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Ferguson S, Jones A, Murray K, Andrew R, Schwessinger B, Borevitz J. Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence. Genome Res 2024; 34:606-619. [PMID: 38589251 PMCID: PMC11146599 DOI: 10.1101/gr.277999.123] [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: 04/19/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024]
Abstract
Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly gene expression and reproduction. Despite the need to conserve genome architecture, a high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. However, within plant genomes, the processes of genome architecture divergence are not well described. Here we use long-read sequencing and de novo assembly of 33 phylogenetically diverse, wild and naturally evolving Eucalyptus species, covering 1-50 million years of diverging genome evolution to measure genome architectural conservation and describe architectural divergence. The investigation of these genomes revealed that following lineage divergence, genome architecture is highly fragmented by rearrangements. As genomes continue to diverge, the accumulation of mutations and the subsequent divergence beyond recognition of rearrangements become the primary driver of genome divergence. The loss of syntenic regions also contribute to genome divergence but at a slower pace than that of rearrangements. We hypothesize that duplications and translocations are potentially the greatest contributors to Eucalyptus genome divergence.
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Affiliation(s)
- Scott Ferguson
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia;
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia;
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- Weigel Department, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Rose Andrew
- Botany & N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
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2
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Schmutzer M, Dasmeh P, Wagner A. Frustration can Limit the Adaptation of Promiscuous Enzymes Through Gene Duplication and Specialisation. J Mol Evol 2024; 92:104-120. [PMID: 38470504 PMCID: PMC10978624 DOI: 10.1007/s00239-024-10161-4] [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: 10/07/2023] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
Abstract
Virtually all enzymes catalyse more than one reaction, a phenomenon known as enzyme promiscuity. It is unclear whether promiscuous enzymes are more often generalists that catalyse multiple reactions at similar rates or specialists that catalyse one reaction much more efficiently than other reactions. In addition, the factors that shape whether an enzyme evolves to be a generalist or a specialist are poorly understood. To address these questions, we follow a three-pronged approach. First, we examine the distribution of promiscuity in empirical enzymes reported in the BRENDA database. We find that the promiscuity distribution of empirical enzymes is bimodal. In other words, a large fraction of promiscuous enzymes are either generalists or specialists, with few intermediates. Second, we demonstrate that enzyme biophysics is not sufficient to explain this bimodal distribution. Third, we devise a constraint-based model of promiscuous enzymes undergoing duplication and facing selection pressures favouring subfunctionalization. The model posits the existence of constraints between the catalytic efficiencies of an enzyme for different reactions and is inspired by empirical case studies. The promiscuity distribution predicted by our constraint-based model is consistent with the empirical bimodal distribution. Our results suggest that subfunctionalization is possible and beneficial only in certain enzymes. Furthermore, the model predicts that conflicting constraints and selection pressures can cause promiscuous enzymes to enter a 'frustrated' state, in which competing interactions limit the specialisation of enzymes. We find that frustration can be both a driver and an inhibitor of enzyme evolution by duplication and subfunctionalization. In addition, our model predicts that frustration becomes more likely as enzymes catalyse more reactions, implying that natural selection may prefer catalytically simple enzymes. In sum, our results suggest that frustration may play an important role in enzyme evolution.
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Affiliation(s)
- Michael Schmutzer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pouria Dasmeh
- Center for Human Genetics, Philipps University of Marburg, Marburg, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Santa Fe Institute, Santa Fe, NM, USA.
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3
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Evans-Yamamoto D, Dubé AK, Saha G, Plante S, Bradley D, Gagnon-Arsenault I, Landry CR. Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event. Mol Biol Evol 2023; 40:msad246. [PMID: 37979156 PMCID: PMC10699747 DOI: 10.1093/molbev/msad246] [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: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
Whole-genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast family Saccharomycetaceae, HRR25 is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy in Saccharomyces cerevisiae where it is now essential, but has been maintained as pairs in at least 7 species post-WGD. In S. cerevisiae, HRR25 encodes the casein kinase 1δ/ε and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicated HRR25 ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay in S. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post-WGD and non-WGD species, and have nonconserved cellular localization, consistent with their ongoing loss of function. The analysis in Naumovozyma castellii shows that the noncomplementing ohnolog is expressed at a lower level and has become nonessential. Taken together, our results indicate that HRR25 orthologs are undergoing gradual nonfunctionalization.
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Affiliation(s)
- Daniel Evans-Yamamoto
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Gourav Saha
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani K K Birla Goa Campus, South Goa, India
| | - Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
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4
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Jia GS, Zhang WC, Liang Y, Liu XH, Rhind N, Pidoux A, Brysch-Herzberg M, Du LL. A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus. G3 (BETHESDA, MD.) 2023; 13:jkad028. [PMID: 36748990 PMCID: PMC10085805 DOI: 10.1093/g3journal/jkad028] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/08/2023]
Abstract
Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes of S. pombe and 3 other fission yeast species S. japonicus, S. octosporus, and S. cryophilus has enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast species S. osmophilus and obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5,098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed that S. osmophilus is most closely related to S. octosporus and these 2 species diverged around 16 million years ago. To demonstrate the utility of this S. osmophilus reference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of 2 types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of 2 types of mitochondrial selfish elements.
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Affiliation(s)
- Guo-Song Jia
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wen-Cai Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yue Liang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xi-Han Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alison Pidoux
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn 74081, Germany
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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5
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Kapetanakis GC, Sousa LS, Felten C, Mues L, Gabant P, Van Nedervelde L, Georis I, André B. Deletion of QDR genes in a bioethanol-producing yeast strain reduces propagation of contaminating lactic acid bacteria. Sci Rep 2023; 13:4986. [PMID: 36973391 PMCID: PMC10043021 DOI: 10.1038/s41598-023-32062-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Bacterial contaminations in yeast fermentation tanks are a recurring problem for the bioethanol production industry. Lactic acid bacteria (LAB), particularly of the genus Lactobacillus, are the most common contaminants. Their proliferation can reduce fermentation efficiency or even impose premature shutdown for cleaning. We have previously reported that laboratory yeast strains naturally excrete amino acids via transporters of the Drug: H+ Antiporter-1 (DHA1) family. This excretion allows yeast to cross-feed LAB, which are most often unable to grow without an external amino acid supply. Whether industrial yeast strains used in bioethanol production likewise promote LAB proliferation through cross-feeding has not been investigated. In this study, we first show that the yeast strain Ethanol Red used in ethanol production supports growth of Lactobacillus fermentum in an amino-acid-free synthetic medium. This effect was markedly reduced upon homozygous deletion of the QDR3 gene encoding a DHA1-family amino acid exporter. We further show that cultivation of Ethanol Red in a nonsterile sugarcane-molasses-based medium is associated with an increase in lactic acid due to LAB growth. When Ethanol Red lacked the QDR1, QDR2, and QDR3 genes, this lactic acid production was not observed and ethanol production was not significantly reduced. Our results indicate that Ethanol Red cultivated in synthetic or molasses medium sustains LAB proliferation in a manner that depends on its ability to excrete amino acids via Qdr transporters. They further suggest that using mutant industrial yeast derivatives lacking DHA1-family amino acid exporters may be a way to reduce the risk of bacterial contaminations during fermentation.
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Affiliation(s)
- George C Kapetanakis
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), Biopark, Gosselies, Belgium
| | - Luis Santos Sousa
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), Biopark, Gosselies, Belgium
| | - Charlotte Felten
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), Biopark, Gosselies, Belgium
| | | | | | | | - Isabelle Georis
- Department of Biochemical Industry, YEaST, LABIRIS, Brussels, Belgium
| | - Bruno André
- Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), Biopark, Gosselies, Belgium.
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6
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Jia Y, Xu M, Hu H, Chapman B, Watt C, Buerte B, Han N, Zhu M, Bian H, Li C, Zeng Z. Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication. BMC Biol 2023; 21:25. [PMID: 36747211 PMCID: PMC9903521 DOI: 10.1186/s12915-022-01503-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date. RESULTS Taking advantage of recently published genomic data in Triticeae, we dissected a divergent homogentisate phytyltransferase (HPT2) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional divergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint. CONCLUSIONS Comparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication. Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.
