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Sun L, Xu Z, Shuai M, Li C, Yang G, Xu S. Natural resistance to cancers in long-lived mammals: genomic mechanisms and experimental evidence to explain Peto's paradox. SCIENCE CHINA. LIFE SCIENCES 2025; 68:1801-1814. [PMID: 40131646 DOI: 10.1007/s11427-024-2838-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Accepted: 01/10/2025] [Indexed: 03/27/2025]
Abstract
Long-lived mammals are reported to have rare or considerably fewer instances of spontaneous tumors, suggesting they might have evolved specific or convergent mechanisms of cancer resistance to extend lifespan; however, the underlying mechanisms remain insufficiently explored. Here, we conducted comparative analysis across 60 mammalian genomes to investigate the genomic features associated with natural cancer resistance. We identified 296 strongly selected genes unique to long-lived species and associated with immune response, DNA repair, and cancer, which might contribute to cancer resistance and lifespan extension in long-lived species. Further, 229 convergent cancer-related genes were detected in the four extremely long-lived species and in-vitro assays confirmed a convergent mutation of LZTS1, shared by bowhead whales and naked mole rats, could suppress cancer development. Importantly, 16 genes were significantly related to both body weight and cancer, defined as candidate genes of Peto's paradox. Of them, the YAP1 gene, harboring the A214S mutation, was identified as a key gene that upregulated tumor suppression genes by localizing to the cytoplasm, which might prohibit cancer development in the large and long-lived cetaceans. These findings provide novel insights into the molecular mechanisms underlying natural cancer resistance in long-lived mammals and the biological basis of Peto's paradox.
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Affiliation(s)
- Linxia Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhikang Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengqi Shuai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Chengxu Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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2
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Lucotte EA, Jay P, Rougemont Q, Boyer L, Cornille A, Snirc A, Labat A, Chahine E, Duhamel M, Namias A, Gendelman J, Ma WJ, Hayes RK, Baruri S, Ham JP, Perlin MH, Hood ME, Rodríguez de la Vega RC, Giraud T. Repeated loss of function at HD mating-type genes and of recombination in anther-smut fungi. Nat Commun 2025; 16:4962. [PMID: 40436846 PMCID: PMC12119880 DOI: 10.1038/s41467-025-60222-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/14/2025] [Indexed: 06/01/2025] Open
Abstract
Basidiomycete fungi typically have two mating-type loci controlling mating compatibility, HD and PR, residing on different chromosomes. Loss-of-function in mating compatibility has been reported at the PR genes in a few heterothallic basidiomycetes, but not for the HD genes. In Microbotryum anther-smut fungi, there have been repeated linkage events between the HD and PR loci through chromosome fusions, leading to non-recombining regions. Here, we found that two sister Microbotryum species parasitizing Dianthus plants, M. superbum and M. shykoffianum, as well as the distantly related M. scorzonerae, have their HD and PR loci on different chromosomes, but with the PR chromosome fused with a part of the ancestral HD chromosome. In addition, recombination suppression has extended stepwise, generating evolutionary strata. In all three species, the HD genes lost their function in mating compatibility, natural diploid strains being often homozygous at the HD locus. Strains could be homozygous for a disrupted HD2 gene, that was hardly expressed during mating. Mating tests confirmed that a single genetic factor controlled mating compatibility and that haploid strains with identical HD alleles could mate and produce hyphae. This study shows that a unifactorial mating-type determinism can evolve, repeatedly, from a bifactorial system, by different mechanisms.
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Affiliation(s)
- Elise A Lucotte
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France.
| | - Paul Jay
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Quentin Rougemont
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Loreleï Boyer
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Amandine Cornille
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France
| | - Alodie Snirc
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Amandine Labat
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Elizabeth Chahine
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Marine Duhamel
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | - Alice Namias
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France
| | | | - Wen-Juan Ma
- Department of Biology, Amherst College, Amherst, MA, USA
- Department of Biology, Research group of Ecology, Evolution and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Roxanne K Hayes
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Shikhi Baruri
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Joseph P Ham
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, MA, USA
| | | | - Tatiana Giraud
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Société Evolution, Gif sur Yvette, France.
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3
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Liu X, Blomme J, Bogaert KA, D'hondt S, Coulembier Vandelannoote E, Wichard T, De Clerck O. Positive selection and relaxed purifying selection contribute to rapid evolution of sex-biased genes in green seaweed Ulva. BMC Ecol Evol 2025; 25:44. [PMID: 40346481 PMCID: PMC12063405 DOI: 10.1186/s12862-025-02382-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Accepted: 04/25/2025] [Indexed: 05/11/2025] Open
Abstract
BACKGROUND The evolution of differences in gamete size and number between sexes is a cornerstone of sexual selection theories. The green macroalga Ulva, with incipient anisogamy and parthenogenetic gametes, provides a unique system to investigate theoretical predictions regarding the evolutionary pressures that drive the transition from isogamy to anisogamy, particularly in relation to gamete size differentiation and sexual selection. Its minimal gamete dimorphism and facultative parthenogenesis enable a rare window into early evolutionary steps toward anisogamy. RESULTS By analyzing the expression profiles of sex-biased genes (SBGs) during gametogenesis, we found that SBGs evolve faster than unbiased genes, driven by higher rates of non-synonymous substitution (dN), indicating that SBGs are under stronger selective pressures. Mating type minus-biased genes (mt-BGs) exhibit higher dN/dS values than mating type plus-biased genes (mt+BGs), suggesting stronger selective pressures on mt-BGs, although this difference was not statistically significant (P = 0.08). Using branch-site and RELAX models, we found positive selection and relaxed purifying selection acting on a significant proportion of SBGs, particularly those associated with flagella function. CONCLUSIONS This study highlights the selective pressures shaping anisogamy and provides insights into the molecular mechanisms underlying its evolution. The faster evolution of SBGs, particularly mt-BGs, and the positive selection on genes associated with motility, such as those related to flagella function, suggest the importance of enhanced gamete motility in the transition to anisogamy. These findings contribute to our understanding of sexual selection and the evolutionary forces that drive the differentiation of gamete size and number between sexes.
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Affiliation(s)
- Xiaojie Liu
- Phycology Research Group, Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, 9000, Belgium
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Jonas Blomme
- Phycology Research Group, Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, 9000, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Kenny A Bogaert
- Phycology Research Group, Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, 9000, Belgium
| | - Sofie D'hondt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
| | - Emma Coulembier Vandelannoote
- Phycology Research Group, Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, 9000, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Olivier De Clerck
- Phycology Research Group, Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, 9000, Belgium.
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Weng Y, Qin D, Li X, Zhou J, Zhang B, Li QQ. Convergent Isobilateral Leaves Increase the Risk for Mangroves Facing Human-Induced Rapid Environmental Changes. PLANT, CELL & ENVIRONMENT 2025; 48:3500-3511. [PMID: 39777404 DOI: 10.1111/pce.15373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 12/27/2024] [Indexed: 01/11/2025]
Abstract
Understanding plant adaptations in extreme environments is crucial, as these adaptations often confer advantages for survival. However, a significant gap exists regarding the genetic mechanisms underlying these adaptations and their responses to human-induced rapid environmental change (HIREC). This study addresses the question of whether genetic convergence occurs among plants with similar adaptive features, specifically focusing on isobilateral leaves in mangrove species. Here, we analyse the genetic convergence of isobilateral leaves in mangroves that have independently adapted to coastal intertidal zones. Our findings reveal that genetic convergence is evident in gene families involved in leaf abaxial and adaxial development, with strong selection pressures identified in photosynthesis and leaf polarity pathways. Despite these adaptations, mangrove species with isobilateral leaves occupy narrower ecological niches and face diminishing suitable habitat areas projected under various HIREC scenarios. These results indicate that while convergent traits enhance local adaptation, they may also increase vulnerability to ongoing environmental changes. This research provides valuable insight into the interplay between genetic adaptation and environmental resilience, underscoring the necessity for targeted biodiversity conservation strategies that safeguard specific adaptive traits amid rapid environmental shifts.
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Affiliation(s)
- Yulin Weng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dandan Qin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xiao Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jiawen Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Bowen Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, California, USA
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5
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Ding Y, Zou M, Guo B. Genomic signatures associated with recurrent scale loss in cyprinid fish. Integr Zool 2025; 20:535-550. [PMID: 38816909 DOI: 10.1111/1749-4877.12851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Scale morphology represents a fundamental feature of fish and a key evolutionary trait underlying fish diversification. Despite frequent and recurrent scale loss throughout fish diversification, comprehensive genome-wide analyses of the genomic signatures associated with scale loss in divergent fish lineages remain scarce. In the current study, we investigated genome-wide signatures, specifically convergent protein-coding gene loss, amino acid substitutions, and cis-regulatory sequence changes, associated with recurrent scale loss in two divergent Cypriniformes lineages based on large-scale genomic, transcriptomic, and epigenetic data. Results demonstrated convergent changes in many genes related to scale formation in divergent scaleless fish lineages, including loss of P/Q-rich scpp genes (e.g. scpp6 and scpp7), accelerated evolution of non-coding elements adjacent to the fgf and fgfr genes, and convergent amino acid changes in genes (e.g. snap29) under relaxed selection. Collectively, these findings highlight the existence of a shared genetic architecture underlying recurrent scale loss in divergent fish lineages, suggesting that evolutionary outcomes may be genetically repeatable and predictable in the convergence of scale loss in fish.
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Affiliation(s)
- Yongli Ding
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
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6
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Policarpo M, Salzburger W, Maumus F, Gilbert C. Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes. Mol Biol Evol 2025; 42:msaf107. [PMID: 40378191 PMCID: PMC12107551 DOI: 10.1093/molbev/msaf107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 04/29/2025] [Accepted: 05/02/2025] [Indexed: 05/18/2025] Open
Abstract
Horizontal gene transfer (HGT) is less frequent in eukaryotes than in prokaryotes, yet can have strong functional implications and was proposed as a causal factor for major adaptations in several eukaryotic lineages. Most cases of eukaryote HGT reported to date are inter-domain transfers, and few studies have investigated eukaryote-to-eukaryote HGTs. Here, we performed a large-scale survey of HGT among 242 species of ray-finned fishes. We found multiple lines of evidence supporting 19 teleost-to-teleost HGT events that involve 17 different genes in 11 teleost fish orders. The genes involved in these transfers show lower synonymous divergence than expected under vertical transmission, their phylogeny is inconsistent with that of teleost fishes, and they occur at non-syntenic positions in donor and recipient lineages. The distribution of HGT events in the teleost tree is heterogenous, with 8 of the 19 transfers occurring between the same two orders (Osmeriformes and Clupeiformes). Though we favor a scenario involving multiple HGT events, future work should evaluate whether hybridization between species belonging to different teleost orders may generate HGT-like patterns. Besides the previously reported transfer of an antifreeze protein, most transferred genes play roles in immunity or are pore-forming proteins, suggesting that such genes may be more likely than others to confer a strong selective advantage to the recipient species. Overall, our work shows that teleost-to-teleost HGT has occurred on multiple occasions, and it will be worth further quantifying these transfers and evaluating their impact on teleost evolution as more genomes are sequenced.
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Affiliation(s)
- Maxime Policarpo
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Florian Maumus
- URGI, INRAE, Université Paris-Saclay, Versailles 78026, France
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette 91198, France
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7
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Zhao X, Liu Y, Yuan B, Cao Z, Yang Y, He C, Chan KC, Xiao S, Lin H, Fang Q, Ye G, Ye X. Genomic signatures associated with the evolutionary loss of egg yolk in parasitoid wasps. Proc Natl Acad Sci U S A 2025; 122:e2422292122. [PMID: 40232796 PMCID: PMC12036997 DOI: 10.1073/pnas.2422292122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Accepted: 03/14/2025] [Indexed: 04/16/2025] Open
Abstract
Trait regression and loss have occurred repeatedly in numerous lineages in response to environmental changes. In parasitoid wasps, a megadiverse group of hymenopteran insects, yolk protein reduction or loss has been observed in many species, likely linked to the transition from ectoparasitism to endoparasitism. However, the genetic basis of this trait and the impact of its loss on genome evolution remain poorly understood. Here, we performed a comparative genomic analysis of 64 hymenopteran insects. The conserved insect yolk protein gene vitellogenin (Vg) underwent five independent loss events in four families, involving 23 of the analyzed endoparasitoid species. Whole-genome alignment suggested that Vg loss occurred during genome rearrangement events. Analysis of Vg receptor gene (VgR) loss, selection, and structural variation in lineages lacking Vg demonstrated functional biases in the patterns of gene loss. The ectoparasitism to endoparasitism transition did not appear to be the primary driver of Vg loss or the subsequent VgR evolution. Together, these findings reveal the genomic changes underlying a unique trait loss in parasitoid wasps. More broadly, this study enhances our understanding of yolk protein loss evolution outside the class Mammalia, highlighting a potential evolutionary trend arising from the availability of an alternative nutrient source for embryonic development.
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Affiliation(s)
- Xianxin Zhao
- State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou310058, China
| | - Yuanyuan Liu
- State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou310058, China
| | - Bo Yuan
- State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou310058, China
| | - Zhichao Cao
- State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou310058, China
| | - Yi Yang
- State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou310058, China
| | - Chun He
- State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou310058, China
| | - Kevin C. Chan
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou215123, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai201203, China
| | - Shan Xiao
- Ningbo Academy of Agricultural Science, Ningbo315100, China
| | - Haiwei Lin
- State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou310058, China
| | - Qi Fang
- State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou310058, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou310058, China
| | - Xinhai Ye
- College of Advanced Agriculture Science, Zhejiang Agriculture and Forestry University, Hangzhou311300, China
- Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Zhejiang Agriculture and Forestry University, Hangzhou311300, China
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8
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Oyeniran KA, Tenibiaje MO. Detectable episodic positive selection in the virion strand a-strain Maize streak virus genes may have a role in its host adaptation. Virus Genes 2025:10.1007/s11262-025-02157-z. [PMID: 40237943 DOI: 10.1007/s11262-025-02157-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 04/06/2025] [Indexed: 04/18/2025]
Abstract
Maize streak virus (MSV) has four genes: cp, encoding the coat protein; mp, the movement protein; and repA and rep, encoding two distinct replication-associated proteins from an alternatively spliced transcript. These genes play roles in encapsidation, movement, replication, and interactions with the external environment, making them prone to stimuli-driven molecular adaptation. We accomplished selection studies on publicly available curated, recombination-free, complete coding sequences for representative A-strain maize streak virus (MSV-A) cp and mp genes. We found evidence of gene-wide selection in these two MSV genes at specific sites within the genes (cp 1.23% and mp 0.99%). Positively selected sites have amino acids that are 60% hydrophilic and 40% hydrophobic in nature. We found significant evidence of positive selection at branches (cp: 0.76 and mp:1.66%) representing the diversity of MSV-A-strain in South Africa, which is related to the MSV-A-matA isolate (GenBank accession number: AF329881), well disseminated and adapted to the maize plant in sub-Saharan Africa. In the mp gene, selection significantly intensified for the overall diversities of the MSV-A sequences and those more related to the MSV-Mat-A isolate. These findings reveal that despite predominantly undergoing non-diversifying selection, the detectable diversifying positive selection observed in these genes may play a major role in MSV-A host adaptive evolution, ensuring sufficient pathogenicity for onward transmission without killing the host.
