here, we leverage 141 whole genome sequences to evaluate the evolutionary history and adaptive potential of single nucleotide premature termination codons (PTCs) in Mexican tetra. We find that cave populations contain significantly more PTCs at high frequency than surface populations. We also find that PTCs occur more frequently in genes with inherent relaxed evolutionary constraint relative to the rest of the genome. Using SLiM to simulate PTC evolution in a cavefish population, we show that the smaller population size and increased genetic drift is sufficient to account for the observed increase in PTC frequency in cave populations without positive selection. Using CRISPR-Cas9, we show that mutation of one of these genes, pde6c, produces phenotypes in surface Mexican tetra that mimic cave-derived traits. Finally, we identify a small subset of candidate genes that contain high-frequency PTCs in cave populations, occur within selective sweeps, and may contribute to beneficial traits such as reduced energy expenditure, suggesting that a handful of PTCs may be adaptive. Overall, our work provides a rare characterization of PTCs across wild populations and finds that they may have an important role in loss-of-function phenotypes, contributing to a growing body of literature showing genome evolution through relaxed constraint in subterranean organisms.","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/PMC11796094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008435","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

Faithful Interpretation of Protein Structures through Weighted Persistent Homology Improves Evolutionary Distance Estimation.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msae271

Léa Bou Dagher, Dominique Madern, Philippe Malbos, Céline Brochier-Armanet

{"title":"Faithful Interpretation of Protein Structures through Weighted Persistent Homology Improves Evolutionary Distance Estimation.","authors":"Léa Bou Dagher, Dominique Madern, Philippe Malbos, Céline Brochier-Armanet","doi":"10.1093/molbev/msae271","DOIUrl":"10.1093/molbev/msae271","url":null,"abstract":"Phylogenetic inference is mainly based on sequence analysis and requires reliable alignments. This can be challenging, especially when sequences are highly divergent. In this context, the use of three-dimensional protein structures is a promising alternative. In a recent study, we introduced an original topological data analysis method based on persistent homology to estimate the evolutionary distances from structures. The method was successfully tested on 518 protein families representing 22,940 predicted structures. However, as anticipated, the reliability of the estimated evolutionary distances was impacted by the quality of the predicted structures and the presence of indels in the proteins. This paper introduces a new topological descriptor, called bio-topological marker (BTM), which provides a more faithful description of the structures, a topological analysis for estimating evolutionary distances from BTMs, and a new weight-filtering method adapted to protein structures. These new developments significantly improve the estimation of evolutionary distances and phylogenies inferred from structures.","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/PMC11789942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143123381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: Evolution of Chromosomal Inversions across an Avian Radiation.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf018

引用次数: 0

Deciphering the Foundations of Mitochondrial Mutational Spectra: Replication-Driven and Damage-Induced Signatures Across Chordate Classes.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msae261

Dmitrii Iliushchenko, Bogdan Efimenko, Alina G Mikhailova, Victor Shamanskiy, Murat K Saparbaev, Bakhyt T Matkarimov, Ilya Mazunin, Alexandr Voronka, Dmitry Knorre, Wolfram S Kunz, Philipp Kapranov, Stepan Denisov, Jacques Fellay, Konstantin Khrapko, Konstantin Gunbin, Konstantin Popadin

{"title":"Deciphering the Foundations of Mitochondrial Mutational Spectra: Replication-Driven and Damage-Induced Signatures Across Chordate Classes.","authors":"Dmitrii Iliushchenko, Bogdan Efimenko, Alina G Mikhailova, Victor Shamanskiy, Murat K Saparbaev, Bakhyt T Matkarimov, Ilya Mazunin, Alexandr Voronka, Dmitry Knorre, Wolfram S Kunz, Philipp Kapranov, Stepan Denisov, Jacques Fellay, Konstantin Khrapko, Konstantin Gunbin, Konstantin Popadin","doi":"10.1093/molbev/msae261","DOIUrl":"10.1093/molbev/msae261","url":null,"abstract":"Mitochondrial DNA (mtDNA) mutagenesis remains poorly understood despite its crucial role in disease, aging, and evolutionary tracing. In this study, we reconstructed a comprehensive 192-component mtDNA mutational spectrum for chordates by analyzing 118,397 synonymous mutations in the CytB gene across 1,697 species and five classes. This analysis revealed three primary forces shaping mtDNA mutagenesis: (i) symmetrical, replication-driven errors by mitochondrial polymerase (POLG), resulting in C > T and A > G mutations that are highly conserved across classes; (ii) asymmetrical, damage-driven C > T mutations on the single-stranded heavy strand with clock-like dynamics; and (iii) asymmetrical A > G mutations on the heavy strand, with dynamics suggesting sensitivity to oxidative damage. The third component, sensitive to oxidative damage, positions mtDNA mutagenesis as a promising marker for metabolic and physiological processes across various classes, species, organisms, tissues, and cells. The deconvolution of the mutational spectra into mutational signatures uncovered deficiencies in both base excision repair (BER) and mismatch repair (MMR) pathways. Further analysis of mutation hotspots, abasic sites, and mutational asymmetries underscores the critical role of single-stranded DNA damage (components ii and iii), which, uncorrected due to BER and MMR deficiencies, contributes roughly as many mutations as POLG-induced errors (component i).","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/PMC11792237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189882","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