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Affiliation(s)
- Yong Jia
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Mingrui Xu
- grid.410595.c0000 0001 2230 9154College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Haifei Hu
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Brett Chapman
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Calum Watt
- grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.516230.30000 0005 0233 6218Intergrain Pty Ltd, Bibra Lake, WA 6163 Australia
| | - B. Buerte
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ning Han
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Muyuan Zhu
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chengdao Li
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Department of Primary Industries and Regional Development, 3-Baron-Hay Court, South Perth, WA, 6151, Australia.
| | - Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China. .,Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, 311121, China.
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7
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Moreira F, Arenas M, Videira A, Pereira F. Evolution of TOP1 and TOP1MT Topoisomerases in Chordata. J Mol Evol 2023; 91:192-203. [PMID: 36651963 PMCID: PMC10081982 DOI: 10.1007/s00239-022-10091-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023]
Abstract
Type IB topoisomerases relax the torsional stress associated with DNA metabolism in the nucleus and mitochondria and constitute important molecular targets of anticancer drugs. Vertebrates stand out among eukaryotes by having two Type IB topoisomerases acting specifically in the nucleus (TOP1) and mitochondria (TOP1MT). Despite their major importance, the origin and evolution of these paralogues remain unknown. Here, we examine the molecular evolutionary processes acting on both TOP1 and TOP1MT in Chordata, taking advantage of the increasing number of available genome sequences. We found that both TOP1 and TOP1MT evolved under strong purifying selection, as expected considering their essential biological functions. Critical active sites, including those associated with resistance to anticancer agents, were found particularly conserved. However, TOP1MT presented a higher rate of molecular evolution than TOP1, possibly related with its specialized activity on the mitochondrial genome and a less critical role in cells. We could place the duplication event that originated the TOP1 and TOP1MT paralogues early in the radiation of vertebrates, most likely associated with the first round of vertebrate tetraploidization (1R). Moreover, our data suggest that cyclostomes present a specialized mitochondrial Type IB topoisomerase. Interestingly, we identified two missense mutations replacing amino acids in the Linker region of TOP1MT in Neanderthals, which appears as a rare event when comparing the genome of both species. In conclusion, TOP1 and TOP1MT differ in their rates of evolution, and their evolutionary histories allowed us to better understand the evolution of chordates.
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Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos S/N 4450-208, Matosinhos, Portugal
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Arnaldo Videira
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Filipe Pereira
- IDENTIFICA Genetic Testing, Rua Simão Bolívar 259 3º Dir Tras, 4470-214, Maia, Portugal.
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
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8
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Mallik S, Tawfik DS, Levy ED. How gene duplication diversifies the landscape of protein oligomeric state and function. Curr Opin Genet Dev 2022; 76:101966. [PMID: 36007298 PMCID: PMC9548406 DOI: 10.1016/j.gde.2022.101966] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 11/29/2022]
Abstract
Oligomeric proteins are central to cellular life and the duplication and divergence of their genes is a key driver of evolutionary innovations. The duplication of a gene coding for an oligomeric protein has numerous possible outcomes, which motivates questions on the relationship between structural and functional divergence. How do protein oligomeric states diversify after gene duplication? In the simple case of duplication of a homo-oligomeric protein gene, what properties can influence the fate of descendant paralogs toward forming independent homomers or maintaining their interaction as a complex? Furthermore, how are functional innovations associated with the diversification of oligomeric states? Here, we review recent literature and present specific examples in an attempt to illustrate and answer these questions.
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Affiliation(s)
- Saurav Mallik
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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9
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Johri P, Gout JF, Doak TG, Lynch M. A Population-Genetic Lens into the Process of Gene Loss Following Whole-Genome Duplication. Mol Biol Evol 2022; 39:msac118. [PMID: 35639978 PMCID: PMC9206413 DOI: 10.1093/molbev/msac118] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Whole-genome duplications (WGDs) have occurred in many eukaryotic lineages. However, the underlying evolutionary forces and molecular mechanisms responsible for the long-term retention of gene duplicates created by WGDs are not well understood. We employ a population-genomic approach to understand the selective forces acting on paralogs and investigate ongoing duplicate-gene loss in multiple species of Paramecium that share an ancient WGD. We show that mutations that abolish protein function are more likely to be segregating in retained WGD paralogs than in single-copy genes, most likely because of ongoing nonfunctionalization post-WGD. This relaxation of purifying selection occurs in only one WGD paralog, accompanied by the gradual fixation of nonsynonymous mutations and reduction in levels of expression, and occurs over a long period of evolutionary time, "marking" one locus for future loss. Concordantly, the fitness effects of new nonsynonymous mutations and frameshift-causing indels are significantly more deleterious in the highly expressed copy compared with their paralogs with lower expression. Our results provide a novel mechanistic model of gene duplicate loss following WGDs, wherein selection acts on the sum of functional activity of both duplicate genes, allowing the two to wander in expression and functional space, until one duplicate locus eventually degenerates enough in functional efficiency or expression that its contribution to total activity is too insignificant to be retained by purifying selection. Retention of duplicates by such mechanisms predicts long times to duplicate-gene loss, which should not be falsely attributed to retention due to gain/change in function.
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Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Jean-Francois Gout
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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10
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Moreira F, Arenas M, Videira A, Pereira F. Evolutionary History of TOPIIA Topoisomerases in Animals. J Mol Evol 2022; 90:149-165. [PMID: 35165762 DOI: 10.1007/s00239-022-10048-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/26/2022] [Indexed: 01/15/2023]
Abstract
TOPIIA topoisomerases are required for the regulation of DNA topology by DNA cleavage and re-ligation and are important targets of antibiotic and anticancer agents. Humans possess two TOPIIA paralogue genes (TOP2A and TOP2B) with high sequence and structural similarity but distinct cellular functions. Despite their functional and clinical relevance, the evolutionary history of TOPIIA is still poorly understood. Here we show that TOPIIA is highly conserved in Metazoa. We also found that TOPIIA paralogues from jawed and jawless vertebrates had different origins related with tetraploidization events. After duplication, TOP2B evolved under a stronger purifying selection than TOP2A, perhaps promoted by the more specialized role of TOP2B in postmitotic cells. We also detected genetic signatures of positive selection in the highly variable C-terminal domain (CTD), possibly associated with adaptation to cellular interactions. By comparing TOPIIA from modern and archaic humans, we found two amino acid substitutions in the TOP2A CTD, suggesting that TOP2A may have contributed to the evolution of present-day humans, as proposed for other cell cycle-related genes. Finally, we identified six residues conferring resistance to chemotherapy differing between TOP2A and TOP2B. These six residues could be targets for the development of TOP2A-specific inhibitors that would avoid the side effects caused by inhibiting TOP2B. Altogether, our findings clarify the origin, diversification and selection pressures governing the evolution of animal TOPIIA.
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Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Arnaldo Videira
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Filipe Pereira
- IDENTIFICA Genetic Testing, Rua Simão Bolívar 259 3º Dir Tras, 4470-214, Maia, Portugal.
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
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11
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Begum T, Serrano‐Serrano ML, Robinson‐Rechavi M. Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tina Begum
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Martha Liliana Serrano‐Serrano
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics Lausanne Switzerland
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12
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Begum T, Robinson-Rechavi M. Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes. Mol Biol Evol 2021; 38:1614-1626. [PMID: 33169790 PMCID: PMC8042747 DOI: 10.1093/molbev/msaa288] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, as genes, like species, are phylogenetically related. Phylogenetic comparative methods should be used to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the “ortholog conjecture,” the hypothesis that functional evolution is faster in paralogs than in orthologs. Although pairwise comparisons of tissue specificity (τ) provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows successful use of phylogenetic methods to study the evolution of gene function and provides some support for the ortholog conjecture using three different phylogenetic approaches.
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Affiliation(s)
- Tina Begum
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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13
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Fernández R, Marcet-Houben M, Legeai F, Richard G, Robin S, Wucher V, Pegueroles C, Gabaldón T, Tagu D. Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum. Mol Biol Evol 2021; 37:2601-2615. [PMID: 32359152 PMCID: PMC7475028 DOI: 10.1093/molbev/msaa110] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there are a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation.