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Affiliation(s)
- Kehinde A Oyeniran
- Department of Biological Sciences, Bamidele Olumilua University of Education Science and Technology, P.M.B. 250, Ikere-Ekiti, Ekiti, Nigeria.
- Plant Systems Biology, International Centre for Genetic Engineering and Biotechnology, Cape Town, 7925, South Africa.
| | - Mobolaji O Tenibiaje
- Department of Computing and Information Science, Bamidele Olumilua University of Education Science and Technology, P.M.B. 250, Ikere-Ekiti, Ekiti, Nigeria
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9
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Xie YY, Wen B, Bai MZ, Guo YY. De Novo Creation of Two Novel Spliceosomal Introns of RECG1 by Intronization of Formerly Exonic Sequences in Orchidaceae. J Mol Evol 2025; 93:267-277. [PMID: 40202594 DOI: 10.1007/s00239-025-10242-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Accepted: 03/21/2025] [Indexed: 04/10/2025]
Abstract
Spliceosomal introns are a key characteristic of eukaryotic genes. However, the origins and mechanisms of new spliceosomal introns remain elusive, and definitive case studies documenting intron creation are still limited. This study examined the RECG1 genes of 49 land plants, including 21 orchids and 28 non-orchid species. Sequence comparison revealed that the fourth intron of Gastrodia and Platanthera (Orchidaceae) is a newly gained spliceosomal intron, originating from the intronization of former exonic sequences. This intronization event was accompanied by the creation of novel recognizable GT/AG splice sites. In contrast, other orchid species lack the corresponding splice sites in the counterpart regions. Moreover, the secondary and tertiary protein structures implied that the intronization events do not affect the protein function. Given the diverse trophic modes of the two genera, we infer that relaxed selection may have contributed to the fluidity of gene structures. This study provides a typical example of de novo lineage-specific intron creation via intronization in orchids supported by multiple lines of evidence, and the two intronization events occurred independently in the same gene. This research enhances our understanding of gene evolution in orchids and provides valuable insights that may assist the annotation of structurally complex genes.
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Affiliation(s)
- Yuan-Yuan Xie
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Bin Wen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Ming-Zhu Bai
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yan-Yan Guo
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China.
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10
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Iverson ENK, Criswell A, Havird JC. Stronger Evidence for Relaxed Selection Than Adaptive Evolution in High-elevation Animal mtDNA. Mol Biol Evol 2025; 42:msaf061. [PMID: 40114504 PMCID: PMC12018679 DOI: 10.1093/molbev/msaf061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 07/04/2024] [Accepted: 07/15/2024] [Indexed: 03/22/2025] Open
Abstract
Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive selection, rather than relaxed purifying selection, has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.
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Affiliation(s)
- Erik N K Iverson
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, USA
| | - Abby Criswell
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, USA
| | - Justin C Havird
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, USA
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11
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Song S, Cao J, Xiang H, Liu Z, Jiang W. Comparative mitogenomic analysis of Chinese cavefish Triplophysa (Cypriniformes: Nemacheilidae): novel gene tandem duplication and evolutionary implications. BMC Genomics 2025; 26:293. [PMID: 40128668 PMCID: PMC11934697 DOI: 10.1186/s12864-025-11486-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 03/13/2025] [Indexed: 03/26/2025] Open
Abstract
BACKGROUND Cavefish exhibit significant morphological changes that result in trade-offs in metabolic requirements and energy utilization in perpetual darkness. As cellular "powerhouses", mitochondria play crucial roles in energy metabolism, suggesting that mitochondrial genes have likely experienced selective pressures during cavefish evolution. RESULTS This study presents the first assembly of the complete mitogenome of Triplophysa yangi, a typical cavefish species in China. The mitogenome is 17,068 bp long, marking the longest recorded for the genus Triplophysa, and includes 13 protein-coding genes (PCGs), 2 rRNAs, 25 tRNAs, and a noncoding control region. An ~ 500 bp insertion between ND2 and WANCY regions was observed, comprising a large intact tandem repeat unit (A'-N'-OL'-C') flanked by two unannotated sequences (U1/U2). The evolutionary origin of this repeat unit may involve either in situ duplication events with subsequent functional divergence-where neofunctionalization, subfunctionalization, or pseudogenization drove differential mutation rates between paralogs-or alternatively, horizontal acquisition from exogenous genetic material that became functionally integrated into the ancestral T. yangi mitogenome through co-option mechanisms. Phylogenetic analyses revealed two major clades within Triplophysa-epigean and hypogean lineages-consistent with previous classifications, while cave-restricted species exhibited signs of parallel evolution within the hypogean lineage. Selective pressure analysis indicated that the hypogean lineage (cave-dwelling groups, II & III) have a significantly increased ratio of nonsynonymous to synonymous substitution rates (ω) compared to the epigean lineage (surface-dwelling group, I), suggesting a combination of adaptive selection and relaxed functional constraints in cave-dwelling species. CONCLUSIONS The duplication of tRNAs in T. yangi and the potential positive selection sites identified in Triplophysa cavefish further indicated adaptive evolution in mitochondrial PCGs in response to extreme subterranean conditions.
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Affiliation(s)
- Shuang Song
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
- National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, Jishou University, Zhangjiajie, 427000, China
| | - Jianhan Cao
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
- National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, Jishou University, Zhangjiajie, 427000, China
| | - Hongmei Xiang
- National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, Jishou University, Zhangjiajie, 427000, China
| | - Zhixiao Liu
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Wansheng Jiang
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China.
- National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoides, Jishou University, Zhangjiajie, 427000, China.
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12
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Ma J, Bechsgaard J, Aagaard A, Villesen P, Bilde T, Schierup MH. The genomic consequences and persistence of sociality in spiders. Genome Res 2025; 35:499-511. [PMID: 39978820 PMCID: PMC11960701 DOI: 10.1101/gr.279503.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 02/04/2025] [Indexed: 02/22/2025]
Abstract
In cooperatively breeding social animals, a few individuals account for all reproduction. In some taxa, sociality is accompanied by a transition from outcrossing to inbreeding. In concert, these traits reduce effective population size, potentially rendering transitions to sociality "evolutionarily dead-ends." We addressed this hypothesis in a comparative genomic study in spiders, in which sociality has evolved independently at least 23 times, but social branches are recent and short. We present genomic evidence for the evolutionary dead-end hypothesis in a spider genus with three independent transitions to sociality. We assembled and annotated high-quality, chromosome-level reference genomes from three pairs of closely related social and subsocial Stegodyphus species. We timed the divergence between the social and subsocial species pairs to be from 1.3 million to 1.8 million years. Social evolution in spiders involves a shift from outcrossing to inbreeding and from an equal to a female-biased sex ratio, causing severe reductions in effective population size and decreased efficacy of selection. We show that transitions to sociality only had full effect on purifying selection at 119, 260, and 279 kya, respectively, and follow similar convergent trajectories of progressive loss of diversity and shifts to an increasingly female-biased sex ratio. This almost deterministic genomic response to sociality may explain why social spider lineages do not persist. What causes species extinction is not clear, but either could be selfish meiotic drive eliminating the production of males or could be an inability to retain genome integrity in the face of extremely reduced efficacy of selection.
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Affiliation(s)
- Jilong Ma
- Bioinformatics Research Center, Aarhus University, Aarhus C, DK-8000, Denmark;
- Department of Biology, Aarhus University, Aarhus C, DK-8000, Denmark
| | - Jesper Bechsgaard
- Department of Biology, Aarhus University, Aarhus C, DK-8000, Denmark
| | - Anne Aagaard
- Department of Biology, Aarhus University, Aarhus C, DK-8000, Denmark
| | - Palle Villesen
- Bioinformatics Research Center, Aarhus University, Aarhus C, DK-8000, Denmark
| | - Trine Bilde
- Department of Biology, Aarhus University, Aarhus C, DK-8000, Denmark;
- Center for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, United Kingdom
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13
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Tressel LG, Shrestha B, Lee C, Choi IS, Ruhlman TA, Cardoso D, Wojciechowski MF, Jansen RK. Plastid-nuclear coevolution of ribosomal protein genes in papilionoid legumes. Mol Phylogenet Evol 2025; 204:108281. [PMID: 39733867 DOI: 10.1016/j.ympev.2024.108281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 12/23/2024] [Accepted: 12/26/2024] [Indexed: 12/31/2024]
Abstract
In plants, cellular function is orchestrated by three distinct genomes located within the nucleus, mitochondrion, and plastid. These genomes are interdependent, requiring tightly coordinated maintenance and expression. Plastids host several multisubunit protein complexes encoded by both the plastid and nuclear genomes. To investigate plastid-nuclear coevolution, this study focused on plastid ribosomal protein genes that are encoded by both plastid and nuclear genomes from 50 taxa across 15 of the 22 early branching major clades of the legume subfamily Papilionoideae. Comparative analysis of substitution rates was conducted across five gene sets: nuclear-encoded plastid-targeted ribosomal protein genes (NuCpRP), nuclear-encoded cytosol-targeted ribosomal genes (NuCyRP), other nuclear-encoded plastid-targeted genes that are not involved in ribosomes (NuCpOT), plastid-encoded ribosomal protein genes (CpRP) and plastid-encoded photosynthesis genes (CpPS).1 Elevated nonsynonymous substitution rates (dN) and ratios of nonsynonymous to synonymous substitution rates (dN/dS; ω) were observed in both CpRP and NuCpRP compared to the other gene sets. Significant differences in dN for CpRP and NuCpRP were found between the papilionoid 50-kb inversion clade and other legumes. Using coevolution statistics and evolutionary rate covariation, strong signals of cytonuclear coevolution were identified, where nonsynonymous substitutions in CpRP and NuCpRP genes co-occur along the same branches of the Papilionoideae phylogeny. Increased ω in a few CpRP genes was due to intensified positive selection whereas most of the CpRP and NuCpRP increased ω was caused by relaxed purifying selection. This pattern not only underscores the role of cytonuclear incompatibility in driving speciation but also highlights its constraints on the genetic enhancement of papilionoid crop species.
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Affiliation(s)
- Lydia G Tressel
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Bikash Shrestha
- DOE, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chaehee Lee
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - In-Su Choi
- Department of Biological Sciences and Biotechnology, Hannam University, Daejeon, South Korea
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Domingos Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, RJ, Brazil
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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14
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Prost S, Elbers JP, Slezacek J, Hykollari A, Fuselli S, Smith S, Fusani L. The unexpected loss of the 'hunger hormone' ghrelin in true passerines: a game changer in migration physiology. ROYAL SOCIETY OPEN SCIENCE 2025; 12:242107. [PMID: 40109942 PMCID: PMC11919490 DOI: 10.1098/rsos.242107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 02/19/2025] [Accepted: 02/21/2025] [Indexed: 03/22/2025]
Abstract
Migratory birds must accumulate large amounts of fat prior to migration to sustain long flights. In passerines, the small body size limits the amount of energy stores that can be transported, and therefore birds undergo cycles of extreme fattening and rapid exhaustion of reserves. Research on these physiological adaptations was rattled by the discovery that birds have lost the main vertebrate regulator of fat deposition, leptin. Recent studies have thus focused on ghrelin, known as 'hunger hormone', a peptide secreted by the gastrointestinal tract to regulate, e.g. food intake and body mass in vertebrates. Studies on domestic species showed that, in birds, ghrelin has effects opposite to those described in mammals such as inhibiting instead of promoting food intake. Furthermore, recent studies have shown that ghrelin administration influences migratory behaviour in passerine birds. Using comparative genomics and immunoaffinity chromatography, we show that ghrelin has been lost in Eupasseres after the basic split from Acanthisitti about 50 Ma. We found that the ghrelin receptor is still conserved in passerines. The maintenance of a functional receptor system suggests that in Eupasserines, another ligand has replaced ghrelin, perhaps to bypass the feedback system that would hinder the large pre-migratory accumulation of subcutaneous fat.
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Affiliation(s)
- Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Jean P Elbers
- Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Julia Slezacek
- Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Alba Hykollari
- Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Silvia Fuselli
- Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Steve Smith
- Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Leonida Fusani
- Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, Austria
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
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15
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Havens JL, Kosakovsky Pond SL, Zehr JD, Pekar JE, Parker E, Worobey M, Andersen KG, Wertheim JO. Dynamics of natural selection preceding human viral epidemics and pandemics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.26.640439. [PMID: 40060453 PMCID: PMC11888428 DOI: 10.1101/2025.02.26.640439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/15/2025]
Abstract
Using a phylogenetic framework to characterize natural selection, we investigate the hypothesis that zoonotic viruses require adaptation prior to zoonosis to sustain human-to-human transmission. Examining the zoonotic emergence of Ebola virus, Marburg virus, influenza A virus, SARS-CoV, and SARS-CoV-2, we find no evidence of a change in the intensity of natural selection immediately prior to a host switch, compared with typical selection within reservoir hosts. We conclude that extensive pre-zoonotic adaptation is not necessary for human-to-human transmission of zoonotic viruses. In contrast, the reemergence of H1N1 influenza A virus in 1977 showed a change in selection, consistent with the hypothesis of passage in a laboratory setting prior to its reintroduction into the human population, purportedly during a vaccine trial. Holistic phylogenetic analysis of selection regimes can be used to detect evolutionary signals of host switching or laboratory passage, providing insight into the circumstances of past and future viral emergence.
