{"title":"Every gain comes with loss: Ecological and physiological shifts associated with polyploidization in a pygmy frog.","authors":"Qiheng Chen, Wei Zhu, Liming Chang, Meihua Zhang, Shouhong Wang, Jiongyu Liu, Ningning Lu, Cheng Li, Feng Xie, Bin Wang, Jianping Jiang","doi":"10.1093/molbev/msaf037","DOIUrl":"https://doi.org/10.1093/molbev/msaf037","url":null,"abstract":"<p><p>Polyploidization plays a pivotal role in vertebrate evolution and diversification. However, the effects of polyploidization on animals across various biological levels, and how these differences drive ecological shifts, remain unclear. Through karyotype analysis and whole-genome sequencing, we identified an autotetraploid Microhyla fissipes from Hainan Island, which shows reproductive isolation and geographic differentiation from its diploid counterpart. Tetraploids exhibited larger cell size, improved tadpole growth rates, and greater whole-body size, along with reduced cell cycle activity. Rather than being simple scaled-up diploids, tetraploids showed shifts in physiological performance, organ allometry, gene expression profiles, and metabolic patterns. Tetraploid adults demonstrated superior jumping ability and increased reproductive investment (e.g., larger gonads and steeper slopes in the relationship between gonadal weight and body weight), suggesting a potential competitive advantage over diploids. However, tetraploids exhibited higher energy expenditure at elevated temperatures, reduced hepatic energy storage, and altered pulmonary regulatory metabolites at 25 oC. Males had smaller relative heart sizes, and females showed flatter slopes in the relationship between heart and lung weight and body weight, indicating reduced investment in cardiopulmonary system. These variations suggest an increased risk of metabolic constraints under heat stress, putting tetraploids at a disadvantage in warmer regions. Importantly, the physiological trade-offs associated with polyploidization help explain the geographical differentiation between diploids and tetraploids, which reflects a climatic boundary, with tetraploids occupying cooler northeastern areas. Our findings identify an autotetraploid frog, report the first autotetraploid genome in amphibians, and demonstrate how vertebrate polyploids physiologically and ecologically diverge from their diploid counterparts.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143364540","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}
Fanny E Hartmann, Ricardo C Rodríguez de la Vega, Arthur Demené, Thomas Badet, Jean-Philippe Vernadet, Quentin Rougemont, Amandine Labat, Alodie Snirc, Lea Stauber, Daniel Croll, Simone Prospero, Cyril Dutech, Tatiana Giraud
{"title":"An inversion polymorphism under balancing selection, involving giant mobile elements, in an invasive fungal pathogen.","authors":"Fanny E Hartmann, Ricardo C Rodríguez de la Vega, Arthur Demené, Thomas Badet, Jean-Philippe Vernadet, Quentin Rougemont, Amandine Labat, Alodie Snirc, Lea Stauber, Daniel Croll, Simone Prospero, Cyril Dutech, Tatiana Giraud","doi":"10.1093/molbev/msaf026","DOIUrl":"https://doi.org/10.1093/molbev/msaf026","url":null,"abstract":"<p><p>Recombination suppression can evolve in sex or mating-type chromosomes, or in autosomal supergenes, with different haplotypes being maintained by balancing selection. In the invasive chestnut blight fungus Cryphonectria parasitica, a genomic region was suggested to lack recombination and to be partially physically linked to the mating-type (MAT) locus based on segregation analyses. Using hundreds of available C. parasitica genomes and generating new high-quality genome assemblies, we show that a ca. 1.2 Mb genomic region proximal to the mating-type locus lacks recombination, with the segregation of two highly differentiated haplotypes in balanced proportions in invasive populations. High-quality genome assemblies further revealed an inversion in one of the haplotypes in the invaded range. The two haplotypes were estimated to have diverged 1.5 million years ago, and each harboured specific genes, some of which likely belonging to Starships. These are large trasnposable elements, mobilized by tyrosine recombinases, able to move accessory genes, and involved in adaptation in multiple fungi. The MAT-proximal region carried genes upregulated under virus infection or vegetative incompatibility reaction. In the native range, the MAT-proximal region also appeared to have a different evolutionary history than the rest of the genome. In all continents, the MAT-Proximal region was enriched in non-synonymous substitutions, in gene presence/absence polymorphism, in tyrosine recombinases and in transposable elements. This study thus sheds light on a case of a large non-recombining region partially linked to a mating compatibility locus, likely maintained by balancing selection on differentiated haplotypes, possibly involved in adaptation in a devastating tree pathogen.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189871","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}