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Affiliation(s)
- Rosa Fernández
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.,Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
| | - Fabrice Legeai
- IGEPP, INRAE, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France.,INRIA, IRISA, Genscale, Campus Beaulieu, Rennes, France
| | - Gautier Richard
- IGEPP, INRAE, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Stéphanie Robin
- IGEPP, INRAE, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France.,INRIA, IRISA, GenOuest Core Facility, Campus Beaulieu, Rennes, France
| | - Valentin Wucher
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Cinta Pegueroles
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.,Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
| | - Denis Tagu
- IGEPP, INRAE, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
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14
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Qi X, An H, Hall TE, Di C, Blischak PD, McKibben MTW, Hao Y, Conant GC, Pires JC, Barker MS. Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. THE NEW PHYTOLOGIST 2021; 230:372-386. [PMID: 33452818 DOI: 10.1111/nph.17194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. In order to test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties of Brassica rapa. Like all 'diploid' flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivated B. rapa accessions. Using a combination of approaches, we identified > 3000 candidate genes associated with the domestication of four major B. rapa crop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non-paleologs. Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.
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Affiliation(s)
- Xinshuai Qi
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tara E Hall
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Chenlu Di
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Paul D Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael T W McKibben
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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15
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Zeng X, Sheng J, Zhu F, Wei T, Zhao L, Hu X, Zheng X, Zhou F, Hu Z, Diao Y, Jin S. Genetic, transcriptional, and regulatory landscape of monolignol biosynthesis pathway in Miscanthus × giganteus. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:179. [PMID: 33117433 PMCID: PMC7590476 DOI: 10.1186/s13068-020-01819-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Miscanthus × giganteus is widely recognized as a promising lignocellulosic biomass crop due to its advantages of high biomass production, low environmental impacts, and the potential to be cultivated on marginal land. However, the high costs of bioethanol production still limit the current commercialization of lignocellulosic bioethanol. The lignin in the cell wall and its by-products released in the pretreatment step is the main component inhibiting the enzymatic reactions in the saccharification and fermentation processes. Hence, genetic modification of the genes involved in lignin biosynthesis could be a feasible strategy to overcome this barrier by manipulating the lignin content and composition of M. × giganteus. For this purpose, the essential knowledge of these genes and understanding the underlying regulatory mechanisms in M. × giganteus is required. RESULTS In this study, MgPAL1, MgPAL5, Mg4CL1, Mg4CL3, MgHCT1, MgHCT2, MgC3'H1, MgCCoAOMT1, MgCCoAOMT3, MgCCR1, MgCCR2, MgF5H, MgCOMT, and MgCAD were identified as the major monolignol biosynthetic genes in M. × giganteus based on genetic and transcriptional evidence. Among them, 12 genes were cloned and sequenced. By combining transcription factor binding site prediction and expression correlation analysis, MYB46, MYB61, MYB63, WRKY24, WRKY35, WRKY12, ERF021, ERF058, and ERF017 were inferred to regulate the expression of these genes directly. On the basis of these results, an integrated model was summarized to depict the monolignol biosynthesis pathway and the underlying regulatory mechanism in M. × giganteus. CONCLUSIONS This study provides a list of potential gene targets for genetic improvement of lignocellulosic biomass quality of M. × giganteus, and reveals the genetic, transcriptional, and regulatory landscape of the monolignol biosynthesis pathway in M. × giganteus.
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Affiliation(s)
- Xiaofei Zeng
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, 430023 People’s Republic of China
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055 People’s Republic of China
| | - Jiajing Sheng
- School of Life Sciences, Nantong University, Nantong, 226019 People’s Republic of China
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Fenglin Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Tianzi Wei
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055 People’s Republic of China
| | - Lingling Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Xiaohu Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Xingfei Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Fasong Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Ying Diao
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, 430023 People’s Republic of China
| | - Surong Jin
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070 People’s Republic of China
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16
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David KT, Oaks JR, Halanych KM. Patterns of gene evolution following duplications and speciations in vertebrates. PeerJ 2020; 8:e8813. [PMID: 32266119 PMCID: PMC7120047 DOI: 10.7717/peerj.8813] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/27/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. METHODS To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. RESULTS Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions.
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Affiliation(s)
- Kyle T. David
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Jamie R. Oaks
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
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17
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Abstract
The root-knot nematodes of the genus Meloidogyne are important and damaging parasites capable of infecting most flowering plants. Within this genus, several species of the Meloidogyne incognita group show evidence of paleopolyploidy in their genomes. We used our software tool POInT, the Polyploidy Orthology Inference Tool, to phylogenetically model the gene losses that followed that polyploidy. These models, and simulations based on them, show that three of these species (M. incognita, M. arenaria and M. javanica) descend from a single common hybridization event that yielded triplicated genomes with three distinguishable subgenomes. While one of the three subgenomes shows elevated gene loss rates relative to the other two, this subgenome does not show elevated sequence divergence. In all three species, ancestral loci where two of the three gene copies have been lost are less likely to have orthologs in Caenorhabditis elegans that are lethal when knocked down than are ancestral loci with surviving duplicate copies.
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18
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Shirai K, Hanada K. Contribution of Functional Divergence Through Copy Number Variations to the Inter-Species and Intra-Species Diversity in Specialized Metabolites. FRONTIERS IN PLANT SCIENCE 2019; 10:1567. [PMID: 31850041 PMCID: PMC6902010 DOI: 10.3389/fpls.2019.01567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/08/2019] [Indexed: 06/10/2023]
Abstract
There is considerable diversity in the specialized metabolites within a single plant species (intra-species) and among different plant species (inter-species). The functional divergence associated with gene duplications largely contributes to the inter-species diversity in the specialized metabolites, whereas the intra-species diversity is due to gene dosage changes via gene duplications [i.e., copy number variants (CNVs)] at the intra-species level of evolution. This is because CNVs are thought to undergo associated with less functional divergence at the intra-species level of evolution. However, functional divergence caused by CNVs may induce specialized metabolite diversity at the intra-species and inter-species levels of evolution. We herein discuss the functional divergence of CNVs in metabolic quantitative trait genes (mQTGs). We focused on 5,654 previously identified mQTGs in 270 Arabidopsis thaliana accessions. The ratio of nonsynonymous to synonymous variations tends to be higher for mQTGs with CNVs than for mQTGs without CNVs within A. thaliana accessions, suggesting that CNVs are responsible for the functional divergence among mQTGs at the intra-species level of evolution. To evaluate the contribution of CNVs to inter-species diversity, we calculated the ratio of nonsynonymous to synonymous substitutions in the Arabidopsis lineage. The ratio tends to be higher for the mQTGs with CNVs than for the mQTGs without CNVs. Additionally, we determined that mQTGs with CNVs are subject to positive selection in the Arabidopsis lineage. Our data suggest that CNVs are closely related to functional divergence contributing to adaptations via the production of diverse specialized metabolites at the intra-species and inter-species levels of evolution.