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Affiliation(s)
- Jennifer L. Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Jordan D. Zehr
- Institute for Genomics and Evolutionary Medicine, Temple University, 19122, Philadelphia, USA
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY 14850, USA
| | - Jonathan E. Pekar
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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16
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Liang X, Wu M, Nong Q, Yang S, Kan T, Feng P. Evolution of UCP1 Gene and Its Significance to Temperature Adaptation in Rodents. Int J Mol Sci 2025; 26:2155. [PMID: 40076776 PMCID: PMC11899873 DOI: 10.3390/ijms26052155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 02/12/2025] [Accepted: 02/24/2025] [Indexed: 03/14/2025] Open
Abstract
Adaptive thermogenesis comprises shivering thermogenesis dependent on skeletal muscles and non-shivering thermogenesis (NST) mediated by uncoupling protein 1 (UCP1). Although the thermogenic function of UCP1 was adopted early in some placental mammals, positive selection predominantly occurred in the ancestral branches of small-bodied species. Some previous studies have revealed that rodents living in northern or high mountain regions adapt to cold environments by increasing NST, whereas those living in tropical and subtropical regions that are not exposed to cold stress express low concentrations of UCP1, indicating that UCP1 may have evolved to adapt to ambient temperatures. In this study, we explored the evolution of UCP1 and its significance to temperature adaptation by performing detailed evolutionary and statistical analyses on 64 rodents with known genomes. As a result, a total of 71 UCP1 gene sequences were obtained, including 47 intact genes, 22 partial genes, and 2 pseudogenes. Further, 47 intact genes and 3 previously published intact UCP1 genes were incorporated into evolutionary analyses, and correlation analyses between evolutionary rate and ambient temperatures (including average annual temperature, maximum temperature, and minimum temperature) of the rodent survives were conducted. The results show that UCP1 is under purifying selection (ω = 0.11), and among rodents with intact UCP1 sequences, Urocitellus parryii and Dicrostonyx groenlandicus-the two species with the lowest ambient temperatures among the rodents used here-have higher evolutionary rates than others. In the statistical analyses, in addition to ambient temperatures, body weight and weight at birth were also taken into account since weight was previously proposed to be linked to UCP1 evolution. The results showed that after controlling for the phylogenetic effect, the maximum temperature was significantly negatively correlated with the evolutionary rate of UCP1, whereas weight did not have a relationship with UCP1 evolutionary rate. Consequently, it is suggested that ambient temperature can drive the evolution of rodent UCP1, thereby enhancing NST adaptation to cold stress.
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Affiliation(s)
- Xinyue Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin 541006, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China
| | - Minyu Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin 541006, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China
| | - Qiuting Nong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin 541006, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China
| | - Siqi Yang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin 541006, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China
| | - Tuo Kan
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin 541006, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China
| | - Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin 541006, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541006, China
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17
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Edlund M, Anderson BM, Su HJ, Robison T, Caraballo-Ortiz MA, Der JP, Nickrent DL, Petersen G. Plastome evolution in Santalales involves relaxed selection prior to loss of ndh genes and major boundary shifts of the inverted repeat. ANNALS OF BOTANY 2025; 135:515-530. [PMID: 39213003 PMCID: PMC11897430 DOI: 10.1093/aob/mcae145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 09/03/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND AND AIMS Biological aspects of haustorial parasitism have significant effects on the configuration of the plastid genome. Approximately half the diversity of haustorial parasites belongs to the order Santalales, where a clearer picture of plastome evolution in relation to parasitism is starting to emerge. However, in previous studies of plastome evolution there is still a notable under-representation of members from non-parasitic and deep-branching hemiparasitic lineages, limiting evolutionary inference around the time of transition to a parasitic lifestyle. To expand taxon sampling relevant to this transition we therefore targeted three families of non-parasites (Erythropalaceae, Strombosiaceae and Coulaceae), two families of root-feeding hemiparasites (Ximeniaceae and Olacaceae) and two families of uncertain parasitic status (Aptandraceae and Octoknemaceae). With data from these lineages we aimed to explore plastome evolution in relation to the evolution of parasitism. METHODS From 29 new samples we sequenced and annotated plastomes and the nuclear ribosomal cistron. We examined phylogenetic patterns, plastome evolution, and patterns of relaxed or intensified selection in plastid genes. Available transcriptome data were analysed to investigate potential transfer of infA to the nuclear genome. RESULTS Phylogenetic relationships indicate a single functional loss of all plastid ndh genes (ndhA-K) in a clade formed by confirmed parasites and Aptandraceae, and the loss coincides with major size and boundary shifts of the inverted repeat (IR) region. Depending on an autotrophic or heterotrophic lifestyle in Aptandraceae, plastome changes are either correlated with or pre-date the evolution of parasitism. Phylogenetic patterns also indicate repeated loss of infA from the plastome, and based on the presence of transcribed sequences with presequences corresponding to thylakoid luminal transit peptides, we infer that the genes were transferred to the nuclear genome. CONCLUSIONS Except for the loss of the ndh complex, relatively few genes have been lost from the plastome in deep-branching root parasites in Santalales. Prior to loss of the ndh genes, they show signs of relaxed selection indicative of their dispensability. To firmly establish a potential correlation between ndh gene loss, plastome instability and evolution of parasitism, it is pertinent to refute or confirm a parasitic lifestyle in all Santalales clades.
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Affiliation(s)
- Maja Edlund
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Benjamin M Anderson
- Western Australia Herbarium, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, 6983, Australia
| | - Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, Taipei 100234, Taiwan
| | - Tanner Robison
- 121 Boyce Thompson Institute, Ithaca, NY 14853, USA
- Plant Biology Section, School of Integrative Plant Science, CALS, Cornell University, Ithaca, NY 14853, USA
| | - Marcos A Caraballo-Ortiz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, MRC-166, PO Box 37012, Washington, DC 22013-7012, USA
| | - Joshua P Der
- Department of Biological Science (MH-282), California State University, Fullerton, PO Box 6850, Fullerton, CA 92834-6850, USA
| | - Daniel L Nickrent
- Plant Biology Section, School of Integrative Plant Science, CALS, Cornell University, Ithaca, NY 14853, USA
| | - Gitte Petersen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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18
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Cai L, Havird JC, Jansen RK. Recombination and retroprocessing in broomrapes reveal a universal roadmap for mitochondrial evolution in heterotrophic plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.14.637881. [PMID: 39990427 PMCID: PMC11844532 DOI: 10.1101/2025.02.14.637881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
The altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance on host-derived nutrients and loss of photosynthesis in holoparasites have led to highly degraded to absent plastid genomes, but its impact on mitochondrial genome (mitogenome) evolution has remained controversial. By examining mitogenomes from 45 Orobanchaceae species including three independent transitions to holoparasitism and key evolutionary intermediates, we identified measurable and predictable genetic alterations in genomic shuffling, RNA editing, and intracellular (IGT) and horizontal gene transfer (HGT) en route to a nonphotosynthetic lifestyle. In-depth comparative analyses revealed DNA recombination and repair processes, especially RNA-mediated retroprocessing, as significant drivers for genome structure evolution. In particular, we identified a novel RNA-mediated IGT and HGT mechanism, which has not been demonstrated in cross-species and inter-organelle transfers. Based on this, we propose a generalized dosage effect mechanism to explain the biased transferability of plastid DNA to mitochondria across green plants, especially in heterotrophic lineages like parasites and mycoheterotrophs. Evolutionary rates scaled with these genomic changes, but the direction and strength of selection varied substantially among genes and clades, resulting in high contingency in mitochondrial genome evolution. Finally, we describe a universal roadmap for mitochondrial evolution in heterotrophic plants where increased recombination and repair activities, rather than relaxed selection alone, lead to differentiated genome structure compared to free-living species.
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19
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Wang J, Chang J, Wang K, Liang B, Zhu Y, Liu Z, Liang X, Chen J, Peng Y, Agnarsson I, Li D, Liu J. Blue light restores functional circadian clocks in eyeless cave spiders. SCIENCE ADVANCES 2025; 11:eadr2802. [PMID: 39937902 PMCID: PMC11817938 DOI: 10.1126/sciadv.adr2802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 01/13/2025] [Indexed: 02/14/2025]
Abstract
Evolution in profound darkness often leads to predictable, convergent traits, such as the loss of vision. Yet, the consequences of such repeated evolutionary experiments remain obscure, especially regarding fundamental regulatory behaviors like circadian rhythms. We studied circadian clocks of blind cave spiders and their sighted relatives. In the field, cave spiders exhibit low per expression and maintain constant activity levels. Curiously, their clocks are not permanently lost; exposure to monochromatic blue light restores both circadian gene expression and behavioral rhythms. Conversely, blocking blue light in sighted relatives induces an arrhythmic "cave phenotype." Our RNA interference experiments suggest that clock genes regulate the rhythmicity of the huddle response, establishing a link between circadian gene networks and this behavioral rhythm. We demonstrate that circadian regulation is readily toggled and may play a latent role, even in constant darkness. Overall, our study expands understanding of circadian clock variations and paves the way for future research on the maintenance of silent phenotypes.
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Affiliation(s)
- Jinhui Wang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
- Arachnid Resource Centre of Hubei & Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jian Chang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
- Arachnid Resource Centre of Hubei & Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Kai Wang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
- Arachnid Resource Centre of Hubei & Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Bing Liang
- Arachnid Resource Centre of Hubei & Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yang Zhu
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zhihua Liu
- Arachnid Resource Centre of Hubei & Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Xitong Liang
- Peking University School of Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Jian Chen
- Arachnid Resource Centre of Hubei & Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yu Peng
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Ingi Agnarsson
- Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, Reykjavik, Iceland
| | - Daiqin Li
- Arachnid Resource Centre of Hubei & Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jie Liu
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, Hubei 430062, China
- Arachnid Resource Centre of Hubei & Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
- School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning, Hubei 437100, China
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20
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Clemons RA, Smith CH, Zamudio KR. Primary regulatory T cell activator FOXP3 is present across Amphibia. Immunogenetics 2025; 77:15. [PMID: 39945843 DOI: 10.1007/s00251-025-01372-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 02/05/2025] [Indexed: 05/09/2025]
Abstract
The overall structure of the immune system is highly conserved across jawed vertebrates, but characterization and description of the immune system is heavily biased toward mammals. One arm of the vertebrate immune system, the adaptive immune system, mounts pathogen-specific responses that tend to be robust and effective at clearing pathogens. This system requires selection against self-recognition and modulation of the immune response. One of the mechanisms of immune modulation is the presence of regulatory T cells that suppress other effector immune cells. Regulatory T cells and their primary activator forkhead box protein P3 (FOXP3) have been well characterized in mammalian models but unexplored in most other vertebrate taxa. Amphibians are a good focal group for the characterization of FOXP3 due to their phylogenetic position on the vertebrate tree of life, and their susceptibility to emerging pathogens. In this study, we mined available transcriptomic and genomic data to confirm the presence of FOXP3 across the amphibian tree of life. We find that FOXP3 is present in all major clades of amphibians. We also test whether selection on FOXP3 shows signatures of intensification among the three main clades of amphibians, which may reflect shifts in the stringency of natural selection on this gene. Our findings provide insights into the evolutionary history of the vertebrate immune system and confirm the conservation of vertebrate immune genes within amphibians.
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Affiliation(s)
- Rebecca A Clemons
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.
| | - Chase H Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kelly R Zamudio
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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21
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Claude SJ, Kamra K, Jung J, Kim HO, Kim JH. Elucidating the evolutionary dynamics of parasitism in Cuscuta: in-depth phylogenetic reconstruction and extensive plastomes reduction. BMC Genomics 2025; 26:137. [PMID: 39939920 PMCID: PMC11823189 DOI: 10.1186/s12864-025-11324-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 02/04/2025] [Indexed: 02/14/2025] Open
Abstract
BACKGROUND The genus Cuscuta L. (Convolvulaceae), commonly known as dodder, is a holoparasite plant that relies on host plants for nutrition, leading to significant genomic changes, particularly in plastomes. This dependency has led to significant reductions and modifications in their plastomes compared to autotrophic plants. In contrast to the well-conserved plastomes of photosynthetic plants, Cuscuta exhibits substantial genomic reductions reflecting the loss of photosynthetic functions and associated genes. RESULT This study examines eight plastomes within Cuscuta and reconstructs the phylogenetic relationships among 40 Cuscuta taxa using five other genera as an outgroup. The size of plastid genome varies significantly, with the smallest being 60 kb and the largest 121 kb, highlighting extensive genomic reduction. In special cases, the subgenera Cuscuta exhibit the loss of inverted repeats, distinguishing from them other subge within the Cuscuta genus. This reduction is most pronounced in genes related to photosynthesis, such as atp, pet, psa, psb, and ycf genes, particularly in the subg. Grammica (Lour.) Peter. The study also notes the frequent and independent loss of the plastid genes infA, rpl23, rpl32, rps15, and rps16 across various angiosperm lineages, often involving transfer to the nuclear genome. In parasitic plants like Cuscuta, the ndh genes, crucial for photosynthesis, are often lost. The study also highlights that in the subg. Grammica, the matK and rpo genes, along with trnR-ACG genes, are lost in parallel, indicating that these parasitic plants do not need matK and rpo genes after the loss of ndh genes for survival. Analysis of selective relaxation pressure on plastid genes shows a reductive trend, with genes such as atp, pet, psa, psb, rpo, and ycf progressively becoming pseudogenes over time, with housekeeping genes like rpl and rps expected to follow. However, the pseudogenization process is specific to the subg. Grammica, Pachystigma (Engelm.) Baker & C.H.Wright, and Cuscuta, rather than in the subg. Monogynella (Des Moul.) Peter, Engl. & Prantl (ancient clade species). CONCLUSION The study of Cuscuta plastomes reveals the profound impact of parasitism on genome evolution, highlighting the complex interplay of gene retention and loss through phylogenomic approaches. This research enriches our understanding of plant genome evolution and the intricate host-parasite relationships. It also sheds light on the evolutionary history and genomic adaptations of Cuscuta, illustrating the diverse strategies enabling subg. Grammica, Pachystigma, Cuscuta, and Monogynella thrive as parasitic species. These findings provide valuable insights into the molecular mechanisms underlying parasitism and its impact on plastid genome organization.
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Affiliation(s)
- Sivagami-Jean Claude
- Department of Life Sciences, Gachon University, 1342, Seongnamdaero, Seongnam-Si, Republic of Korea
| | - Kashish Kamra
- Department of Life Sciences, Gachon University, 1342, Seongnamdaero, Seongnam-Si, Republic of Korea
| | - Joonhyung Jung
- Department of Life Sciences, Gachon University, 1342, Seongnamdaero, Seongnam-Si, Republic of Korea
- Division of Forest Biodiversity, Korea National Arboretum, 509, Gwangneungsumogwon-Ro, Pocheon-Si, Republic of Korea
| | - Hye One Kim
- Department of Life Sciences, Gachon University, 1342, Seongnamdaero, Seongnam-Si, Republic of Korea
| | - Joo-Hwan Kim
- Department of Life Sciences, Gachon University, 1342, Seongnamdaero, Seongnam-Si, Republic of Korea.