Jess D Hebert, Yuning J Tang, Márton Szamecz, Laura Andrejka, Steven S Lopez, Dmitri A Petrov, Gábor Boross, Monte M Winslow
{"title":"Combinatorial in vivo genome editing identifies widespread epistasis and an accessible fitness landscape during lung tumorigenesis.","authors":"Jess D Hebert, Yuning J Tang, Márton Szamecz, Laura Andrejka, Steven S Lopez, Dmitri A Petrov, Gábor Boross, Monte M Winslow","doi":"10.1093/molbev/msaf023","DOIUrl":"10.1093/molbev/msaf023","url":null,"abstract":"<p><p>Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with inactivation of pairs of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings expand our understanding of the evolutionary interactions that drive tumorigenesis in vivo.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189873","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}
Kate R Castellano, Michelle L Neitzey, Andrew Starovoitov, Gabriel A Barrett, Noah M Reid, Vidya S Vuruputoor, Cynthia N Webster, Jessica M Storer, Nicole R Pauloski, Natalie J Ameral, Susan L McEvoy, M Conor McManus, Jonathan B Puritz, Jill L Wegrzyn, Rachel J O'Neill
{"title":"Genome assembly of a living fossil, the Atlantic horseshoe crab Limulus polyphemus, reveals lineage-specific whole genome duplications, transposable element-based centromeres and a ZW sex chromosome system.","authors":"Kate R Castellano, Michelle L Neitzey, Andrew Starovoitov, Gabriel A Barrett, Noah M Reid, Vidya S Vuruputoor, Cynthia N Webster, Jessica M Storer, Nicole R Pauloski, Natalie J Ameral, Susan L McEvoy, M Conor McManus, Jonathan B Puritz, Jill L Wegrzyn, Rachel J O'Neill","doi":"10.1093/molbev/msaf021","DOIUrl":"https://doi.org/10.1093/molbev/msaf021","url":null,"abstract":"<p><p>Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and most contiguous and complete assembly to date, for Limulus polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin-detection pathway components Factor C and Factor G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189880","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}
Menno J de Jong, Gabriel Anaya, Aidin Niamir, Javier Pérez-González, Camilla Broggini, Alberto Membrillo Del Pozo, Marcel Nebenfuehr, Eva de la Peña, Jordi Ruiz-Olmo, Jose Manuel Seoane, Giovanni Vedel, Aurelie Barboiron, Luděk Bartoš, Elena Buzan, Ruth F Carden, Giorgi Darchiashvili, Gačić Dragan, Alain C Frantz, Adrien Gérard, Araceli Gort-Esteve, Etienne Guillaumat, Anja Hantschmann, Mahmoud-Reza Hemami, Jacob Höglund, Joost F de Jong, Niko Kerdikoshvili, Christian Kern, Dean Konjevic, Petr Koubek, Nikoleta Karaiskou, Maryline Pellerin, Jarmila Krojerová-Prokešová, Allan D McDevitt, Stefan Merker, Markus Pfenninger, Knut H Røed, Christine Saint-Andrieux, Fatih Sarigol, Maciej Sykut, Alexandros Triantafyllidis, Josephine Pemberton, Urmas Saarma, Laura Iacolina, Magdalena Niedziałkowska, Frank E Zachos, Juan Carranza, Axel Janke
{"title":"Red deer resequencing reveals the importance of sex chromosomes for reconstructing Late Quaternary events.","authors":"Menno J de Jong, Gabriel Anaya, Aidin Niamir, Javier Pérez-González, Camilla Broggini, Alberto Membrillo Del Pozo, Marcel Nebenfuehr, Eva de la Peña, Jordi Ruiz-Olmo, Jose Manuel Seoane, Giovanni Vedel, Aurelie Barboiron, Luděk Bartoš, Elena Buzan, Ruth F Carden, Giorgi Darchiashvili, Gačić Dragan, Alain C Frantz, Adrien Gérard, Araceli Gort-Esteve, Etienne Guillaumat, Anja Hantschmann, Mahmoud-Reza Hemami, Jacob Höglund, Joost F de Jong, Niko Kerdikoshvili, Christian Kern, Dean Konjevic, Petr Koubek, Nikoleta Karaiskou, Maryline Pellerin, Jarmila Krojerová-Prokešová, Allan D McDevitt, Stefan Merker, Markus Pfenninger, Knut H Røed, Christine Saint-Andrieux, Fatih Sarigol, Maciej Sykut, Alexandros Triantafyllidis, Josephine Pemberton, Urmas Saarma, Laura Iacolina, Magdalena Niedziałkowska, Frank E Zachos, Juan Carranza, Axel Janke","doi":"10.1093/molbev/msaf031","DOIUrl":"https://doi.org/10.1093/molbev/msaf031","url":null,"abstract":"<p><p>Sex chromosomes differ in their inheritance properties from autosomes, and hence may encode complementary information about past demographic events. We compiled and analysed a range-wide resequencing dataset of the red deer (Cervus elaphus), one of the few Eurasian herbivores of the Late Pleistocene megafauna still found throughout much of its historic range. Our analyses of 144 whole genomes reveal striking discrepancies between the population clusters suggested by autosomal and X-chromosomal data. We postulate that the genetic legacy of Late Glacial population structure is better captured and preserved by the X chromosome than by autosomes, for two reasons. First, X chromosomes have a lower Ne and hence lose genetic variation faster during isolation in glacial refugia, causing increased population differentiation. Second, following postglacial recolonisation and secondary contact, immigrant males pass on their X chromosomes to female offspring only, which effectively halves the migration rate when gene flow is male-mediated. Our study illustrates how a comparison between autosomal and sex chromosomal phylogeographic signals unravels past demographic processes which otherwise would remain hidden.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143255850","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}