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19
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Furman BLS, Dang UJ, Evans BJ, Golding GB. Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus). J Evol Biol 2018; 31:1945-1958. [DOI: 10.1111/jeb.13391] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/26/2018] [Accepted: 10/06/2018] [Indexed: 12/22/2022]
Affiliation(s)
| | - Utkarsh J. Dang
- Department of Health Outcomes and Administrative Sciences; School of Pharmacy and Pharmaceutical Sciences; Binghamton University; State University of New York; Binghamton NY USA
| | - Ben J. Evans
- Department of Biology; McMaster University; Hamilton ON Canada
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20
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Zhao L, Han L, Xiao C, Lin X, Xu C, Yang C. Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids. BMC Genomics 2018; 19:756. [PMID: 30340512 PMCID: PMC6194744 DOI: 10.1186/s12864-018-5150-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022] Open
Abstract
Background In diverse plant taxa, whole-genome duplication (WGD) events are major sources of phenotypic novelty. Studies of gene expression in synthetic polyploids have shown immediate expression and functional partitioning of duplicated genes among different tissues. Many studies of the tissue-specific homeolog expression partitioning have focused on allopolyploids that have very different parental genomes, while few studies have focused on autopolyploids or allopolyploids that have similar parental genomes. Results In this study, we used a set of reciprocal F1 hybrids and synthetic tetraploids constructed from subspecies (japonica and indica) of Asian rice (Oryza sativa L.) as a model to gain insights into the expression partitioning of homeologs among tissues in a developmental context. We assayed the tissue-specific silencing (TSS) of the parental homeologs of 30 key genes in the hybrids and tetraploids relative to the in vitro “hybrids” (parental mixes) using Sequenom MassARRAY. We found that the parental mix and synthetic tetraploids had higher frequencies of homeolog TSS than the F1, revealing an instantaneous role of WGD on homeolog expression partitioning. Conclusions Our observations contradicted those of previous studies in which newly formed allopolyploids had a low TSS frequency, similar to that of F1 hybrids, suggesting that the impact of WGD on homeolog expression requires a longer time to manifest. In addition, we found that the TSS frequency in the tetraploids varied at different growth stages and that roots had a much higher frequency of TSS than leaves, which indicated that developmental and metabolic traits may influence the expression states of duplicated genes in newly formed plant polyploids. Electronic supplementary material The online version of this article (10.1186/s12864-018-5150-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Long Zhao
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Han
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chaoxia Xiao
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunwu Yang
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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21
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Hao Y, Washburn JD, Rosenthal J, Nielsen B, Lyons E, Edger PP, Pires JC, Conant GC. Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived. Genome Biol Evol 2018; 10:999-1011. [PMID: 29617811 PMCID: PMC5887293 DOI: 10.1093/gbe/evy061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2018] [Indexed: 11/21/2022] Open
Abstract
Genes that are inherently subject to strong selective constraints tend to be overretained in duplicate after polyploidy. They also continue to experience similar, but somewhat relaxed, constraints after that polyploidy event. We sought to assess for how long the influence of polyploidy is felt on these genes’ selective pressures. We analyzed two nested polyploidy events in Brassicaceae: the At-α genome duplication that is the most recent polyploidy in the model plant Arabidopsis thaliana and a more recent hexaploidy shared by the genus Brassica and its relatives. By comparing the strength and direction of the natural selection acting at the population and at the species level, we find evidence for continued intensified purifying selection acting on retained duplicates from both polyploidies even down to the present. The constraint observed in preferentially retained genes is not a result of the polyploidy event: the orthologs of such genes experience even stronger constraint in nonpolyploid outgroup genomes. In both the Arabidopsis and Brassica lineages, we further find evidence for segregating mildly deleterious variants, confirming that the population-level data uncover patterns not visible with between-species comparisons. Using the A. thaliana metabolic network, we also explored whether network position was correlated with the measured selective constraint. At both the population and species level, nodes/genes tended to show similar constraints to their neighbors. Our results paint a picture of the long-lived effects of polyploidy on plant genomes, suggesting that even yesterday’s polyploids still have distinct evolutionary trajectories.
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Affiliation(s)
- Yue Hao
- Bioinformatics Research Center, North Carolina State University
| | | | | | - Brandon Nielsen
- Department of Biology and Geosciences, Clarion University of Pennsylvania
| | - Eric Lyons
- School of Plant Sciences, University of Arizona
| | - Patrick P Edger
- Department of Horticulture, Michigan State University.,Ecology, Evolutionary Biology and Behavior Program, Michigan State University
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri- Columbia.,Informatics Institute, University of Missouri- Columbia
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University.,Informatics Institute, University of Missouri- Columbia.,Division of Animal Sciences, University of Missouri- Columbia.,Program in Genetics, North Carolina State University.,Department of Biological Sciences, North Carolina State University
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22
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Mattenberger F, Sabater-Muñoz B, Toft C, Sablok G, Fares MA. Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina. DNA Res 2018. [PMID: 28633360 PMCID: PMC5726480 DOI: 10.1093/dnares/dsx025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Gene duplication is an important source of novelties and genome complexity. What genes are preserved as duplicated through long evolutionary times can shape the evolution of innovations. Identifying factors that influence gene duplicability is therefore an important aim in evolutionary biology. Here, we show that in the yeast Saccharomyces cerevisiae the levels of gene expression correlate with gene duplicability, its divergence, and transcriptional plasticity. Genes that were highly expressed before duplication are more likely to be preserved as duplicates for longer evolutionary times and wider phylogenetic ranges than genes that were lowly expressed. Duplicates with higher expression levels exhibit greater divergence between their gene copies. Duplicates that exhibit higher expression divergence are those enriched for TATA-containing promoters. These duplicates also show transcriptional plasticity, which seems to be involved in the origin of adaptations to environmental stresses in yeast. While the expression properties of genes strongly affect their duplicability, divergence and transcriptional plasticity are enhanced after gene duplication. We conclude that highly expressed genes are more likely to be preserved as duplicates due to their promoter architectures, their greater tolerance to expression noise, and their ability to reduce the noise-plasticity conflict.
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Affiliation(s)
- Florian Mattenberger
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Systems Biology of Molecular Interactions and Regulation Department, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones, Científicas-Universitat de Valencia (CSIC-UV), Valencia 46980, Spain
| | - Beatriz Sabater-Muñoz
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Systems Biology of Molecular Interactions and Regulation Department, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones, Científicas-Universitat de Valencia (CSIC-UV), Valencia 46980, Spain.,Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
| | - Christina Toft
- Department of Genetics, University of Valencia, Burjasot, Valencia 46100, Spain.,Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Burjasot, Valencia, Spain
| | - Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Mario A Fares
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Systems Biology of Molecular Interactions and Regulation Department, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones, Científicas-Universitat de Valencia (CSIC-UV), Valencia 46980, Spain.,Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
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23
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Alvarez-Ponce D, Feyertag F, Chakraborty S. Position Matters: Network Centrality Considerably Impacts Rates of Protein Evolution in the Human Protein-Protein Interaction Network. Genome Biol Evol 2018; 9:1742-1756. [PMID: 28854629 PMCID: PMC5570066 DOI: 10.1093/gbe/evx117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2017] [Indexed: 02/06/2023] Open
Abstract
The proteins of any organism evolve at disparate rates. A long list of factors affecting rates of protein evolution have been identified. However, the relative importance of each factor in determining rates of protein evolution remains unresolved. The prevailing view is that evolutionary rates are dominantly determined by gene expression, and that other factors such as network centrality have only a marginal effect, if any. However, this view is largely based on analyses in yeasts, and accurately measuring the importance of the determinants of rates of protein evolution is complicated by the fact that the different factors are often correlated with each other, and by the relatively poor quality of available functional genomics data sets. Here, we use correlation, partial correlation and principal component regression analyses to measure the contributions of several factors to the variability of the rates of evolution of human proteins. For this purpose, we analyzed the entire human protein–protein interaction data set and the human signal transduction network—a network data set of exceptionally high quality, obtained by manual curation, which is expected to be virtually free from false positives. In contrast with the prevailing view, we observe that network centrality (measured as the number of physical and nonphysical interactions, betweenness, and closeness) has a considerable impact on rates of protein evolution. Surprisingly, the impact of centrality on rates of protein evolution seems to be comparable, or even superior according to some analyses, to that of gene expression. Our observations seem to be independent of potentially confounding factors and from the limitations (biases and errors) of interactomic data sets.
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24
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Ascencio D, Ochoa S, Delaye L, DeLuna A. Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts. BMC Evol Biol 2017; 17:40. [PMID: 28166720 PMCID: PMC5294719 DOI: 10.1186/s12862-017-0895-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 01/26/2017] [Indexed: 11/25/2022] Open
Abstract
Background Whole-genome duplication (WGD) events have shaped the genomes of eukaryotic organisms. Relaxed selection after duplication along with inherent functional constraints are thought to determine the fate of the paralogs and, ultimately, the evolution of gene function. Here, we investigated the rate of protein evolution (as measured by dN/dS ratios) before and after the WGD in the hemiascomycete yeasts, and the way in which changes in such rates relate to molecular and biological function. Results For most groups of orthologous genes (81%) we observed a change in the rates of evolution after genome duplication. Genes with atypically-low dN/dS ratio before the WGD were prone to increase their rates of evolution after duplication. Importantly, the paralogs were often different in their rates of evolution after the WGD (50% cases), however, this was more consistent with an asymmetric deceleration in the protein-evolution rates, rather than an asymmetric increase of the initial rates. Functional-category analysis showed that regulatory proteins such as protein kinases and transcription factors were enriched in genes that increase their rates of evolution after the WGD. While changes in the rate of protein-sequence evolution were associated to protein abundance, content of disordered regions, and contribution to fitness, these features were an attribute of specific functional classes. Conclusions Our results indicate that strong purifying selection in ancestral pre-duplication sequences is a strong predictor of increased rates after the duplication in yeasts and that asymmetry in evolution rate is established during the deceleration phase. In addition, changes in the rates at which paralogous sequences evolve before and after WGD are different for specific protein functions; increased rates of protein evolution after duplication occur preferentially in specific protein functions. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0895-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diana Ascencio
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Soledad Ochoa
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Luis Delaye
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico.