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22
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Zhao Q, Xie F, He Q, Wang L, Guo K, Zhang C, Wang Y. Whole-genome relaxed selection and molecular constraints in Triplophysa under adapted Qinghai-Tibetan Plateau. BMC Genomics 2025; 26:123. [PMID: 39924476 PMCID: PMC11808961 DOI: 10.1186/s12864-025-11290-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 01/24/2025] [Indexed: 02/11/2025] Open
Abstract
High-altitude environments are inhospitable, but Triplophysa, the largest taxon among the three major fish groups in the Qinghai-Tibetan Plateau (QTP), is an exception. However, the evolutionary profiling of the common ancestor and its contribution to the adaptation of existing QTP native species is unclear.We researched the comparative genomics of Triplophysa species and found that the genome-wide genes of Triplophysa and its ancestry have the characteristics of rapid evolution.Moreover, the rapid evolution of the ancestral genes was caused by relaxed selection. Natural selection analysis showed that more ancestral relaxed selection genes were under strongly purifying selection and showed higher expression in QTP endemic Triplophysa species.The change in natural selection might be associated with the adaptation to QTP. It should be noted that SPT5 homolog, DSIF elongation factor subunit (supt5h) experienced relaxed selection in common ancestral populations of Triplophysa but under purifying selection in extant species, which might be related to hypoxia adaptation of QTP. In summary, the extant species in different environments were used to infer the evolutionary profile of the common ancestor and to identify candidate genes based on changes in natural selection. Our work might provide new clues for understanding adaptation to extreme environments.
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Affiliation(s)
- Qingyuan Zhao
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China.
| | - Fei Xie
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qiuyue He
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lulu Wang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China
| | - Kenan Guo
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China
| | - Cong Zhang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yong Wang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China.
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Méndez MJN, Amini SS, Santos JC, Saal J, Wake MH, Ron SR, Tarvin RD. Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.07.636964. [PMID: 39975400 PMCID: PMC11839130 DOI: 10.1101/2025.02.07.636964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Visual systems are tuned to animals' ecologies, evolving in response to specific light environments and visual needs. Ecological transitions to fossorial lifestyles impose strong selective pressures favoring morphological adaptations for underground life, such as increased skull ossification and reduced eye protrusion. Fossoriality may simultaneously relax constraints on other aspects of vision leading to diminished visual capabilities. Caecilians (Gymnophiona)-specialized, fossorial amphibians-possess reduced eyes covered by skin or bone. For years, these traits, along with the presence of a single photoreceptor expressing one functional opsin gene, have been interpreted as evidence of limited visual capabilities, including an inability to focus or perceive color. Our results challenge these assumptions: we identified the long-wavelength-sensitive (LWS) opsin gene in 11 species of caecilians spanning 8 of 10 recognized families. Molecular evidence indicates that LWS is intact and transcribed in the eye of at least one species (Caecilia orientalis). Anatomical observations from five caecilian families indicate highly organized retinae even in families with vestigial eyes. While the presence of cone cells in our study species remains uncertain, a putatively functional LWS gene suggests that the visual capabilities of caecilians and the role of light perception in their ecology may be underestimated.
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Affiliation(s)
- Maria José Navarrete Méndez
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA 94720
- Department of Biological Sciences, St John's University, NY, USA 11439
| | - Sina S Amini
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA 94720
| | | | - Jacob Saal
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA 94720
| | - Marvalee H Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA 94720
| | - Santiago R Ron
- Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Rebecca D Tarvin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA 94720
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Smith CR, Kaltenegger E, Teisher J, Moore AJ, Straub SCK, Livshultz T. Homospermidine synthase evolution and the origin(s) of pyrrolizidine alkaloids in Apocynaceae. AMERICAN JOURNAL OF BOTANY 2025; 112:e16458. [PMID: 39887714 PMCID: PMC11848025 DOI: 10.1002/ajb2.16458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 10/11/2024] [Accepted: 10/12/2024] [Indexed: 02/01/2025]
Abstract
PREMISE Enzymes that are encoded by paralogous genes and produce identical specialized metabolites in distantly related plant lineages are strong evidence of parallel phenotypic evolution. Inference of phenotypic homology for metabolites produced by orthologous genes is less straightforward, since orthologs may be recruited in parallel into novel pathways. In prior research on pyrrolizidine alkaloids (PAs), specialized metabolites of Apocynaceae, the evolution of homospermidine synthase (HSS), an enzyme of PA biosynthesis, was reconstructed and a single origin of PAs inferred because HSS enzymes of all known PA-producing Apocynaceae species are orthologous and descended from an ancestral enzyme with the motif (VXXXD) of an optimized HSS. METHODS We increased sampling, tested the effect of amino acid motif on HSS function, revisited motif evolution, and tested for selection to infer evolution of HSS function and its correlation with phenotype. RESULTS Some evidence supports a single origin of PAs: an IXXXD HSS-like gene, similar in function to VXXXD HSS, evolved in the shared ancestor of all PA-producing species; loss of HSS function occurred multiple times via pseudogenization and perhaps via evolution of an IXXXN motif. Other evidence indicates multiple origins: the VXXXD motif, highly correlated with the PA phenotype, evolved two or four times independently; the ancestral IXXXD gene was not under positive selection, while some VXXXD genes were; and substitutions at sites experiencing positive selection occurred on multiple branches in the HSS-like gene tree. CONCLUSIONS The complexity of the genotype-function-phenotype map confounds the inference of PA homology from HSS-like gene evolution in Apocynaceae.
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Affiliation(s)
- Chelsea R. Smith
- Botany DepartmentAcademy of Natural Sciences of Drexel UniversityPhiladelphiaPAUSA
- Department of Biodiversity, Earth, and Environmental SciencesDrexel UniversityPhiladelphiaPAUSA
| | - Elisabeth Kaltenegger
- Botanisches Institut und Botanischer GartenChristian‐Albrechts‐Universitӓt zu KielKielGermany
| | - Jordan Teisher
- Botany DepartmentAcademy of Natural Sciences of Drexel UniversityPhiladelphiaPAUSA
- MO Herbarium, Missouri Botanical GardenSt. LouisMOUSA
| | - Abigail J. Moore
- School of Biological Sciences, University of OklahomaNormanOKUSA
| | | | - Tatyana Livshultz
- Botany DepartmentAcademy of Natural Sciences of Drexel UniversityPhiladelphiaPAUSA
- Department of Biodiversity, Earth, and Environmental SciencesDrexel UniversityPhiladelphiaPAUSA
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25
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Arya M, Ghosh A, Tyagi K, Tyagi I, Bisht SS, Kumar V. Characterization of Complete Mitochondrial Genome of Badri Breed of Bos indicus (Bovidae: Bovinae): Selection Pressure and Comparative Analysis. Biochem Genet 2025; 63:43-66. [PMID: 38407767 DOI: 10.1007/s10528-024-10691-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/05/2024] [Indexed: 02/27/2024]
Abstract
High-altitude mammals are often subject to specific environmental obstacles, which exert selective pressure on their physiological and morphological traits, hence driving their evolutionary processes. It is anticipated that these circumstances will lead to the adaptive evolution of protein-coding genes (PCGs) in the mitochondrial genome, which play a crucial role in the oxidative phosphorylation system. In this study, we have generated the complete mitochondrial genome of the Badri breed of Bos indicus inhabiting a high-altitude environment to test the signatures of adaptive evolution on PCGs and their phylogenetic relationships. The complete mitogenome of the Badri breed is 16,339 bp and most tRNAs showed typical clover-leaf secondary structure with a few exceptions, like trnS1 and trnS2 without DHU arm and trnK without DHU loop. Comparative analysis of PCGs indicated that cox1 is the most conserved, while atp6 is the most variable gene. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated the purifying selection (Ka/Ks < 1) in the protein-coding genes that shape the diversity in mitogenome of Bos indicus. Furthermore, Branch-site model (BSM) suggested that cox1, cox2, nad3, nad4L, and nad6 underwent stronger purifying selection (ω < 1) than other PCGs in 15 breeds of 4 species, including Badri. BSM also detected 10 positive sites in PCGs and one in 13 PCGs concatenated dataset. Additional analyses in Datamonkey indicated 11 positive sites and 23 purifying sites in the concatenated dataset, a relaxation of selection strength in nad3, and no evidence of episodic diversifying selection in any PCGs. Phylogeny revealed the sister relationship of the Badri with other breeds of Bos indicus as well as Bos frontalis (Gayal-2). The mitogenome of the Badri breed is an important genomic resource for conservation genetics of this species and also contributes to the understanding of the adaptive evolution of mitochondrial protein coding genes.
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Affiliation(s)
- Mansi Arya
- Department of Zoology, Kumaun University, Nainital, Uttarakhand, India
| | - Abhishek Ghosh
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Inderjeet Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Satpal Singh Bisht
- Department of Zoology, Kumaun University, Nainital, Uttarakhand, India
- Vice Chancellor, Soban Singh Jeena University, Almora, Uttarakahand, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
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26
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York JM, Taylor TN, LaPotin S, Lu Y, Mueller U. Hymenopteran-specific TRPA channel from the Texas leaf cutter ant (Atta texana) is heat and cold activated and expression correlates with environmental temperature. INSECT SCIENCE 2025; 32:301-320. [PMID: 38605428 PMCID: PMC11824891 DOI: 10.1111/1744-7917.13364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/13/2024]
Abstract
Leaf cutting ants of the genus Atta cultivate fungal gardens, carefully modifying environmental conditions to maintain optimal temperature for fungal growth. Antennal nerves from Atta are highly temperature sensitive, but the underlying molecular sensor is unknown. Here, we utilize Atta texana (Texas leaf cutter ant) to investigate the molecular basis of ant temperature sensation and how it might have evolved as the range expanded northeast across Texas from ancestral populations in Mexico. We focus on transient receptor potential (TRP) channel genes, the best characterized temperature sensor proteins in animals. Atta texana antennae express 6 of 13 Hymenopteran TRP channel genes and sequences are under a mix of relaxed and intensified selection. In a behavioral assay, we find A. texana workers prefer 24 °C (range 21-26 °C) for fungal growth. There was no evidence of regulatory evolution across a temperature transect in Texas, but instead Hymenoptera-specific TRPA (HsTRPA) expression highly correlated with ambient temperature. When expressed in vitro, HsTRPA from A. texana is temperature activated with Q10 values exceeding 100 on initial exposure to temperatures above 33 °C. Surprisingly, HsTRPA also appears to be activated by cooling, and therefore to our knowledge, the first non-TRPA1 ortholog to be described with dual heat/cold activation and the first in any invertebrate.
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Affiliation(s)
- Julia M. York
- Department of Evolution, Ecology, and BehaviorUniversity of Illinois Urbana‐ChampaignUrbanaUSA
- Department of Integrative BiologyUniversity of Texas at AustinAustinUSA
- Institute for NeuroscienceUniversity of Texas at AustinAustinUSA
| | - Timothy N. Taylor
- Department of Integrative BiologyUniversity of Texas at AustinAustinUSA
| | - Sarah LaPotin
- Institute for NeuroscienceUniversity of Texas at AustinAustinUSA
- Department of Human GeneticsUniversity of UtahSalt Lake CityUSA
| | - Ying Lu
- Department of Integrative BiologyUniversity of Texas at AustinAustinUSA
- Institute for NeuroscienceUniversity of Texas at AustinAustinUSA
| | - Ulrich Mueller
- Department of Integrative BiologyUniversity of Texas at AustinAustinUSA
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27
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Yang F, Cao LJ, Nguyen P, Ma ZZ, Chen JC, Song W, Wei SJ. Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths. Genome Res 2025; 35:66-77. [PMID: 39762048 PMCID: PMC11789632 DOI: 10.1101/gr.279569.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 11/26/2024] [Indexed: 01/24/2025]
Abstract
Sex chromosomes can expand through fusion with autosomes, thereby acquiring unique evolutionary patterns. In butterflies and moths (Lepidoptera), these sex chromosome-autosome (SA) fusions occur relatively frequently, suggesting possible evolutionary advantages. Here, we investigated how SA fusion affects chromosome features and molecular evolution in leafroller moths (Lepidoptera: Tortricidae). Phylogenomic analysis showed that Tortricidae diverged ∼124 million years ago, accompanied by an SA fusion between the Merian elements M(20 + 17) and MZ. In contrast to partial autosomal fusions, the fused neo-Z Chromosome developed a hierarchical architecture, in which the three elements exhibit heterogeneous sequence features and evolutionary patterns. Specifically, the M17 part had a distinct base composition and chromatin domains. Unlike M20 and MZ, M17 was expressed at the same levels as autosomes in both sexes, compensating for the lost gene dosage in females. Concurrently, the SA fusion drove M17 as an evolutionary hotspot, accelerating the evolution of several genes related to ecological adaptation (e.g., ABCCs) and facilitating the divergence of closely related species, whereas the undercompensated M20 did not show such an effect. Thus, accelerated evolution under a novel pattern of dosage compensation may have favored the adaptive radiation of this group. This study demonstrates the association between a karyotype variant and adaptive evolution and explains the recurrent SA fusion in the Lepidoptera.
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Affiliation(s)
- Fangyuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Institute of Zoology, Chinese Academy of Science, Beijing 100101, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 Ceske Budejovice, Czech Republic
| | - Zhong-Zheng Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wei Song
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China;
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28
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Zeng J, Zhang X, Huang C, Tian S, Zhao H. Dampened TLR2-mediated Inflammatory Signaling in Bats. Mol Biol Evol 2025; 42:msae253. [PMID: 39663845 PMCID: PMC11702297 DOI: 10.1093/molbev/msae253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Revised: 11/29/2024] [Accepted: 12/03/2024] [Indexed: 12/13/2024] Open
Abstract
Bats are considered natural hosts for numerous viruses. Their ability to carry viruses that cause severe diseases or even death in other mammals without falling ill themselves has attracted widespread research attention. Toll-like receptor 2 forms heterodimers with Toll-like receptor 1 or Toll-like receptor 6 on cell membranes, recognizing specific pathogen-associated molecular patterns and playing a key role in innate immune responses. Previous studies have shown that moderate Toll-like receptor 2-mediated immune signals aid in pathogen clearance, while excessive or inappropriate Toll-like receptor 2-mediated immune signals can cause self-damage. In this study, we observed that TLR2, unlike TLR1 or TLR6, has undergone relaxed selection in bats compared with other mammals, indicating a reduced functional constraint on TLR2 specifically in bats. Indeed, our cell-based functional assays demonstrated that the ability of Toll-like receptor 2 to bind with Toll-like receptor 1 or Toll-like receptor 6 was significantly reduced in bats, leading to dampened inflammatory signaling. We identified mutations unique to bats that were responsible for this observation. Additionally, we found that mutations at residues 375 and 376 of Toll-like receptor 2 in the common ancestor of bats also resulted in reduced inflammatory response, suggesting that this reduction occurred early in bat evolution. Together, our study reveals that the Toll-like receptor 2-mediated inflammatory response has been specifically dampened in bats, which may be one of the reasons why they could harbor many viruses without falling ill.