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":"https://doi.org/10.1093/molbev/msaf030","url":null,"abstract":"<p><p>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.</p>","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":"143080479","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}
{"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":"<p><p>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.</p>","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}
Apurva Narechania, Dean Bobo, Rob DeSalle, Barun Mathema, Barry Kreiswirth, Paul J Planet
{"title":"What do we gain when tolerating loss? The information bottleneck wrings out recombination.","authors":"Apurva Narechania, Dean Bobo, Rob DeSalle, Barun Mathema, Barry Kreiswirth, Paul J Planet","doi":"10.1093/molbev/msaf029","DOIUrl":"https://doi.org/10.1093/molbev/msaf029","url":null,"abstract":"<p><p>Most microbes have the capacity to acquire genetic material from their environment. Recombination of foreign DNA yields genomes that are, at least in part, incongruent with the vertical history of their species. Dominant approaches for detecting these transfers are phylogenetic, requiring a painstaking series of analyses including alignment and tree reconstruction. But these methods do not scale. Here we propose an unsupervised, alignment-free and tree-free technique based on the sequential information bottleneck (SIB), an optimization procedure designed to extract some portion of relevant information from one random variable conditioned on another. In our case, this joint probability distribution tabulates occurrence counts of k-mers against their genomes of origin with the expectation that recombination will create a strong signal that unifies certain sets of co-occuring k-mers. We conceptualize the technique as a rate-distortion problem, measuring distortion in the relevance information as k-mers are compressed into clusters based on their co-occurrence in the source genomes. The result is fast, model-free, lossy compression of k-mers into learned groups of shared genome sequence, differentiating recombined elements from the vertically inherited core. We show that the technique yields a new recombination measure based purely on information, divorced from any biases and limitations inherent to alignment and phylogeny.</p>","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":"143080484","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}
{"title":"An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses.","authors":"Yue Yang, Xinyi Zhang, Tingting Chen, Fengyuan Wu, Yu S Huang, Yanhua Qu, Miao Xu, Liang Ma, Mo Liu, Weiwei Zhai","doi":"10.1093/molbev/msaf009","DOIUrl":"10.1093/molbev/msaf009","url":null,"abstract":"<p><p>The study of mutational processes in somatic genomes has gained recent momentum, uncovering a wide array of endogenous and exogenous factors associated with somatic changes. However, the overall landscape of mutational processes in germline mutations across the tree of life and associated evolutionary driving forces are rather unclear. In this study, we analyzed mutational processes in single-stranded RNA (ssRNA) viruses which are known to jump between different hosts with divergent exogenous environments. We found that mutational spectra in different ssRNA viruses differ significantly and are mainly associated with their genetic divergence. Surprisingly, host environments contribute much less significantly to the mutational spectrum, challenging the prevailing view that the exogenous cellular environment is a major determinant of the mutational spectrum in viruses. To dissect the evolutionary forces shaping viral spectra, we selected two important scenarios, namely the inter-host evolution between different viral strains as well as the intra-host evolution. In both scenarios, we found mutational spectra change significantly through space and time, strongly correlating with levels of natural selection. Combining the mutations across all ssRNA viruses, we identified a suite of mutational signatures with varying degrees of similarity to somatic signatures in humans, indicating universal and divergent mutational processes across the tree of life. Taken together, we unraveled an unprecedented dynamic landscape of mutational processes in ssRNA viruses, pinpointing important evolutionary forces shaping fast evolution of mutational spectra in different species.</p>","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/PMC11796089/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008405","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}
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":"<p><p>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.</p>","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}