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25
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Panchy N, Lehti-Shiu M, Shiu SH. Evolution of Gene Duplication in Plants. PLANT PHYSIOLOGY 2016; 171:2294-316. [PMID: 27288366 PMCID: PMC4972278 DOI: 10.1104/pp.16.00523] [Citation(s) in RCA: 784] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/17/2016] [Indexed: 05/18/2023]
Abstract
Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.
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Affiliation(s)
- Nicholas Panchy
- Genetics Program (N.P., S.-H.S.) and Department of Plant Biology (M.L.-S., S.-H.S.), Michigan State University, East Lansing, Michigan 48824
| | - Melissa Lehti-Shiu
- Genetics Program (N.P., S.-H.S.) and Department of Plant Biology (M.L.-S., S.-H.S.), Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Genetics Program (N.P., S.-H.S.) and Department of Plant Biology (M.L.-S., S.-H.S.), Michigan State University, East Lansing, Michigan 48824
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26
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Comparing the Statistical Fate of Paralogous and Orthologous Sequences. Genetics 2016; 204:475-482. [PMID: 27474728 DOI: 10.1534/genetics.116.193912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/26/2016] [Indexed: 02/01/2023] Open
Abstract
For several decades, sequence alignment has been a widely used tool in bioinformatics. For instance, finding homologous sequences with a known function in large databases is used to get insight into the function of nonannotated genomic regions. Very efficient tools like BLAST have been developed to identify and rank possible homologous sequences. To estimate the significance of the homology, the ranking of alignment scores takes a background model for random sequences into account. Using this model we can estimate the probability to find two exactly matching subsequences by chance in two unrelated sequences. For two homologous sequences, the corresponding probability is much higher, which allows us to identify them. Here we focus on the distribution of lengths of exact sequence matches between protein-coding regions of pairs of evolutionarily distant genomes. We show that this distribution exhibits a power-law tail with an exponent [Formula: see text] Developing a simple model of sequence evolution by substitutions and segmental duplications, we show analytically and computationally that paralogous and orthologous gene pairs contribute differently to this distribution. Our model explains the differences observed in the comparison of coding and noncoding parts of genomes, thus providing a better understanding of statistical properties of genomic sequences and their evolution.
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27
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Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FEG, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SMJ, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PWH, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 2016; 48:427-37. [PMID: 26950095 PMCID: PMC4817229 DOI: 10.1038/ng.3526] [Citation(s) in RCA: 405] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 02/12/2016] [Indexed: 12/16/2022]
Abstract
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Andrew R Gehrke
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Jeremy Pasquier
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Julian Catchen
- Department of Animal Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Aaron M Berlin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S Campbell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Daniel Barrell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Kyle J Martin
- Department of Zoology, University of Oxford, Oxford, UK
| | - John F Mulley
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Vydianathan Ravi
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Alison P Lee
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Tetsuya Nakamura
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Shaohua Fan
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dustin Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Cristian Cañestro
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Felix E G Beaudry
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Yi Sun
- Center for Circadian Clocks, Soochow University, Suzhou, China
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Michael J Beam
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Mikio Ishiyama
- Department of Dental Hygiene, Nippon Dental University College at Niigata, Niigata, Japan
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steffi Kehr
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Marcia Lara
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - John H Letaw
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Gary W Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA
| | - Ronda T Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA
| | - Masato Mikami
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Niigata, Niigata, Japan
| | - Tatsuya Ota
- Department of Evolutionary Studies of Biosystems, SOKENDAI (Graduate University for Advanced Studies), Hayama, Japan
| | - Nil Ratan Saha
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Louise Williams
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou, China
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - John S Taylor
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Brazil
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
- International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
| | - Chris T Amemiya
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Yann Guiguen
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Julien Bobe
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Neil H Shubin
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | | | - Jessica Alföldi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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28
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Ames RM, Talavera D, Williams SG, Robertson DL, Lovell SC. Binding interface change and cryptic variation in the evolution of protein-protein interactions. BMC Evol Biol 2016; 16:40. [PMID: 26892785 PMCID: PMC4758157 DOI: 10.1186/s12862-016-0608-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 02/02/2016] [Indexed: 12/03/2022] Open
Abstract
Background Physical interactions between proteins are essential for almost all biological functions and systems. To understand the evolution of function it is therefore important to understand the evolution of molecular interactions. Of key importance is the evolution of binding specificity, the set of interactions made by a protein, since change in specificity can lead to “rewiring” of interaction networks. Unfortunately, the interfaces through which proteins interact are complex, typically containing many amino-acid residues that collectively must contribute to binding specificity as well as binding affinity, structural integrity of the interface and solubility in the unbound state. Results In order to study the relationship between interface composition and binding specificity, we make use of paralogous pairs of yeast proteins. Immediately after duplication these paralogues will have identical sequences and protein products that make an identical set of interactions. As the sequences diverge, we can correlate amino-acid change in the interface with any change in the specificity of binding. We show that change in interface regions correlates only weakly with change in specificity, and many variants in interfaces are functionally equivalent. We show that many of the residue replacements within interfaces are silent with respect to their contribution to binding specificity. Conclusions We conclude that such functionally-equivalent change has the potential to contribute to evolutionary plasticity in interfaces by creating cryptic variation, which in turn may provide the raw material for functional innovation and coevolution. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0608-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryan M Ames
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK. .,Current address: Wellcome Trust Centre for Biomedical Modelling and Analysis, University of Exeter, RILD Level 3, Exeter, EX2 5DW, UK.
| | - David Talavera
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK. .,Current address: Institute of Cardiovascular Sciences, Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Simon G Williams
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK. .,Current address: Institute of Cardiovascular Sciences, Faculty of Medical and Human Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - David L Robertson
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Simon C Lovell
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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29
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Compensatory Drift and the Evolutionary Dynamics of Dosage-Sensitive Duplicate Genes. Genetics 2015; 202:765-74. [PMID: 26661114 DOI: 10.1534/genetics.115.178137] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 12/06/2015] [Indexed: 11/18/2022] Open
Abstract
Dosage-balance selection preserves functionally redundant duplicates (paralogs) at the optimum for their combined expression. Here we present a model of the dynamics of duplicate genes coevolving under dosage-balance selection. We call this the compensatory drift model. Results show that even when strong dosage-balance selection constrains total expression to the optimum, expression of each duplicate can diverge by drift from its original level. The rate of divergence slows as the strength of stabilizing selection, the size of the mutation effect, and/or the size of the population increases. We show that dosage-balance selection impedes neofunctionalization early after duplication but can later facilitate it. We fit this model to data from sodium channel duplicates in 10 families of teleost fish; these include two convergent lineages of electric fish in which one of the duplicates neofunctionalized. Using the model, we estimated the strength of dosage-balance selection for these genes. The results indicate that functionally redundant paralogs still may undergo radical functional changes after a prolonged period of compensatory drift.
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30
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MglC, a Paralog of Myxococcus xanthus GTPase-Activating Protein MglB, Plays a Divergent Role in Motility Regulation. J Bacteriol 2015; 198:510-20. [PMID: 26574508 PMCID: PMC4719450 DOI: 10.1128/jb.00548-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/05/2015] [Indexed: 01/01/2023] Open
Abstract
In order to optimize interactions with their environment and one another, bacteria regulate their motility. In the case of the rod-shaped cells of Myxococcus xanthus, regulated motility is essential for social behaviors. M. xanthus moves over surfaces using type IV pilus-dependent motility and gliding motility. These two motility systems are coordinated by a protein module that controls cell polarity and consists of three polarly localized proteins, the small G protein MglA, the cognate MglA GTPase-activating protein MglB, and the response regulator RomR. Cellular reversals are induced by the Frz chemosensory system, and the output response regulator of this system, FrzZ, interfaces with the MglA/MglB/RomR module to invert cell polarity. Using a computational approach, we identify a paralog of MglB, MXAN_5770 (MglC). Genetic epistasis experiments demonstrate that MglC functions in the same pathway as MglA, MglB, RomR, and FrzZ and is important for regulating cellular reversals. Like MglB, MglC localizes to the cell poles asymmetrically and with a large cluster at the lagging pole. Correct polar localization of MglC depends on RomR and MglB. Consistently, MglC interacts directly with MglB and the C-terminal output domain of RomR, and we identified a surface of MglC that is necessary for the interaction with MglB and for MglC function. Together, our findings identify an additional member of the M. xanthus polarity module involved in regulating motility and demonstrate how gene duplication followed by functional divergence can add a layer of control to the complex cellular processes of motility and motility regulation.