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Affiliation(s)
- Jiaming Zeng
- Key Laboratory of Biodiversity and Environment on the Qinghai–Tibetan Plateau, Ministry of Education, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072 Hubei, China
| | - Xiangyi Zhang
- Key Laboratory of Biodiversity and Environment on the Qinghai–Tibetan Plateau, Ministry of Education, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072 Hubei, China
| | - Chen Huang
- Key Laboratory of Biodiversity and Environment on the Qinghai–Tibetan Plateau, Ministry of Education, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072 Hubei, China
| | - Shilin Tian
- Key Laboratory of Biodiversity and Environment on the Qinghai–Tibetan Plateau, Ministry of Education, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072 Hubei, China
| | - Huabin Zhao
- Key Laboratory of Biodiversity and Environment on the Qinghai–Tibetan Plateau, Ministry of Education, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan 430072 Hubei, China
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29
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Masubuchi T, Chen L, Marcel N, Wen GA, Caron C, Zhang J, Zhao Y, Morris GP, Chen X, Hedrick SM, Lu LF, Wu C, Zou Z, Bui JD, Hui E. Functional differences between rodent and human PD-1 linked to evolutionary divergence. Sci Immunol 2025; 10:eads6295. [PMID: 39752535 PMCID: PMC11774210 DOI: 10.1126/sciimmunol.ads6295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 12/04/2024] [Indexed: 01/30/2025]
Abstract
Mechanistic understanding of the inhibitory immunoreceptor PD-1 is largely based on mouse models, but human and mouse PD-1 share only 59.6% amino acid identity. Here, we found that human PD-1 is more inhibitory than mouse PD-1, owing to stronger interactions with the ligands PD-L1 and PD-L2 and more efficient recruitment of the effector phosphatase Shp2. In a mouse melanoma model with adoptively transferred T cells, humanization of a PD-1 intracellular domain disrupted the antitumor activity of CD8+ T cells and increased the magnitude of anti-PD-1 response. We identified a motif highly conserved across vertebrate PD-1 orthologs, absent in rodents, as a key determinant for differential Shp2 recruitment. Evolutionary analysis suggested that PD-1 underwent a rodent lineage-specific functional attenuation during evolution. Together, our study uncovers species-specific features of the PD-1 pathway, with implications for PD-1 evolution and differential anti-PD-(L)1 responses in mouse models and human patients.
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Affiliation(s)
- Takeya Masubuchi
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Lin Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Nimi Marcel
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - George A. Wen
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Christine Caron
- Department of Pathology, University of California San Diego, La Jolla, CA 92093
| | - Jibin Zhang
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Yunlong Zhao
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Gerald P. Morris
- Department of Pathology, University of California San Diego, La Jolla, CA 92093
| | - Xu Chen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093
| | - Stephen M. Hedrick
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Li-Fan Lu
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhengting Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jack D. Bui
- Department of Pathology, University of California San Diego, La Jolla, CA 92093
| | - Enfu Hui
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
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Barrett CF, Pace MC, Corbett CW, Kennedy AH, Thixton-Nolan HL, Freudenstein JV. Organellar phylogenomics at the epidendroid orchid base, with a focus on the mycoheterotrophic Wullschlaegelia. ANNALS OF BOTANY 2024; 134:1207-1228. [PMID: 38804968 PMCID: PMC11688536 DOI: 10.1093/aob/mcae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND AND AIMS Heterotrophic plants have long been a challenge for systematists, exemplified by the base of the orchid subfamily Epidendroideae, which contains numerous mycoheterotrophic species. METHODS Here we address the utility of organellar genomes in resolving relationships at the epidendroid base, specifically employing models of heterotachy, or lineage-specific rate variation over time. We further conduct comparative analyses of plastid genome evolution in heterotrophs and structural variation in matK. KEY RESULTS We present the first complete plastid genomes (plastomes) of Wullschlaegelia, the sole genus of the tribe Wullschlaegelieae, revealing a highly reduced genome of 37 kb, which retains a fraction of the genes present in related autotrophs. Plastid phylogenomic analyses recovered a strongly supported clade composed exclusively of mycoheterotrophic species with long branches. We further analysed mitochondrial gene sets, which recovered similar relationships to those in other studies using nuclear data, but the placement of Wullschlaegelia remains uncertain. We conducted comparative plastome analyses among Wullschlaegelia and other heterotrophic orchids, revealing a suite of correlated substitutional and structural changes relative to autotrophic species. Lastly, we investigated evolutionary and structural variation in matK, which is retained in Wullschlaegelia and a few other 'late stage' heterotrophs and found evidence for structural conservation despite rapid substitution rates in both Wullschlaegelia and the leafless Gastrodia. CONCLUSIONS Our analyses reveal the limits of what the plastid genome can tell us on orchid relationships in this part of the tree, even when applying parameter-rich heterotachy models. Our study underscores the need for increased taxon sampling across all three genomes at the epidendroid base, and illustrates the need for further research on addressing heterotachy in phylogenomic analyses.
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Affiliation(s)
- Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Matthew C Pace
- New York Botanical Garden, Bronx, New York, NY 10458, USA
| | - Cameron W Corbett
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Aaron H Kennedy
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-APHIS, Beltsville, MD 20705, USA
| | | | - John V Freudenstein
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43212, USA
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31
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Pollard MD, Meyer WK, Puckett EE. Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets. Genome Res 2024; 34:2176-2189. [PMID: 39578099 PMCID: PMC11694762 DOI: 10.1101/gr.278930.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 10/16/2024] [Indexed: 11/24/2024]
Abstract
Mammalia comprises a great diversity of diet types and associated adaptations. An understanding of the genomic mechanisms underlying these adaptations may offer insights for improving human health. Comparative genomic studies of diet that employ taxonomically restricted analyses or simplified diet classifications may suffer reduced power to detect molecular convergence associated with diet evolution. Here, we use a quantitative carnivory score-indicative of the amount of animal protein in the diet-for 80 mammalian species to detect significant correlations between the relative evolutionary rates of genes and changes in diet. We have identified six genes-ACADSB, CLDN16, CPB1, PNLIP, SLC13A2, and SLC14A2-that experienced significant changes in evolutionary constraint alongside changes in carnivory score, becoming less constrained in lineages evolving more herbivorous diets. We further consider the biological functions associated with diet evolution and observe that pathways related to amino acid and lipid metabolism, biological oxidation, and small molecule transport experienced reduced purifying selection as lineages became more herbivorous. Liver and kidney functions show similar patterns of constraint with dietary change. Our results indicate that these functions are important for the consumption of animal matter and become less important with the evolution of increasing herbivory. So, genes expressed in these tissues experience a relaxation of evolutionary constraint in more herbivorous lineages.
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Affiliation(s)
- Matthew D Pollard
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152, USA;
- Center for Biodiversity Research, University of Memphis, Memphis, Tennessee 38152, USA
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Emily E Puckett
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, Tennessee 38152, USA
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32
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Sullivan SA, Orosco JC, Callejas-Hernández F, Blow F, Lee H, Ranallo-Benavidez T, Peters A, Raidal S, Girard YA, Johnson CK, Rogers K, Gerhold R, Mangelson H, Liachko I, Srivastava H, Chandler C, Berenberg D, Bonneau RA, Huang PJ, Yeh YM, Lee CC, Liu H, Tang P, Chen TW, Schatz MC, Carlton JM. Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.22.629724. [PMID: 39763951 PMCID: PMC11703204 DOI: 10.1101/2024.12.22.629724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2025]
Abstract
Trichomonas vaginalis is the causative agent of the venereal disease trichomoniasis which infects men and women globally and is associated with serious outcomes during pregnancy and cancers of the human reproductive tract. Trichomonads parasitize a range of hosts in addition to humans including birds, livestock, and domesticated animals. Recent genetic analysis of trichomonads recovered from columbid birds has provided evidence that these parasite species undergo frequent host-switching, and that a current epoch spillover event from columbids likely gave rise to T. vaginalis in humans. We undertook a comparative evolutionary genomics study of seven trichomonad species, generating chromosome-scale reference genomes for T. vaginalis and its avian sister species Trichomonas stableri, and assemblies of five other species that infect birds and mammals. Human-infecting trichomonad lineages have undergone recent and convergent genome size expansions compared to their avian sister species, and the major contributor to their increased genome size is increased repeat expansions, especially multicopy gene families and transposable elements, with genetic drift likely a driver due to relaxed selection. Trichomonads have independently host-switched twice from birds to humans, and genes implicated in the transition to the human host include those associated with host tissue adherence and phagocytosis, extracellular vesicles, and CAZyme virulence factors.
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Affiliation(s)
- Steven A. Sullivan
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jordan C. Orosco
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Francisco Callejas-Hernández
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Frances Blow
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Hayan Lee
- Department of Computer Science, Johns Hopkins Whiting School of Engineering, 3400 N Charles St Malone Hall 323, Baltimore, MD 21211, USA
| | - Timothy Ranallo-Benavidez
- Department of Computer Science, Johns Hopkins Whiting School of Engineering, 3400 N Charles St Malone Hall 323, Baltimore, MD 21211, USA
| | - Andrew Peters
- Charles Sturt University, The Grange Chancellery, Panorama Avenue, Bathurst, New South Wales, Australia 2795
| | - Shane Raidal
- Charles Sturt University, The Grange Chancellery, Panorama Avenue, Bathurst, New South Wales, Australia 2795
| | - Yvette A. Girard
- One Health Institute, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, Davis, CA, 95616, USA
| | - Christine K. Johnson
- One Health Institute, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, Davis, CA, 95616, USA
| | - Krysta Rogers
- Wildlife Health Laboratory, California Department of Fish & Wildlife, 1701 Nimbus Road, Suite D Rancho Cordova, CA 95670, USA
| | - Richard Gerhold
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Ivan Liachko
- Phase Genomics, 1617 8th Ave N, Seattle, WA 98109, USA
| | - Harsh Srivastava
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chris Chandler
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Daniel Berenberg
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Richard A. Bonneau
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Po-Jung Huang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Chi-Ching Lee
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Hsuan Liu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Petrus Tang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan
| | - Ting-Wen Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins Whiting School of Engineering, 3400 N Charles St Malone Hall 323, Baltimore, MD 21211, USA
| | - Jane M. Carlton
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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33
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Kopania EEK, Thomas GWC, Hutter CR, Mortimer SME, Callahan CM, Roycroft E, Achmadi AS, Breed WG, Clark NL, Esselstyn JA, Rowe KC, Good JM. Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents. Evolution 2024; 79:11-27. [PMID: 39392918 DOI: 10.1093/evolut/qpae146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 09/19/2024] [Accepted: 10/09/2024] [Indexed: 10/13/2024]
Abstract
It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morphology and production. We combined phenotypic and genomic data to perform phylogenetic comparisons of male reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass (RTM), presumably reflecting reduced sperm competition. Several sperm traits were associated with RTM, suggesting that mating system evolution selects for convergent suites of traits related to sperm competitive ability. We predicted that sperm competition would also drive more rapid molecular divergence in species with large testes. Contrary to this, we found that many spermatogenesis genes evolved more rapidly in species with smaller RTM due to relaxed purifying selection. While some reproductive genes evolved rapidly under recurrent positive selection, relaxed selection played a greater role in underlying rapid evolution in small testes species. Our work demonstrates that postcopulatory sexual selection can impose strong purifying selection shaping the evolution of male reproduction and that broad patterns of molecular evolution may help identify genes that contribute to male fertility.
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Affiliation(s)
- Emily E K Kopania
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gregg W C Thomas
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Informatics Group, Harvard University, Cambridge, MA, USA
| | - Carl R Hutter
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | | | - Colin M Callahan
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Emily Roycroft
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Department of Sciences, Museums Victoria Research Institute, Melbourne, VIC, Australia
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Anang S Achmadi
- Museum Zoologicum Bogoriense, Research Center for Biology, Cibinong, Indonesia
| | - William G Breed
- School of Biological Sciences and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Nathan L Clark
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jacob A Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Kevin C Rowe
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Department of Sciences, Museums Victoria Research Institute, Melbourne, VIC, Australia
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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34
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Tom MT, Brand P, Bucks S, Zhang J, Escobar Huezo ME, Hansson BS, Bisch-Knaden S. Gene expansion in the hawkmoth Manduca sexta drives evolution of food-associated odorant receptors. iScience 2024; 27:111317. [PMID: 39640564 PMCID: PMC11617253 DOI: 10.1016/j.isci.2024.111317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 09/30/2024] [Accepted: 10/30/2024] [Indexed: 12/07/2024] Open
Abstract
In insects, odorant receptors (ORs) are required for the detection of most olfactory cues. We investigated the function of a clade of four duplicated ORs in the hawkmoth Manduca sexta and found that these paralogs encode broadly tuned receptors with overlapping but distinct response spectra. Two paralogs, which arose after divergence from a related lineage, show high sensitivity to floral esters released by a nectar-rich plant frequently visited by M. sexta. Functional imaging in mutant moths lacking one of the paralogs suggests that olfactory sensory neurons expressing this OR target a previously identified feeding-associated glomerulus in the primary olfactory center of the brain. However, only the response of this glomerulus to the single ligand unique to the now mutated OR disappeared, suggesting neuronal coexpression of the paralogs. Our results suggest a link between the studied OR expansion and enhanced detection of odors emitted by valuable nectar sources in M. sexta.