Multilevel Gene Expression Changes in Lineages Containing Adaptive Copy Number Variants.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-03 DOI: 10.1093/molbev/msaf005

Pieter Spealman, Carolina de Santana, Titir De, David Gresham

{"title":"Multilevel Gene Expression Changes in Lineages Containing Adaptive Copy Number Variants.","authors":"Pieter Spealman, Carolina de Santana, Titir De, David Gresham","doi":"10.1093/molbev/msaf005","DOIUrl":"10.1093/molbev/msaf005","url":null,"abstract":"Copy number variants (CNVs) are an important class of genetic variation that can mediate rapid adaptive evolution. Whereas, CNVs can increase the relative fitness of the organism, they can also incur a cost due to the associated increased gene expression and repetitive DNA. We previously evolved populations of Saccharomyces cerevisiae over hundreds of generations in glutamine-limited (Gln-) chemostats and observed the recurrent evolution of CNVs at the GAP1 locus. To understand the role that gene expression plays in adaptation, both in relation to the adaptation of the organism to the selective condition and as a consequence of the CNV, we measured the transcriptome, translatome, and proteome of 4 strains of evolved yeast, each with a unique CNV, and their ancestor in Gln- chemostats. We find CNV-amplified genes correlate with higher mRNA abundance; however, this effect is reduced at the level of the proteome, consistent with post-transcriptional dosage compensation. By normalizing each level of gene expression by the abundance of the preceding step we were able to identify widespread differences in the efficiency of each level of gene expression. Genes with significantly different translational efficiency were enriched for potential regulatory mechanisms including either upstream open reading frames, RNA-binding sites for Ssd1, or both. Genes with lower protein expression efficiency were enriched for genes encoding proteins in protein complexes. Taken together, our study reveals widespread changes in gene expression at multiple regulatory levels in lineages containing adaptive CNVs highlighting the diverse ways in which genome evolution shapes gene expression.","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/PMC11789944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143029213","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

Convergent evolution of cysteine-rich keratins in horny teeth of jawless vertebrates and in cornified skin appendages of amniotes.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-02-01 DOI: 10.1093/molbev/msaf028

Attila Placido Sachslehner, Leopold Eckhart

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 : 2025-01-30 DOI: 10.1093/molbev/msaf025

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

引用次数: 0

Comparative population genomics unveils congruent secondary suture zone in Southwest Pacific Hydrothermal Vents.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-30 DOI: 10.1093/molbev/msaf024

Tran Lu Y Adrien, Stéphanie Ruault, Claire Daguin-Thiébaut, Anne-Sophie Le Port, Marion Ballenghien, Jade Castel, Pierre-Alexandre Gagnaire, Nicolas Bierne, Sophie Arnaud-Haond, Camille Poitrimol, Eric Thiébaut, François H Lallier, Thomas Broquet, Didier Jollivet, François Bonhomme, Stéphane Hourdez

{"title":"Comparative population genomics unveils congruent secondary suture zone in Southwest Pacific Hydrothermal Vents.","authors":"Tran Lu Y Adrien, Stéphanie Ruault, Claire Daguin-Thiébaut, Anne-Sophie Le Port, Marion Ballenghien, Jade Castel, Pierre-Alexandre Gagnaire, Nicolas Bierne, Sophie Arnaud-Haond, Camille Poitrimol, Eric Thiébaut, François H Lallier, Thomas Broquet, Didier Jollivet, François Bonhomme, Stéphane Hourdez","doi":"10.1093/molbev/msaf024","DOIUrl":"https://doi.org/10.1093/molbev/msaf024","url":null,"abstract":"How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure across lineages. To shed light on the factors that shape community-level genetic variation and to improve our understanding of deep-sea biogeographic patterns, we conducted a comparative population genomics study on seven hydrothermal vent species co-distributed in the Back-Arc Basins (BABs) of the Southwest Pacific region. Using ddRAD-seq, we compared the range-wide distribution of genomic diversity across species and discovered a shared phylogeographic break. Demogenetic inference revealed shared histories of lineage divergence and a secondary contact. Low levels of asymmetric gene flow probably occurred in most species between the Woodlark and North Fiji basins, but the exact location of contact zones varied from species to species. For two species, we found individuals from the two lineages co-occurring in sympatry in Woodlark Basin. Although species exhibit congruent patterns of spatial structure (Eastern vs Western sites), they also show variation in the degree of divergence among lineages across the suture zone. Our results also show heterogeneous gene flow across the genome, indicating possible partial reproductive isolation between lineages and early speciation. Our comparative study highlights the pivotal role of historical and contemporary factors, underscoring the need for a comprehensive approach-especially in addressing knowledge gaps on the life history traits of deep-sea species.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066410","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