IMPORTANCE Gene duplication and the subsequent divergence of the duplicated genes are important evolutionary mechanisms for increasing both biological complexity and regulation of biological processes. The bacterium Myxococcus xanthus is a soil bacterium with an unusually large genome that carries out several social processes, including predation of other bacterial species and formation of multicellular, spore-filled fruiting bodies. One feature of the large M. xanthus genome is that it contains many gene duplications. Here, we compare the products of one example of gene duplication and divergence, in which a paralog of the cognate MglA GTPase-activating protein MglB has acquired a different and opposing role in the regulation of cellular polarity and motility, processes critical to the bacterium's social behaviors.
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Dudzic JP, Kondo S, Ueda R, Bergman CM, Lemaitre B. Drosophila innate immunity: regional and functional specialization of prophenoloxidases. BMC Biol 2015; 13:81. [PMID: 26437768 PMCID: PMC4595066 DOI: 10.1186/s12915-015-0193-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/17/2015] [Indexed: 01/08/2023] Open
Abstract
Background The diversification of immune systems during evolution involves the expansion of particular gene families in given phyla. A better understanding of the metazoan immune system requires an analysis of the logic underlying such immune gene amplification. This analysis is now within reach due to the ease with which we can generate multiple mutations in an organism. In this paper, we analyze the contribution of the three Drosophila prophenoloxidases (PPOs) to host defense by generating single, double and triple mutants. PPOs are enzymes that catalyze the production of melanin at the site of infection and around parasites. They are the rate-limiting enzymes that contribute to the melanization reaction, a major immune mechanism of arthropods. The number of PPO-encoding genes is variable among insects, ranging from one in the bee to ten in the mosquito. Results By analyzing mutations alone and in combination, we ascribe a specific function to each of the three PPOs of Drosophila. Our study confirms that two PPOs produced by crystal cells, PPO1 and PPO2, contribute to the bulk of melanization in the hemolymph, upon septic or clean injury. In contrast, PPO3, a PPO restricted to the D. melanogaster group, is expressed in lamellocytes and contributes to melanization during the encapsulation process. Interestingly, another overlapping set of PPOs, PPO2 and PPO3, achieve melanization of the capsule upon parasitoid wasp infection. Conclusions The use of single or combined mutations allowed us to show that each PPO mutant has a specific phenotype, and that knocking out two of three genes is required to abolish fully a particular function. Thus, Drosophila PPOs have partially overlapping functions to optimize melanization in at least two conditions: following injury or during encapsulation. Since PPO3 is restricted to the D. melanogaster group, this suggests that production of PPO by lamellocytes emerged as a recent defense mechanism against parasitoid wasps. We conclude that differences in spatial localization, immediate or late availability, and mode of activation underlie the functional diversification of the three Drosophila PPOs, with each of them having non-redundant but overlapping functions. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0193-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jan P Dudzic
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland.
| | - Shu Kondo
- Invertebrate Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, 411-8540, Japan.
| | - Ryu Ueda
- Invertebrate Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, 411-8540, Japan.
| | - Casey M Bergman
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
| | - Bruno Lemaitre
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland.
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Radó-Trilla N, Arató K, Pegueroles C, Raya A, de la Luna S, Albà MM. Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors. Mol Biol Evol 2015; 32:2263-72. [PMID: 25931513 PMCID: PMC4540963 DOI: 10.1093/molbev/msv103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The high regulatory complexity of vertebrates has been related to two rounds of whole genome duplication (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families originated during the 2R-WGD contains LCRs. The number of gene duplicates with LCRs is 155 out of 550 analyzed (28%), about twice as many as the number of single copy genes with LCRs (15 out of 115, 13%). In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.
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Affiliation(s)
- Núria Radó-Trilla
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Krisztina Arató
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Cinta Pegueroles
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Alicia Raya
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Susana de la Luna
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K, Amselem J, Beckerich JM, Henrissat B, Van de Peer Y, Wincker P, Souciet JL, Gabaldón T, Tinsley CR, Casaregola S. Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Sci Rep 2015; 5:11571. [PMID: 26108467 PMCID: PMC4479816 DOI: 10.1038/srep11571] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/29/2015] [Indexed: 12/13/2022] Open
Abstract
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi-yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
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Affiliation(s)
- Guillaume Morel
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Lieven Sterck
- Department of Plant Systems Biology VIB, Technologiepark 927, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Dominique Swennen
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Djamila Onesime
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Anthony Levasseur
- INRA UMR1163, Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, Polytech Marseille, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | - Noémie Jacques
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Sandrine Mallet
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Arnaux Couloux
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Karine Labadie
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Joëlle Amselem
- INRA UR1164, Unité de Recherche Génomique – Info, 78000 Versailles, France
| | - Jean-Marie Beckerich
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | | | - Yves Van de Peer
- Department of Plant Systems Biology VIB, Technologiepark 927, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
- Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
| | - Patrick Wincker
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
- CNRS UMR 8030, 2 Rue Gaston Crémieux, Évry, 91000, France
- Université d’Evry, Bd François Mitterand, Evry,91025, France
| | - Jean-Luc Souciet
- Université de Strasbourg, CNRS UMR7156, Strasbourg, 67000, France
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Colin R. Tinsley
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Serge Casaregola
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
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Dujon B. Basic principles of yeast genomics, a personal recollection: Graphical Abstract Figure. FEMS Yeast Res 2015; 15:fov047. [DOI: 10.1093/femsyr/fov047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2015] [Indexed: 12/12/2022] Open
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Evans BJ, Kwon T. Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs (Xenopus). Cytogenet Genome Res 2015; 145:243-52. [PMID: 26066830 DOI: 10.1159/000431108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genome duplication creates redundancy in proteins and their interaction networks, and subsequent smaller-scale gene duplication can further amplify genetic redundancy. Mutations then lead to the loss, maintenance or functional divergence of duplicated genes. Genome duplication occurred many times in African clawed frogs (genus Xenopus), and almost all extant species in this group evolved from a polyploid ancestor. To better understand the nature of selective constraints in a polyploid genome, we examined molecular polymorphism and divergence of duplicates and single-copy genes in 2 tetraploid African clawed frog species, Xenopus laevis and X. victorianus. We found that molecular polymorphism in the coding regions of putative duplicated genes was higher than in singletons, but not significantly so. Our findings also suggest that transcriptome evolution in polyploids is influenced by variation in the genome-wide mutation rate, and do not reject the hypothesis that gene dosage balance is also important.
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Affiliation(s)
- Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ont., Canada
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Andersson DI, Jerlström-Hultqvist J, Näsvall J. Evolution of new functions de novo and from preexisting genes. Cold Spring Harb Perspect Biol 2015; 7:7/6/a017996. [PMID: 26032716 DOI: 10.1101/cshperspect.a017996] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
How the enormous structural and functional diversity of new genes and proteins was generated (estimated to be 10(10)-10(12) different proteins in all organisms on earth [Choi I-G, Kim S-H. 2006. Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci 103: 14056-14061] is a central biological question that has a long and rich history. Extensive work during the last 80 years have shown that new genes that play important roles in lineage-specific phenotypes and adaptation can originate through a multitude of different mechanisms, including duplication, lateral gene transfer, gene fusion/fission, and de novo origination. In this review, we focus on two main processes as generators of new functions: evolution of new genes by duplication and divergence of pre-existing genes and de novo gene origination in which a whole protein-coding gene evolves from a noncoding sequence.