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Affiliation(s)
- Megha Treesa Tom
- Department of Evolutionary Neuroethology, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Philipp Brand
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, NY, USA
| | - Sascha Bucks
- Department of Evolutionary Neuroethology, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Jin Zhang
- Department of Evolutionary Neuroethology, Max-Planck Institute for Chemical Ecology, Jena, Germany
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | | | - Bill S. Hansson
- Department of Evolutionary Neuroethology, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Sonja Bisch-Knaden
- Department of Evolutionary Neuroethology, Max-Planck Institute for Chemical Ecology, Jena, Germany
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35
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Siozios S, Nadal-Jimenez P, Azagi T, Sprong H, Frost CL, Parratt SR, Taylor G, Brettell L, Liew KC, Croft L, King KC, Brockhurst MA, Hypša V, Novakova E, Darby AC, Hurst GDD. Genome dynamics across the evolutionary transition to endosymbiosis. Curr Biol 2024; 34:5659-5670.e7. [PMID: 39549700 DOI: 10.1016/j.cub.2024.10.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 04/12/2024] [Accepted: 10/15/2024] [Indexed: 11/18/2024]
Abstract
Endosymbiosis-where a microbe lives and replicates within a host-is an important contributor to organismal function that has accelerated evolutionary innovations and catalyzed the evolution of complex life. The evolutionary processes associated with transitions to endosymbiosis, however, are poorly understood. Here, we leverage the wide diversity of host-associated lifestyles of the genus Arsenophonus to reveal the complex evolutionary processes that occur during the transition to a vertically transmitted endosymbiotic lifestyle from strains maintained solely by horizontal (infectious) transmission. We compared the genomes of 38 strains spanning diverse lifestyles from horizontally transmitted pathogens to obligate interdependent endosymbionts. Among culturable strains, we observed those with vertical transmission had larger genome sizes than closely related horizontally transmitting counterparts, consistent with evolutionary innovation and the rapid gain of new functions. Increased genome size was a consequence of prophage and plasmid acquisition, including a cargo of type III effectors, alongside the concomitant loss of CRISPR-Cas genome defense systems, enabling mobile genetic element expansion. Persistent endosymbiosis was also associated with loss of type VI secretion, which we hypothesize to be a consequence of reduced microbe-microbe competition. Thereafter, the transition to endosymbiosis with strict vertical inheritance was associated with the expected relaxation of purifying selection, gene pseudogenization, metabolic degradation, and genome reduction. We argue that reduced phage predation in endosymbiotic niches drives the loss of genome defense systems driving rapid genome expansion upon the adoption of endosymbiosis and vertical transmission. This remodeling enables rapid horizontal gene transfer-mediated evolutionary innovation and precedes the reductive evolution traditionally associated with adaptation to endosymbiosis.
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Affiliation(s)
- Stefanos Siozios
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L59 7ZB, UK.
| | - Pol Nadal-Jimenez
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L59 7ZB, UK
| | - Tal Azagi
- Centre for Infectious Diseases Research, National Institute for Public Health and the Environment, 3720 BA Bilthoven, the Netherlands
| | - Hein Sprong
- Centre for Infectious Diseases Research, National Institute for Public Health and the Environment, 3720 BA Bilthoven, the Netherlands
| | - Crystal L Frost
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L59 7ZB, UK
| | - Steven R Parratt
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L59 7ZB, UK
| | - Graeme Taylor
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Laura Brettell
- School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK
| | - Kwee Chin Liew
- NSW Health Pathology Infectious Diseases Department, Wollongong Hospital, Wollongong, NSW, Australia
| | - Larry Croft
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, VIC 3216, Australia
| | - Kayla C King
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L59 7ZB, UK; Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology & Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Michael A Brockhurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L59 7ZB, UK; Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Dover Street, Manchester M13 9PT, UK
| | - Václav Hypša
- Department of Parasitology, Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Eva Novakova
- Department of Parasitology, Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Alistair C Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L59 7ZB, UK
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L59 7ZB, UK.
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36
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Zuo B, Chen R, Tang X, Shao Y, Liu X, Nneji LM, Sun Y. Genomic Insights Into Genetic Basis of Evolutionary Conservatism and Innovation in Frogs. Integr Zool 2024. [PMID: 39663509 DOI: 10.1111/1749-4877.12931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 10/12/2024] [Accepted: 11/11/2024] [Indexed: 12/13/2024]
Abstract
Examining closely related species evolving in similar environments offers valuable insights into the mechanisms driving phylogenetic conservatism and evolutionary lability. This can elucidate the intricate relationship between inheritance and environmental factors. Nonetheless, the precise genomic dynamics and molecular underpinnings of this process remain enigmatic. This study explores the evolutionary conservatism and adaptation exhibited by two closely related high-altitude frog species: Nanorana parkeri and N. pleskei. We assembled a high-quality genome for Tibetan N. pleskei and compared it to the genomes of N. parkeri and their lowland relatives. Our findings reveal that these two Tibetan frog species diverged approximately 16.6 million years ago, pointing to a possible ancestral colonization of high-elevation habitats. Following this colonization, significant adaptive evolution occurred in both coding and non-coding regions of the ancestral lineage. This evolution led to notable phenotypic alterations, as evidenced by the reduced body size. Also, due to purifying selection, most ancestral adaptive features persisted in descendant species, indicating a strong element of evolutionary conservatism. However, descendant species evolved novel adaptations to exacerbated environmental challenges in the Tibet Plateau, mainly related to hypoxia response. Furthermore, our analysis underscores the critical role of regulatory variations in descendant adaptive evolution. Notably, hub genes in networks, such as EGLN3, accumulated more variations in regulatory regions as they were transmitted from ancestors to descendants. In sum, our study sheds light on the profound and lasting impact of genetic heritage on species' adaptive evolution.
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Affiliation(s)
- Bin Zuo
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Rongmei Chen
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Xiaolong Tang
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaolong Liu
- School of Life Sciences, Southwest University, Chongqing, China
| | - Lotanna M Nneji
- Department of Biology, Howard University, Washington, DC, USA
| | - Yanbo Sun
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
- Southwest United Graduate School, Kunming, China
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37
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Ward CM, Onetto CA, Borneman AR. Adaptation During the Shift from Entomopathogen to Endosymbiont Is Accompanied by Gene Loss and Intensified Selection. Genome Biol Evol 2024; 16:evae251. [PMID: 39561190 PMCID: PMC11632363 DOI: 10.1093/gbe/evae251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 11/10/2024] [Accepted: 11/14/2024] [Indexed: 11/21/2024] Open
Abstract
Fungi have been found to be associated with many insect species, with some species transitioning to reside within insects as symbionts. However, the evolutionary pressures and genomic consequences associated with this transition are not well understood. Pathogenic fungi of the genus Ophiocordyceps have undergone multiple, independent transitions from pathogen to endosymbiont lifestyles, where they reside within the fatty tissues of infected soft-scale insects transgenerationally without killing their hosts. To gain an understanding of the genomic adaptations underlying this life history shift, long-read sequencing was utilized to assemble the genomes of both the soft-scale insect Parthenolecanium corni and its Ophiocordyceps endosymbiont from a single insect. Assembly and metagenomic-based binning produced a highly contiguous genome for Pa. corni and a chromosome-level assembly for the Ophiocordyceps endosymbiont. The endosymbiont genome was characterized by 524 gene loss events compared to free-living pathogenic Ophiocordyceps relatives, with predicted roles in hyphal growth, cell wall integrity, metabolism, gene regulation, and toxin production. Contrasting patterns of selection were observed between the nuclear and mitochondrial genomes specific to the endosymbiont lineage. Intensified selection was most frequently observed across orthologs in the nuclear genome, whereas selection on most mitochondrial genes was found to be relaxed. Scans for positive selection were enriched within the fatty acid metabolism pathway with endosymbiont specific selection within three adjacent enzymes catalyzing the conversion of acetoacetate to acetyl-coenzyme A, suggesting that the endosymbiont lineage is under selective pressure to effectively exploit the lipid rich environment of the insect fat bodies in which it is found.
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Affiliation(s)
- Chris M Ward
- Australian Wine Research Institute, Glen Osmond, Australia
| | - Cristobal A Onetto
- Australian Wine Research Institute, Glen Osmond, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Anthony R Borneman
- Australian Wine Research Institute, Glen Osmond, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
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38
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Li J, Guo C, Xie M, Wang K, Wang X, Zou B, Hou F, Ran C, Bi S, Xu Y, Hua Y. Genomic signatures of sensory adaptation and evolution in pangolins. BMC Genomics 2024; 25:1176. [PMID: 39633301 PMCID: PMC11616205 DOI: 10.1186/s12864-024-11063-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 11/18/2024] [Indexed: 12/07/2024] Open
Abstract
BACKGROUND Pangolin is one of the most endangered mammals with many peculiar characteristics, yet the understanding of its sensory systems is still superficial. Studying the genomic basis of adaptation and evolution of pangolin's sensory system is expected to provide further potential assistance for their conservation in the future. RESULTS In this study, we performed a comprehensive comparative genomic analysis to explore the signature of sensory adaptation and evolution in pangolins. By comparing with the aardvark, Cape golden mole, and short-beaked echidna, 124 and 152 expanded gene families were detected in the genome of the Chinese and Malayan pangolins, respectively. The enrichment analyses showed olfactory-related genomic convergence among five concerned mammals. We found 769 and 733 intact OR genes, and 704 and 475 OR pseudogenes in the Chinese and Malayan pangolin species, respectively. Compared to other mammals, far more intact members of OR6 and OR14 were identified in pangolins, particularly for four genes with large copy numbers (OR6C2, OR14A2, OR14C36, and OR14L1). On the genome-wide scale, 1,523, 1,887, 1,110, and 2,732 genes were detected under positive selection (PSGs), intensified selection (ISGs), rapid evolution (REGs), and relaxed selection (RSGs) in pangolins. GO terms associated with visual perception were enriched in PSGs, ISGs, and REGs. Those related to rhythm and sound perception were enriched in both ISGs and REGs, ear development and morphogenesis were enriched in ISGs, and mechanical stimulus and temperature adaptation were enriched in RSGs. The convergence of two vision-related PSGs (OPN4 and ATXN7), with more than one parallel substituted site, was detected among five concerned mammals. Additionally, the absence of intact genes of PKD1L3, PKD2L1, and TAS1R2 and just six single-copy TAS2Rs (TAS2R1, TAS2R4, TAS2R7, TAS2R38, TAS2R40, and TAS2R46) were found in pangolins. Interestingly, we found two large insertions in TAS1R3, distributed in the N-terminal ectodomain, just in pangolins. CONCLUSIONS We found new features related to the adaptation and evolution of pangolin-specific sensory characteristics across the genome. These are expected to provide valuable and useful genome-wide genetic information for the future breeding and conservation of pangolins.
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Affiliation(s)
- Jun Li
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China
| | - Ce Guo
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China
| | - Meiling Xie
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China
| | - Kai Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Xianghe Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Bishan Zou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Fanghui Hou
- Guangdong Wildlife Rescue Monitoring Center, Guangzhou, 510520, China
- Pangolin Conservation Research Center of National Forestry and Grassland Administration, Guangzhou, 510520, China
| | - Chongyang Ran
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Shiman Bi
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China.
| | - Yan Hua
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China.
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Santos PKF, Kapheim KM. Convergent Evolution Associated with the Loss of Developmental Diapause May Promote Extended Lifespan in Bees. Genome Biol Evol 2024; 16:evae255. [PMID: 39579066 PMCID: PMC11632380 DOI: 10.1093/gbe/evae255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 11/11/2024] [Accepted: 11/14/2024] [Indexed: 11/25/2024] Open
Abstract
Diapause has long been proposed to play a significant role in the evolution of eusociality in Hymenoptera. Recent studies have shown that shifts in the diapause stage precede social evolution in wasps and bees; however, the genomic basis remains unknown. Given the overlap in molecular pathways that regulate diapause and lifespan, we hypothesized that the evolutionary loss of developmental diapause may lead to extended lifespan among adults, which is a prerequisite for the evolution of eusociality. To test whether the loss of prepupal diapause is followed by genomic changes associated with lifespan extension, we compared 27 bee genomes with or without prepupal diapause. Our results point to several potential mechanisms for lifespan extension in species lacking prepupal diapause, including the loss of the growth hormone PTTH and its receptor TORSO, along with convergent selection in genes known to regulate lifespan in animals. Specifically, we observed purifying selection of prolongevity genes and relaxed selection of antilongevity genes within the IIS/TOR pathway in species that have lost prepupal diapause. Changes in selection pressures on this pathway may lead to the evolution of new phenotypes, such as lifespan extension and altered responses to nutritional signals that are crucial for social evolution.
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Affiliation(s)
| | - Karen M Kapheim
- Department of Biology, Utah State University, Logan, UT 84322, USA
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de Cássia Bisio M, Dos Santos EM, Santos CA, Chahad-Ehlers S, de Brito RA. Molecular evolution and genetic diversity of defective chorion 1 in Anastrepha fraterculus and Anastrepha obliqua (Diptera, Tephritidae). Dev Genes Evol 2024; 234:153-171. [PMID: 39509071 DOI: 10.1007/s00427-024-00723-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 10/17/2024] [Indexed: 11/15/2024]
Abstract
The family Tephritidae comprises numerous fruit fly species, some of which are economically significant, such as several in the genus Anastrepha. Most pest species in this genus belong to the fraterculus group, characterized by closely related species that are difficult to differentiate due to recent divergence and gene flow. Identifying genetic markers for their study is paramount for understanding the group's evolution and eventual phytosanitary control. Because there is variation in eggshell morphology among species in the genus, the study of the rapidly evolving defective chorion 1 (dec-1) gene, which is crucial for chorion formation and reproduction, could provide relevant information for Anastrepha differentiation. We compared transcriptome sequences of dec-1 from two of the most important pest species in the genus, Anastrepha fraterculus and Anastrepha obliqua to dec-1 sequences from Anastrepha ludens, which was used for structure prediction. Furthermore, we amplified a conserved exon across populations of these species. These data revealed three alternative transcripts in A. fraterculus and A. obliqua, consistent with patterns found in other Tephritidae; we obtained orthologous sequences for these other tephritids from NCBI to investigate patterns of selection affecting this gene at different hierarchical levels using different methods. These analyses show a general pattern of purifying selection across the whole gene and throughout its history at different hierarchical levels, from populations to more distantly related species. That notwithstanding, we still found evidence of positive and episodic diversifying selection at different levels. Different parts of the gene have shown distinct evolutionary rates, which were associated with the diverse proproteins produced by posttranslational changes of DEC-1, with proproteins that are incorporated in the chorion earlier in egg formation being in general more conserved than others that are incorporated later. This correlation appears more evident in certain lineages, including the branch that separates Anastrepha, as well as other internal branches that differentiate species within the genus. Our data showed that this gene shows remarkable variation across its different exons, which has proven to be informative at different evolutionary levels. These changes hold promise not only for studying differentiation in Anastrepha but also for the eventual management of selected pest species.
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Affiliation(s)
- Mariana de Cássia Bisio
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Via Washington Luis Km 235, São Carlos, SP, 13565-905, Brazil
| | - Edyane Moraes Dos Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Via Washington Luis Km 235, São Carlos, SP, 13565-905, Brazil
| | - Camilla Alves Santos
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências - Universidade de São Paulo., São Paulo, SP, 05508-090, Brazil
| | - Samira Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Via Washington Luis Km 235, São Carlos, SP, 13565-905, Brazil
| | - Reinaldo Alves de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Via Washington Luis Km 235, São Carlos, SP, 13565-905, Brazil.
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Vazquez JM, Lauterbur ME, Mottaghinia S, Bucci M, Fraser D, Gray-Sandoval G, Gaucherand L, Haidar ZR, Han M, Kohler W, Lama TM, Le Corf A, Loyer C, Maesen S, McMillan D, Li S, Lo J, Rey C, Capel SLR, Singer M, Slocum K, Thomas W, Tyburec JD, Villa S, Miller R, Buchalski M, Vazquez-Medina JP, Pfeffer S, Etienne L, Enard D, Sudmant PH. Extensive longevity and DNA virus-driven adaptation in nearctic Myotis bats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.10.617725. [PMID: 39416019 PMCID: PMC11482938 DOI: 10.1101/2024.10.10.617725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
The genus Myotis is one of the largest clades of bats, and exhibits some of the most extreme variation in lifespans among mammals alongside unique adaptations to viral tolerance and immune defense. To study the evolution of longevity-associated traits and infectious disease, we generated near-complete genome assemblies and cell lines for 8 closely related species of Myotis. Using genome-wide screens of positive selection, analyses of structural variation, and functional experiments in primary cell lines, we identify new patterns of adaptation contributing to longevity, cancer resistance, and viral interactions in bats. We find that Myotis bats have some of the most significant variation in cancer risk across mammals and demonstrate a unique DNA damage response in primary cells of the long-lived M. lucifugus. We also find evidence of abundant adaptation in response to DNA viruses - but not RNA viruses - in Myotis and other bats in sharp contrast with other mammals, potentially contributing to the role of bats as reservoirs of zoonoses. Together, our results demonstrate how genomics and primary cells derived from diverse taxa uncover the molecular bases of extreme adaptations in non-model organisms.
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Affiliation(s)
- Juan M Vazquez
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA USA
- These authors contributed equally
| | - M. Elise Lauterbur
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ USA
- Current affiliation: Department of Biology, University of Vermont, Burlington, VT USA
- These authors contributed equally
| | - Saba Mottaghinia
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, UCBL1, CNRS UMR5308, Ecole Normale Supérieure ENS de Lyon, Université de Lyon, Lyon, France
| | - Melanie Bucci
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ USA
| | - Devaughn Fraser
- Wildlife Genetics Research Unit, Wildlife Health Laboratory, California Department of Fish and Wildlife, Sacramento, CA, United States
- Current affiliation: Wildlife Diversity Program, Wildlife Division, Connecticut Department of Energy and Environmental Protection, Burlington, CT, United States
| | | | - Léa Gaucherand
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Zeinab R Haidar
- Department of Biology, California State Polytechnic University, Humboldt, Arcata, CA USA
- Current affiliation: Western EcoSystems Technology Inc, Cheyenne, WY USA
| | - Melissa Han
- Department of Pathology and Clinical Laboratories, University of Michigan, Ann Arbor, MI USA
| | - William Kohler
- Department of Pathology and Clinical Laboratories, University of Michigan, Ann Arbor, MI USA
| | - Tanya M. Lama
- Department of Biological Sciences, Smith College, Northampton, MA USA
| | - Amandine Le Corf
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, UCBL1, CNRS UMR5308, Ecole Normale Supérieure ENS de Lyon, Université de Lyon, Lyon, France
| | - Clara Loyer
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, UCBL1, CNRS UMR5308, Ecole Normale Supérieure ENS de Lyon, Université de Lyon, Lyon, France
| | - Sarah Maesen
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, UCBL1, CNRS UMR5308, Ecole Normale Supérieure ENS de Lyon, Université de Lyon, Lyon, France
| | - Dakota McMillan
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA USA
- Department of Science and Biotechnology, Berkeley City College, Berkeley, CA USA
| | - Stacy Li
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA USA
| | - Johnathan Lo
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA USA
| | - Carine Rey
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, UCBL1, CNRS UMR5308, Ecole Normale Supérieure ENS de Lyon, Université de Lyon, Lyon, France
| | - Samantha LR Capel
- Current affiliation: Wildlife Diversity Program, Wildlife Division, Connecticut Department of Energy and Environmental Protection, Burlington, CT, United States
| | - Michael Singer
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA USA
| | | | - William Thomas
- Department of Ecology and Evolution, Stony Brook University, Stony Brook NY USA
| | | | - Sarah Villa
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA USA
| | - Richard Miller
- Department of Pathology and Clinical Laboratories, University of Michigan, Ann Arbor, MI USA
| | - Michael Buchalski
- Wildlife Genetics Research Unit, Wildlife Health Laboratory, California Department of Fish and Wildlife, Sacramento, CA, United States
| | | | - Sébastien Pfeffer
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Lucie Etienne
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, UCBL1, CNRS UMR5308, Ecole Normale Supérieure ENS de Lyon, Université de Lyon, Lyon, France
- Senior author
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ USA
- Senior author
- These authors contributed equally
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA USA
- Senior author
- These authors contributed equally
- Lead contact
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Zarate S, Bertram MR, Rodgers C, Reed K, Pelzel-McCluskey A, Gomez-Romero N, Rodriguez LL, Mayo C, Mire C, Pond SLK, Velazquez-Salinas L. Phylogenomic Signatures of a Lineage of Vesicular Stomatitis Indiana Virus Circulating During the 2019-2020 Epidemic in the United States. Viruses 2024; 16:1803. [PMID: 39599917 PMCID: PMC11598840 DOI: 10.3390/v16111803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 11/14/2024] [Accepted: 11/15/2024] [Indexed: 11/29/2024] Open
Abstract
For the first time, we describe phylogenomic signatures of an epidemic lineage of vesicular stomatitis Indiana virus (VSIV). We applied multiple evolutionary analyses to a dataset of 87 full-length genome sequences representing the circulation of an epidemic VSIV lineage in the US between 2019 and 2020. Based on phylogenetic analyses, we predicted the ancestral relationship of this lineage with a specific group of isolates circulating in the endemic zone of Chiapas, Mexico. Subsequently, our findings indicate that the lineage diversified into at least four different subpopulations during its circulation in the US. We identified single nucleotide polymorphisms (SNPs) that differentiate viral subpopulations and assessed their potential relevance using comparative phylogenetic methods, highlighting the preponderance of synonymous mutations during the differentiation of these populations. Purifying selection was the main evolutionary force favoring the conservation of this epidemic phenotype, with P and G genes as the main drivers of the evolution of this lineage. Our analyses identified multiple codon sites under positive selection and the association of these sites with specific functional domains at P, M, G, and L proteins. Based on ancestral reconstruction analyses, we showed the potential relevance of some of the sites identified under positive selection to the adaptation of the epidemic lineage at the population level. Finally, using a representative group of viruses from Colorado, we established a positive correlation between genetic and geographical distances, suggesting that positive selection on specific codon positions might have favored the adaptation of different subpopulations to circulation in specific geographical settings. Collectively, our study reveals the complex dynamics that accompany the evolution of an epidemic lineage of VSIV in nature. Our analytical framework provides a model for conducting future evolutionary analyses. The ultimate goal is to support the implementation of an early warning system for vesicular stomatitis virus in the US, enabling early detection of epidemic precursors from Mexico.
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Affiliation(s)
- Selene Zarate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de Mexico, Ciudad de Mexico 03100, Mexico
| | - Miranda R. Bertram
- National Bio-and Agro-defense Facility, Agricultural Research Services, United States Department of Agriculture, Manhattan, KS 66506, USA; (M.R.B.); (L.L.R.); (C.M.)
| | - Case Rodgers
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA; (C.R.); (K.R.); (C.M.)
| | - Kirsten Reed
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA; (C.R.); (K.R.); (C.M.)
| | - Angela Pelzel-McCluskey
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Fort Collins, CO 80521, USA;
| | - Ninnet Gomez-Romero
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Av. Universidad No. 3000 Col Copilco Universidad, Mexico City 14510, Mexico;
| | - Luis L. Rodriguez
- National Bio-and Agro-defense Facility, Agricultural Research Services, United States Department of Agriculture, Manhattan, KS 66506, USA; (M.R.B.); (L.L.R.); (C.M.)
| | - Christie Mayo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA; (C.R.); (K.R.); (C.M.)
| | - Chad Mire
- National Bio-and Agro-defense Facility, Agricultural Research Services, United States Department of Agriculture, Manhattan, KS 66506, USA; (M.R.B.); (L.L.R.); (C.M.)
| | - Sergei L. Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Lauro Velazquez-Salinas
- National Bio-and Agro-defense Facility, Agricultural Research Services, United States Department of Agriculture, Manhattan, KS 66506, USA; (M.R.B.); (L.L.R.); (C.M.)
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Magpali L, Ramos E, Picorelli A, Freitas L, Nery MF. Molecular evolution of toothed whale genes reveals adaptations to echolocating in different environments. BMC Genomics 2024; 25:1049. [PMID: 39506652 PMCID: PMC11542384 DOI: 10.1186/s12864-024-10910-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 10/16/2024] [Indexed: 11/08/2024] Open
Abstract
BACKGROUND Echolocation was a key development in toothed whale evolution, enabling their adaptation and diversification across various environments. Previous bioacoustic and morphological studies suggest that environmental pressures have influenced the evolution of echolocation in toothed whales. This hypothesis demands further investigation, especially regarding the molecular mechanisms involved in the adaptive radiation of toothed whales across multiple habitats. Here we show that the coding sequences of four hearing genes involved in echolocation (CDH23, prestin, TMC1, and CLDN14) have different signatures of molecular evolution among riverine, coastal, and oceanic dolphins, suggesting that the evolutionary constraints of these habitats shaped the underlying genetic diversity of the toothed whale sonar. RESULTS Our comparative analysis across 37 odontocete species revealed patterns of accelerated evolution within coastal and riverine lineages, supporting the hypothesis that shallow habitats pose specific selective pressures to sonar propagation, which are not found in the deep ocean. All toothed whales with genes evolving under positive selection are shallow coastal species, including three species that have recently diverged from freshwater lineages (Cephalorhynchus commersonii, Sotalia guianensis, and Orcaella heinsohni - CDH23), and three species that operate specialized Narrow Band High Frequency (NBHF) Sonars (Phocoena sinus - prestin, Neophocaena phocaenoides - TMC1 and Cephalorhynchus commersonii - CDH23). For river dolphins and deep-diving toothed whales, we found signatures of positive selection and molecular convergence affecting specific sites on CDH23, TMC1, and prestin. Positively selected sites (PSS) were different in number, identity, and substitution rates (dN/dS) across riverine, coastal, and oceanic toothed whales. CONCLUSION Here we shed light on potential molecular mechanisms underlying the diversification of toothed whale echolocation. Our results suggest that toothed whale hearing genes changed under different selective pressures in coastal, riverine, and oceanic environments.
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Affiliation(s)
- L Magpali
- Laboratório de Genômica Evolutiva, Departamento de Genética, Microbiologia e Imunologia, Universidade Estadual de Campinas (Unicamp), Evolução, Campinas, São Paulo, Brasil
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - E Ramos
- Laboratório de Genômica Evolutiva, Departamento de Genética, Microbiologia e Imunologia, Universidade Estadual de Campinas (Unicamp), Evolução, Campinas, São Paulo, Brasil
- Zoological Institute, Department of Environmental Science, University of Basel, Basel, Switzerland
- Natural History Museum Basel, Basel, Switzerland
| | - A Picorelli
- Laboratório de Genômica Evolutiva, Departamento de Genética, Microbiologia e Imunologia, Universidade Estadual de Campinas (Unicamp), Evolução, Campinas, São Paulo, Brasil
| | - L Freitas
- Laboratório de Genômica Evolutiva, Departamento de Genética, Microbiologia e Imunologia, Universidade Estadual de Campinas (Unicamp), Evolução, Campinas, São Paulo, Brasil
| | - M F Nery
- Laboratório de Genômica Evolutiva, Departamento de Genética, Microbiologia e Imunologia, Universidade Estadual de Campinas (Unicamp), Evolução, Campinas, São Paulo, Brasil.
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Low GW, Pavlova A, Gan HM, Ko MC, Sadanandan KR, Lee YP, Amos JN, Austin L, Falk S, Dowling DK, Sunnucks P. Accelerated differentiation of neo-W nuclear-encoded mitochondrial genes between two climate-associated bird lineages signals potential co-evolution with mitogenomes. Heredity (Edinb) 2024; 133:342-354. [PMID: 39174672 PMCID: PMC11527876 DOI: 10.1038/s41437-024-00718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
There is considerable evidence for mitochondrial-nuclear co-adaptation as a key evolutionary driver. Hypotheses regarding the roles of sex-linkage have emphasized Z-linked nuclear genes with mitochondrial function (N-mt genes), whereas it remains contentious whether the perfect co-inheritance of W genes with mitogenomes could hinder or facilitate co-adaptation. Young (neo-) sex chromosomes that possess relatively many N-mt genes compared to older chromosomes provide unprecedented hypothesis-testing opportunities. Eastern Yellow Robin (EYR) lineages in coastal and inland habitats with different climates are diverged in mitogenomes, and in a ~ 15.4 Mb nuclear region enriched with N-mt genes, in contrast with otherwise-similar nuclear genomes. This nuclear region maps to passerine chromosome 1A, previously found to be neo-sex in the inland EYR genome. To compare sex-linked Chr1A-derived genes between lineages, we assembled and annotated the coastal EYR genome. We found that: (i) the coastal lineage shares a similar neo-sex system with the inland lineage, (ii) neo-W and neo-Z N-mt genes are not more diverged between lineages than are comparable non-N-mt genes, and showed little evidence for broad positive selection, (iii) however, W-linked N-mt genes are more diverged between lineages than are their Z-linked gametologs. The latter effect was ~7 times stronger for N-mt than non-N-mt genes, suggesting that W-linked N-mt genes might have diverged between lineages under environmental selection through co-evolution with mitogenomes. Finally, we identify a candidate gene driver for divergent selection, NDUFA12. Our data represent a rare example suggesting a possible role for W-associated mitochondrial-nuclear interactions in climate-associated adaptation and lineage differentiation.
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Affiliation(s)
- Gabriel Weijie Low
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany.
- National Parks Board, 1 Cluny Road, Singapore Botanical Gardens, Singapore, 259569, Singapore.