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Affiliation(s)
- Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Joakim Näsvall
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
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Lipids containing medium-chain fatty acids are specific to post-whole genome duplication Saccharomycotina yeasts. BMC Evol Biol 2015; 15:97. [PMID: 26018144 PMCID: PMC4446107 DOI: 10.1186/s12862-015-0369-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 04/29/2015] [Indexed: 12/04/2022] Open
Abstract
Background Yeasts belonging to the subphylum Saccharomycotina have been used for centuries in food processing and, more recently, biotechnology. Over the past few decades, these yeasts have also been studied in the interest of their potential to produce oil to replace fossil resources. Developing yeasts for massive oil production requires increasing yield and modifying the profiles of the fatty acids contained in the oil to satisfy specific technical requirements. For example, derivatives of medium-chain fatty acids (MCFAs, containing 6–14 carbons) are used for the production of biodiesels, cleaning products, lubricants and cosmetics. Few studies are available in the literature on the production of MCFAs in yeasts. Results We analyzed the MCFA content in Saccharomyces cerevisiae grown in various conditions. The results revealed that MCFAs preferentially accumulated when cells were grown on synthetic media with a high C/N ratio at low temperature (23 °C). Upon screening deletion mutant strains for genes encoding lipid droplet-associated proteins, we found two genes, LOA1 and TGL3, involved in MCFA homeostasis. A phylogenetic analysis on 16 Saccharomycotina species showed that fatty acid profiles differed drastically among yeasts. Interestingly, MCFAs are only present in post-whole genome duplication yeast species. Conclusions In this study, we produced original data on fatty acid diversity in yeasts. We demonstrated that yeasts are amenable to genetic and metabolic engineering to increase their MCFA production. Furthermore, we revealed that yeast lipid biodiversity has not been fully explored, but that yeasts likely harbor as-yet-undiscovered strains or enzymes that can contribute to the production of high-value fatty acids for green chemistry. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0369-2) contains supplementary material, which is available to authorized users.
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Fares MA. The origins of mutational robustness. Trends Genet 2015; 31:373-81. [PMID: 26013677 DOI: 10.1016/j.tig.2015.04.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 11/17/2022]
Abstract
Biological systems are resistant to genetic changes; a property known as mutational robustness, the origin of which remains an open question. In recent years, researchers have explored emergent properties of biological systems and mechanisms of genetic redundancy to reveal how mutational robustness emerges and persists. Several mechanisms have been proposed to explain the origin of mutational robustness, including molecular chaperones and gene duplication. The latter has received much attention, but its role in robustness remains controversial. Here, I examine recent findings linking genetic redundancy through gene duplication and mutational robustness. Experimental evolution and genome resequencing have made it possible to test the role of gene duplication in tolerating mutations at both the coding and regulatory levels. This evidence as well as previous findings on regulatory reprogramming of duplicates support the role of gene duplication in the origin of robustness.
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Affiliation(s)
- Mario A Fares
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain; Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin, Ireland.
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Tanaka K, Diekmann Y, Hazbun A, Hijazi A, Vreede B, Roch F, Sucena É. Multispecies Analysis of Expression Pattern Diversification in the Recently Expanded Insect Ly6 Gene Family. Mol Biol Evol 2015; 32:1730-47. [PMID: 25743545 PMCID: PMC4476152 DOI: 10.1093/molbev/msv052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gene families often consist of members with diverse expression domains reflecting their functions in a wide variety of tissues. However, how the expression of individual members, and thus their tissue-specific functions, diversified during the course of gene family expansion is not well understood. In this study, we approached this question through the analysis of the duplication history and transcriptional evolution of a rapidly expanding subfamily of insect Ly6 genes. We analyzed different insect genomes and identified seven Ly6 genes that have originated from a single ancestor through sequential duplication within the higher Diptera. We then determined how the original embryonic expression pattern of the founding gene diversified by characterizing its tissue-specific expression in the beetle Tribolium castaneum, the butterfly Bicyclus anynana, and the mosquito Anopheles stephensi and those of its duplicates in three higher dipteran species, representing various stages of the duplication history (Megaselia abdita, Ceratitis capitata, and Drosophila melanogaster). Our results revealed that frequent neofunctionalization episodes contributed to the increased expression breadth of this subfamily and that these events occurred after duplication and speciation events at comparable frequencies. In addition, at each duplication node, we consistently found asymmetric expression divergence. One paralog inherited most of the tissue-specificities of the founder gene, whereas the other paralog evolved drastically reduced expression domains. Our approach attests to the power of combining a well-established duplication history with a comprehensive coverage of representative species in acquiring unequivocal information about the dynamics of gene expression evolution in gene families.
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Affiliation(s)
| | | | | | - Assia Hijazi
- Centre de Biologie du Développement, CNRS UMR 5547, Université de Toulouse UPS, Toulouse, France
| | | | - Fernando Roch
- Centre de Biologie du Développement, CNRS UMR 5547, Université de Toulouse UPS, Toulouse, France
| | - Élio Sucena
- Instituto Gulbenkian de Ciência, Oeiras, Portugal Departamento de Biologia Animal, Faculdade de Ciências, Edifício C2, Universidade de Lisboa, Lisboa, Portugal
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Nguyen Ba AN, Strome B, Hua JJ, Desmond J, Gagnon-Arsenault I, Weiss EL, Landry CR, Moses AM. Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences. PLoS Comput Biol 2014; 10:e1003977. [PMID: 25474245 PMCID: PMC4256066 DOI: 10.1371/journal.pcbi.1003977] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/07/2014] [Indexed: 11/18/2022] Open
Abstract
Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared null distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication. How a protein is controlled is intimately linked to its function. Therefore, evolution can drive the functional divergence of proteins by tweaking their regulation, even if enzymatic capacities are preserved. Changes in posttranslational regulation (protein phosphorylation, degradation, subcellular localization, etc.) could therefore represent key mechanisms in functional divergence and lead to different phenotypic outcomes. Since disordered protein regions contain sites of protein modification and interaction (known as short linear motifs) and evolve rapidly relative to domains encoding enzymatic functions, these regions are good candidates to harbour sequence changes that underlie changes in function. In this study, we develop a statistical framework to identify changes in rate of evolution specific to protein regulatory sequences and identify hundreds of short linear motifs in disordered regions that are likely to have diverged after the whole-genome duplication in budding yeast. We show that these divergent motifs are much more frequent in paralogs than in single-copy proteins, and that they are more frequent in duplicate pairs that have functionally diverged. Our analysis suggests that changes in short linear motifs in disordered protein regions could be important molecular mechanisms of functional divergence after gene duplication.
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Affiliation(s)
- Alex N Nguyen Ba
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Bob Strome
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Jun Jie Hua
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Jonathan Desmond
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Isabelle Gagnon-Arsenault
- Département de Biologie, IBIS and PROTEO, Pavillon Charles-Eugene-Marchand, Laval University, Québec City, Canada
| | - Eric L Weiss
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Christian R Landry
- Département de Biologie, IBIS and PROTEO, Pavillon Charles-Eugene-Marchand, Laval University, Québec City, Canada
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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Conant GC. Comparative genomics as a time machine: how relative gene dosage and metabolic requirements shaped the time-dependent resolution of yeast polyploidy. Mol Biol Evol 2014; 31:3184-93. [PMID: 25158798 DOI: 10.1093/molbev/msu250] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Using a phylogenetic model of evolution after genome duplication (i.e., polyploidy) and 12 yeast genomes with a shared genome duplication, I show that the loss of duplicate genes after that duplication occurred in three phases. First, losses that occurred immediately after the event were biased toward genes functioning in DNA repair and organellar functions. Then, the main group of duplicate losses appear to have been shaped by a requirement to maintain balance in protein levels: There is a strong statistical association between the number of protein interactions a gene's product is involved in and its propensity to have remained in duplicate. Moreover, when duplicated genes with interactions were lost, it was more common than expected for both members of an interaction pair to have been lost on the same branch of the phylogeny. Finally, in the third phase of the resolution process, overretention of duplicated enzymes carrying high flux and of duplicated genes involved in transcriptional regulation became dominant. I speculate that initial retention of such genes by a requirement to maintain gene dosage set the stage for the later functional changes that then maintained these duplicates for long periods.
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Affiliation(s)
- Gavin C Conant
- Informatics Institute, University of Missouri, Columbia Division of Animal Sciences, University of Missouri, Columbia
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42
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Vanneste K, Baele G, Maere S, Van de Peer Y. Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res 2014; 24:1334-47. [PMID: 24835588 PMCID: PMC4120086 DOI: 10.1101/gr.168997.113] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 05/16/2014] [Indexed: 02/02/2023]
Abstract
Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous-Paleogene (K-Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K-Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids.
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Affiliation(s)
- Kevin Vanneste
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven B-3000, Belgium
| | - Steven Maere
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria 0002, South Africa
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43
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Pich I Roselló O, Kondrashov FA. Long-term asymmetrical acceleration of protein evolution after gene duplication. Genome Biol Evol 2014; 6:1949-55. [PMID: 25070510 PMCID: PMC4159008 DOI: 10.1093/gbe/evu159] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on how long the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolution must end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in the mammalian lineage. We find that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications. We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event.