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- Patriot Biotech Sdn Bhd, 47500, Subang Jaya, Selangor, Malaysia
| | - Meng-Ching Ko
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany
| | - Keren R Sadanandan
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany
| | - Yin Peng Lee
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220, Australia
| | - J Nevil Amos
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Arthur Rylah Institute for Environmental Research, Heidelberg, VIC 3084, Australia
| | - Lana Austin
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Stephanie Falk
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
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Ruesink-Bueno IL, Drews A, O’Connor EA, Westerdahl H. Expansion of MHC-IIB Has Constrained the Evolution of MHC-IIA in Passerines. Genome Biol Evol 2024; 16:evae236. [PMID: 39462092 PMCID: PMC11562119 DOI: 10.1093/gbe/evae236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 09/22/2024] [Accepted: 10/17/2024] [Indexed: 10/29/2024] Open
Abstract
The major histocompatibility complex (MHC) is central in adaptive immunity, with the highly polymorphic MHC genes encoding antigen-presenting molecules. Two MHC class II (MHC-II) loci, DA1 and DA2, predate the radiation of extant birds and persist throughout much of the avian phylogeny. Within each locus, the MHC-II molecules are encoded by A-genes (DAA) and B-genes (DAB), which are arranged in A-B dyads. However, in passerines (order Passeriformes), the DA2 locus has been lost, and the ancestral A-B dyad at the DA1 locus has been replaced by a putatively single A-gene (DAA1) and an array of highly polymorphic B-genes (DAB1). In this study, we genotyped the DAA1 gene of 15 passerine species and confirmed that passerines possess just one copy of DAA1. We then compared selection patterns in DAA1 between passerines and nonpasserines and found that exon 2, which encodes the antigen-presenting domain, has been subject to weaker positive selection and stronger negative selection in passerines compared with nonpasserines. Additional comparisons showed that the patterns of selection in the passerine DAA1 gene are unlikely to be related to the loss of the DA2 locus. Instead, our findings suggest that the expansion of DAB1 (MHC-IIB) has imposed an evolutionary constraint on the passerine DAA1 (MHC-IIA) gene. We speculate that this constraint may be the result of each DAA1 chain forming heterodimers with many different DAB1 chains.
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Affiliation(s)
| | - Anna Drews
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Emily Amelia O’Connor
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Helena Westerdahl
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
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Calamari ZT, Song A, Cohen E, Akter M, Das Roy R, Hallikas O, Christensen MM, Li P, Marangoni P, Jernvall J, Klein OD. Bank vole genomics links determinate and indeterminate growth of teeth. BMC Genomics 2024; 25:1000. [PMID: 39472825 PMCID: PMC11523675 DOI: 10.1186/s12864-024-10901-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Accepted: 10/14/2024] [Indexed: 11/02/2024] Open
Abstract
BACKGROUND Continuously growing teeth are an important innovation in mammalian evolution, yet genetic regulation of continuous growth by stem cells remains incompletely understood. Dental stem cells responsible for tooth crown growth are lost at the onset of tooth root formation. Genetic signaling that initiates this loss is difficult to study with the ever-growing incisor and rooted molars of mice, the most common mammalian dental model species, because signals for root formation overlap with signals that pattern tooth size and shape (i.e., cusp patterns). Bank and prairie voles (Cricetidae, Rodentia, Glires) have evolved rooted and unrooted molars while retaining similar size and shape, providing alternative models for studying roots. RESULTS We assembled a de novo genome of Myodes glareolus, a vole with high-crowned, rooted molars, and performed genomic and transcriptomic analyses in a broad phylogenetic context of Glires (rodents and lagomorphs) to assess differential selection and evolution in tooth forming genes. Bulk transcriptomics comparisons of embryonic molar development between bank voles and mice demonstrated overall conservation of gene expression levels, with species-specific differences corresponding to the accelerated and more extensive patterning of the vole molar. We leverage convergent evolution of unrooted molars across the clade to examine changes that may underlie the evolution of unrooted molars. We identified 15 dental genes with changing synteny relationships and six dental genes undergoing positive selection across Glires, two of which were undergoing positive selection in species with unrooted molars, Dspp and Aqp1. Decreased expression of both genes in prairie voles with unrooted molars compared to bank voles supports the presence of positive selection and may underlie differences in root formation. CONCLUSIONS Our results support ongoing evolution of dental genes across Glires and identify candidate genes for mechanistic studies of root formation. Comparative research using the bank vole as a model species can reveal the complex evolutionary background of convergent evolution for ever-growing molars.
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Affiliation(s)
- Zachary T Calamari
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY, 10010, USA.
- The Graduate Center, City University of New York, 365 Fifth Ave, New York, NY, 10016, USA.
- Program in Craniofacial Biology, Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
| | - Andrew Song
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY, 10010, USA
- Cornell University, 616 Thurston Ave, Ithaca, NY, 14853, USA
| | - Emily Cohen
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY, 10010, USA
- New York University College of Dentistry, 345 E 34th St, New York, NY, 10010, USA
| | - Muspika Akter
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY, 10010, USA
| | - Rishi Das Roy
- Institute of Biotechnology, University of Helsinki, Helsinki, FI-00014, Finland
| | - Outi Hallikas
- Institute of Biotechnology, University of Helsinki, Helsinki, FI-00014, Finland
| | - Mona M Christensen
- Institute of Biotechnology, University of Helsinki, Helsinki, FI-00014, Finland
| | - Pengyang Li
- Program in Craniofacial Biology, Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children's, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA, 90048, USA
- Department of Bioengineering, Stanford University, 443 Via Ortega, Rm 119, Stanford, CA, 94305, USA
| | - Pauline Marangoni
- Program in Craniofacial Biology, Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children's, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA, 90048, USA
| | - Jukka Jernvall
- Institute of Biotechnology, University of Helsinki, Helsinki, FI-00014, Finland
- Department of Geosciences and Geography, University of Helsinki, Helsinki, FI-00014, Finland
| | - Ophir D Klein
- Program in Craniofacial Biology, Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Department of Pediatrics, Cedars-Sinai Guerin Children's, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA, 90048, USA.
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Borujeni PM, Salavati R. Revisiting the functional annotation of TriTryp using sequence similarity tools. Heliyon 2024; 10:e39243. [PMID: 39640808 PMCID: PMC11620254 DOI: 10.1016/j.heliyon.2024.e39243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 09/24/2024] [Accepted: 10/10/2024] [Indexed: 12/07/2024] Open
Abstract
Trypanosomatids are the causative agents of deadly diseases in humans and livestock. Given the high phylogenetic distance of trypanosomatids from model organisms, these organisms have ample unannotated genes. Manual functional annotation is time-consuming, highlighting the importance of automated functional annotation tools. The development of automated functional tools is a hot research topic, and multiple tools have been developed for the task. PANNZER2 is an automated functional annotation tool that merely relies on the sequence similarity of the query to the annotated proteins. We tried PANNZER2 on Trypanosoma brucei, the most studied organism among trypanosomatids, to see if it could improve our knowledge of the functions of the genes. Even with the availability of automated annotation tools like InterPro2GO in databases such as TriTrypDB, PANNZER2 has made surprisingly confident predictions for some hypothetical proteins in T. brucei. In this study, we identify gaps in such annotations because of not employing pairwise sequence alignment tools in TriTrypDB's automated annotation process. Our findings demonstrate that even the use of stringent cutoffs can successfully annotate a significant number of proteins. Additionally, we discovered that adjusting the open reading frames in certain genes leads to sequences with increased sequence signature coverage-characterized by the length covered by at least one sequence signature-compared to the original sequences. This enhanced sequence signature coverage suggests these genomic fragments could be pseudogenes. To facilitate further exploration, we developed a script to help identify potential pseudogenes within an organism's genome, offering researchers a new tool for genomic analysis and understanding. We extended all our analysis to Trypanosoma cruzi and Leishmania major to assess the impact of this approach across different species. Our study demonstrates that by utilizing pairwise sequence similarity alignment, even with stringent cutoffs, we can attribute 2986, 3953, and 3798 new GO terms to the genomes of T. brucei, T. cruzi, and L. major. Additionally, we found that 210, 239, and 29 genes exhibit increased sequence signature coverage following frame correction, suggesting the presence of pseudogenes.
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Affiliation(s)
| | - Reza Salavati
- Institute of Parasitology, McGill University, Canada
- Department of Biochemistry, McGill University, Canada
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48
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Doellman MM, Sun Y, Barcenas-Peña A, Lumbsch HT, Grewe F. Rethinking asexuality: the enigmatic case of functional sexual genes in Lepraria (Stereocaulaceae). BMC Genomics 2024; 25:1003. [PMID: 39455957 PMCID: PMC11515122 DOI: 10.1186/s12864-024-10898-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024] Open
Abstract
BACKGROUND The ubiquity of sex across eukaryotes, given its high costs, strongly suggests it is evolutionarily advantageous. Asexual lineages can avoid, for example, the risks and energetic costs of recombination, but suffer short-term reductions in adaptive potential and long-term damage to genome integrity. Despite these costs, lichenized fungi have frequently evolved asexual reproduction, likely because it allows the retention of symbiotic algae across generations. The lichenized fungal genus Lepraria is thought to be exclusively asexual, while its sister genus Stereocaulon completes a sexual reproductive cycle. A comparison of sister sexual and asexual clades should shed light on the evolution of asexuality in lichens in general, as well as the apparent long-term maintenance of asexuality in Lepraria, specifically. RESULTS In this study, we assembled and annotated representative long-read genomes from the putatively asexual Lepraria genus and its sexual sister genus Stereocaulon, and added short-read assemblies from an additional 22 individuals across both genera. Comparative genomic analyses revealed that both genera were heterothallic, with intact mating-type loci of both idiomorphs present across each genus. Additionally, we identified and assessed 29 genes involved in meiosis and mitosis and 45 genes that contribute to formation of fungal sexual reproductive structures (ascomata). All genes were present and appeared functional in nearly all Lepraria, and we failed to identify a general pattern of relaxation of selection on these genes across the Lepraria lineage. Together, these results suggest that Lepraria may be capable of sexual reproduction, including mate recognition, meiosis, and production of ascomata. CONCLUSIONS Despite apparent maintenance of machinery essential for fungal sex, over 200 years of careful observations by lichenologists have produced no evidence of canonical sexual reproduction in Lepraria. We suggest that Lepraria may have instead evolved a form of parasexual reproduction, perhaps by repurposing MAT and meiosis-specific genes. This may, in turn, allow these lichenized fungi to avoid long-term consequences of asexuality, while maintaining the benefit of an unbroken bond with their algal symbionts.
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Affiliation(s)
- Meredith M Doellman
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL, 60605, USA
| | - Yukun Sun
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL, 60605, USA
| | - Alejandrina Barcenas-Peña
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL, 60605, USA
| | - H Thorsten Lumbsch
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL, 60605, USA
| | - Felix Grewe
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL, 60605, USA.
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49
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Farrand ZM, Galbreath KE, Teeter KC. Evidence of Intraspecific Adaptive Variation in the American Pika (Ochotona princeps) on a Continental Scale Using a Target Enrichment and Mitochondrial Genome Skimming Approach. Mol Ecol 2024:e17557. [PMID: 39425616 DOI: 10.1111/mec.17557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/23/2024] [Accepted: 09/26/2024] [Indexed: 10/21/2024]
Abstract
Montane landscapes present an array of abiotic challenges that drive adaptive evolution amongst organisms. These adaptations can promote habitat specialisation, which may heighten the risk of extirpation from environmental change. For example, higher metabolic rates in an endothermic species may contribute to heightened cold tolerance, whilst simultaneously limiting heat tolerance. Here, using the climate-sensitive American pika (Ochotona princeps), we test for evidence of intraspecific adaptive variation amongst environmental gradients across the Intermountain West of North America. We leveraged results from previous studies on pika adaptation to generate a custom nuclear target enrichment design to sequence several hundred candidate genes related to cold, hypoxia and dietary detoxification. We also applied a 'genome skimming' approach to sequence mitochondrial DNA. Using genotype-environment association tests, we identified rare genomic variants associated with elevation and temperature variation amongst populations. Amongst mitochondrial genes, we identified intraspecific variation in selective signals and significant changes to the amino acid property equilibrium constant, which may relate to electron transport chain efficiency. These results illustrate a complex dynamic of adaptive variation amongst O. princeps where lineages and populations have adapted to unique regional conditions. Some of the clearest signals of selection were in a genetic lineage that includes pikas of the Great Basin region, which is also where recent localised extirpations have taken place and highlights the risk of losing adaptive alleles during environmental change.
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Affiliation(s)
- Zachery M Farrand
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biology, Northern Michigan University, Marquette, Michigan, USA
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, Michigan, USA
| | - Katherine C Teeter
- Department of Biology, Northern Michigan University, Marquette, Michigan, USA
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50
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Cicconardi F, Morris BJ, Martelossi J, Ray DA, Montgomery SH. Novel Sex-Specific Genes and Diverse Interspecific Expression in the Antennal Transcriptomes of Ithomiine Butterflies. Genome Biol Evol 2024; 16:evae218. [PMID: 39373182 PMCID: PMC11500719 DOI: 10.1093/gbe/evae218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/08/2024] Open
Abstract
The olfactory sense is crucial for organisms, facilitating environmental recognition and interindividual communication. Ithomiini butterflies exemplify this importance not only because they rely strongly on olfactory cues for both inter- and intra-sexual behaviors, but also because they show convergent evolution of specialized structures within the antennal lobe, called macroglomerular complexes (MGCs). These structures, widely absent in butterflies, are present in moths where they enable heightened sensitivity to, and integration of, information from various types of pheromones. In this study, we investigate chemosensory evolution across six Ithomiini species and identify possible links between expression profiles and neuroanatomical. To enable this, we sequenced four new high-quality genome assemblies and six sex-specific antennal transcriptomes for three of these species with different MGC morphologies. With extensive genomic analyses, we found that the expression of antennal transcriptomes across species exhibit profound divergence, and identified highly expressed ORs, which we hypothesize may be associated to MGCs, as highly expressed ORs are absent in Methona, an Ithomiini lineage which also lacks MGCs. More broadly, we show how antennal sexual dimorphism is prevalent in both chemosensory genes and non-chemosensory genes, with possible relevance for behavior. As an example, we show how lipid-related genes exhibit consistent sexual dimorphism, potentially linked to lipid transport or host selection. In this study, we investigate the antennal chemosensory adaptations, suggesting a link between genetic diversity, ecological specialization, and sensory perception with the convergent evolution of MCGs. Insights into chemosensory gene evolution, expression patterns, and potential functional implications enhance our knowledge of sensory adaptations and sexual dimorphisms in butterflies, laying the foundation for future investigations into the genetic drivers of insect behavior, adaptation, and speciation.
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Affiliation(s)
- Francesco Cicconardi
- School of Biological Sciences, Bristol University, 24 Tyndall Ave, Bristol BS8 1TQ, UK
| | - Billy J Morris
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Jacopo Martelossi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Stephen H Montgomery
- School of Biological Sciences, Bristol University, 24 Tyndall Ave, Bristol BS8 1TQ, UK
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