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Affiliation(s)
- Oriol Pich I Roselló
- Facultat de Medicina, Universitat de Barcelona (UB), SpainBioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, SpainUniversitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, SpainUniversitat Pompeu Fabra (UPF), Barcelona, SpainInstitució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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44
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Andreani J, Guerois R. Evolution of protein interactions: From interactomes to interfaces. Arch Biochem Biophys 2014; 554:65-75. [DOI: 10.1016/j.abb.2014.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/28/2014] [Accepted: 05/12/2014] [Indexed: 12/16/2022]
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45
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Conant GC, Birchler JA, Pires JC. Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. CURRENT OPINION IN PLANT BIOLOGY 2014; 19:91-8. [PMID: 24907529 DOI: 10.1016/j.pbi.2014.05.008] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 05/06/2014] [Accepted: 05/08/2014] [Indexed: 05/04/2023]
Abstract
Requirements to maintain dosage balance shape many genome-scale patterns in organisms, including the resolution of whole genome duplications (WGD), as well as the varied effects of aneuploidy, segmental duplications, tandem duplications, gene copy number variations (CNV), and epigenetic marks. Like neofunctionalization and subfunctionalization, the impact of absolute and relative dosage varies over time. These variations are of particular importance in understanding the role of dosage in the evolution of polyploid organisms. Numerous investigations have found the consequences of polyploidy remain distinct from small-scale duplications (SSD). This observation is significant as all flowering plants have experienced at least two ancient polyploid events, and many angiosperm lineages have undergone additional rounds of polyploidy. Intriguingly, recent studies indicate a link between how epigenetic marks in recent allopolyploids may induce immediate changes in gene expression and the longer-term patterns of biased fractionation and chromosomal evolution. We argue that dosage effects represent one aspect of an emerging pluralistic framework, a framework that will use biophysics, genomic technologies, and systems-level models of cells to broaden our view of how genomes evolve.
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Affiliation(s)
- Gavin C Conant
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States; Informatics Institute, University of Missouri, Columbia, MO 65211, United States.
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
| | - J Chris Pires
- Informatics Institute, University of Missouri, Columbia, MO 65211, United States; Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
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46
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Zarin T, Moses AM. Insights into molecular evolution from yeast genomics. Yeast 2014; 31:233-41. [PMID: 24760744 DOI: 10.1002/yea.3018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 12/13/2022] Open
Abstract
Enabled by comparative genomics, yeasts have increasingly developed into a powerful model system for molecular evolution. Here we survey several areas in which yeast studies have made important contributions, including regulatory evolution, gene duplication and divergence, evolution of gene order and evolution of complexity. In each area we highlight key studies and findings based on techniques ranging from statistical analysis of large datasets to direct laboratory measurements of fitness. Future work will combine traditional evolutionary genetics analysis and experimental evolution with tools from systems biology to yield mechanistic insight into complex phenotypes.
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Affiliation(s)
- Taraneh Zarin
- Department of Cell and Systems Biology, University of Toronto, ON, Canada
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47
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Moghe GD, Hufnagel DE, Tang H, Xiao Y, Dworkin I, Town CD, Conner JK, Shiu SH. Consequences of Whole-Genome Triplication as Revealed by Comparative Genomic Analyses of the Wild Radish Raphanus raphanistrum and Three Other Brassicaceae Species. THE PLANT CELL 2014; 26:1925-1937. [PMID: 24876251 PMCID: PMC4079359 DOI: 10.1105/tpc.114.124297] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/30/2014] [Accepted: 04/30/2014] [Indexed: 05/18/2023]
Abstract
Polyploidization events are frequent among flowering plants, and the duplicate genes produced via such events contribute significantly to plant evolution. We sequenced the genome of wild radish (Raphanus raphanistrum), a Brassicaceae species that experienced a whole-genome triplication event prior to diverging from Brassica rapa. Despite substantial gene gains in these two species compared with Arabidopsis thaliana and Arabidopsis lyrata, ∼70% of the orthologous groups experienced gene losses in R. raphanistrum and B. rapa, with most of the losses occurring prior to their divergence. The retained duplicates show substantial divergence in sequence and expression. Based on comparison of A. thaliana and R. raphanistrum ortholog floral expression levels, retained radish duplicates diverged primarily via maintenance of ancestral expression level in one copy and reduction of expression level in others. In addition, retained duplicates differed significantly from genes that reverted to singleton state in function, sequence composition, expression patterns, network connectivity, and rates of evolution. Using these properties, we established a statistical learning model for predicting whether a duplicate would be retained postpolyploidization. Overall, our study provides new insights into the processes of plant duplicate loss, retention, and functional divergence and highlights the need for further understanding factors controlling duplicate gene fate.
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Affiliation(s)
- Gaurav D Moghe
- Programs in Genetics and Quantitative Biology, Michigan State University, East Lansing, Michigan 48824
| | - David E Hufnagel
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, Maryland 20850
| | - Yongli Xiao
- National Institute of Allergy and Infectious Disease, National Institute of Health, Bethesda, Maryland 20892
| | - Ian Dworkin
- Department of Zoology, Michigan State University, East Lansing, Michigan 48824
| | | | - Jeffrey K Conner
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 Kellogg Biological Station, Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Programs in Genetics and Quantitative Biology, Michigan State University, East Lansing, Michigan 48824 Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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48
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Sequence and structure space model of protein divergence driven by point mutations. J Theor Biol 2013; 330:1-8. [DOI: 10.1016/j.jtbi.2013.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 03/07/2013] [Accepted: 03/18/2013] [Indexed: 12/11/2022]
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49
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Reece-Hoyes JS, Pons C, Diallo A, Mori A, Shrestha S, Kadreppa S, Nelson J, Diprima S, Dricot A, Lajoie BR, Ribeiro PSM, Weirauch MT, Hill DE, Hughes TR, Myers CL, Walhout AJM. Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. Mol Cell 2013; 51:116-27. [PMID: 23791784 DOI: 10.1016/j.molcel.2013.05.018] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/28/2013] [Accepted: 05/15/2013] [Indexed: 10/26/2022]
Abstract
Gene duplication results in two identical paralogs that diverge through mutation, leading to loss or gain of interactions with other biomolecules. Here, we comprehensively characterize such network rewiring for C. elegans transcription factors (TFs) within and across four newly delineated molecular networks. Remarkably, we find that even highly similar TFs often have different interaction degrees and partners. In addition, we find that most TF families have a member that is highly connected in multiple networks. Further, different TF families have opposing correlations between network connectivity and phylogenetic age, suggesting that they are subject to different evolutionary pressures. Finally, TFs that have similar partners in one network generally do not in another, indicating a lack of pressure to retain cross-network similarity. Our multiparameter analyses provide unique insights into the evolutionary dynamics that shaped TF networks.
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50
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Pegueroles C, Laurie S, Albà MM. Accelerated evolution after gene duplication: a time-dependent process affecting just one copy. Mol Biol Evol 2013; 30:1830-42. [PMID: 23625888 DOI: 10.1093/molbev/mst083] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Gene duplication is widely regarded as a major mechanism modeling genome evolution and function. However, the mechanisms that drive the evolution of the two, initially redundant, gene copies are still ill defined. Many gene duplicates experience evolutionary rate acceleration, but the relative contribution of positive selection and random drift to the retention and subsequent evolution of gene duplicates, and for how long the molecular clock may be distorted by these processes, remains unclear. Focusing on rodent genes that duplicated before and after the mouse and rat split, we find significantly increased sequence divergence after duplication in only one of the copies, which in nearly all cases corresponds to the novel daughter copy, independent of the mechanism of duplication. We observe that the evolutionary rate of the accelerated copy, measured as the ratio of nonsynonymous to synonymous substitutions, is on average 5-fold higher in the period spanning 4-12 My after the duplication than it was before the duplication. This increase can be explained, at least in part, by the action of positive selection according to the results of the maximum likelihood-based branch-site test. Subsequently, the rate decelerates until purifying selection completely returns to preduplication levels. Reversion to the original rates has already been accomplished 40.5 My after the duplication event, corresponding to a genetic distance of about 0.28 synonymous substitutions per site. Differences in tissue gene expression patterns parallel those of substitution rates, reinforcing the role of neofunctionalization in explaining the evolution of young gene duplicates.
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Affiliation(s)
- Cinta Pegueroles
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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