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del Arco A, Fischer MG, Becks L. Evolution of exploitation and replication of giant viruses and virophages. Virus Evol 2024; 10:veae021. [PMID: 38562952 PMCID: PMC10984621 DOI: 10.1093/ve/veae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/05/2024] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
Tripartite biotic interactions are inherently complex, and the strong interdependence of species and often one-sided exploitation can make these systems vulnerable to extinction. The persistence of species depends then on the balance between exploitation and avoidance of exploitation beyond the point where sustainable resource use is no longer possible. We used this general prediction to test the potential role of trait evolution for persistence in a tripartite microbial system consisting of a marine heterotrophic flagellate preyed upon by a giant virus, which in turn is parasitized by a virophage. Host and virophage may benefit from this interaction because the virophage reduces the harmful effects of the giant virus on the host population and the virophage can persist integrated into the host genome when giant viruses are scarce. We grew hosts and virus in the presence and absence of the virophage over ∼280 host generations and tested whether levels of exploitation and replication in the giant virus and/or virophage population evolved over the course of the experiment, and whether the changes were such that they could avoid overexploitation and extinction. We found that the giant virus evolved toward lower levels of replication and the virophage evolved toward increased replication but decreased exploitation of the giant virus. These changes reduced overall host exploitation by the virus and virus exploitation by the virophage and are predicted to facilitate persistence.
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Affiliation(s)
- Ana del Arco
- Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Mainaustraße 252, Konstanz/Egg 78464, Germany
| | - Matthias G Fischer
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Lutz Becks
- Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Mainaustraße 252, Konstanz/Egg 78464, Germany
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2
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Winters NP, Wafula EK, Knollenberg BJ, Hämälä T, Timilsena PR, Perryman M, Zhang D, Sheaffer LL, Praul CA, Ralph PE, Prewitt S, Leandro-Muñoz ME, Delgadillo-Duran DA, Altman NS, Tiffin P, Maximova SN, dePamphilis CW, Marden JH, Guiltinan MJ. A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora. BMC Biol 2024; 22:38. [PMID: 38360697 PMCID: PMC10870529 DOI: 10.1186/s12915-024-01831-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Plants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree crop Theobroma cacao L., as well as four non-cacao Theobroma species, with the goal of identifying genetic elements essential for protection against the oomycete pathogen Phytophthora palmivora. RESULTS We began by creating a new, highly contiguous genome assembly for the P. palmivora-resistant genotype SCA 6 (Additional file 1: Tables S1-S5), deposited in GenBank under accessions CP139290-CP139299. We then used this high-quality assembly to combine RNA and whole-genome sequencing data to discover several genes and pathways associated with resistance. Many of these are unique, i.e., differentially regulated in only one of the four populations (diverged 40 k-900 k generations). Among the pathways shared across all populations is phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One gene in this pathway, caffeoyl shikimate esterase (CSE), was upregulated across all four populations following pathogen treatment, indicating its broad importance for cacao's defense response. Further experimental evidence suggests this gene hydrolyzes caffeoyl shikimate to create caffeic acid, an antimicrobial compound and known inhibitor of Phytophthora spp. CONCLUSIONS Our results indicate most expression variation associated with resistance is unique to populations. Moreover, our findings demonstrate the value of using a broad sample of evolutionarily diverged populations for revealing the genetic bases of cacao resistance to P. palmivora. This approach has promise for further revealing and harnessing valuable genetic resources in this and other long-generation plants.
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Affiliation(s)
- Noah P Winters
- IGDP Ecology, The Pennsylvania State University, 422 Huck Life Sciences Building, University Park, PA, 16803, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | | | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Prakash R Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Melanie Perryman
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, USA
| | - Lena L Sheaffer
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Craig A Praul
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Paula E Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sarah Prewitt
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Naomi S Altman
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Siela N Maximova
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Claude W dePamphilis
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA
| | - James H Marden
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Mark J Guiltinan
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
- Department of Biology, The Pennsylvania State University, University Park, PA, USA.
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
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3
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Stevens L, Martínez-Ugalde I, King E, Wagah M, Absolon D, Bancroft R, Gonzalez de la Rosa P, Hall JL, Kieninger M, Kloch A, Pelan S, Robertson E, Pedersen AB, Abreu-Goodger C, Buck AH, Blaxter M. Ancient diversity in host-parasite interaction genes in a model parasitic nematode. Nat Commun 2023; 14:7776. [PMID: 38012132 PMCID: PMC10682056 DOI: 10.1038/s41467-023-43556-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
Host-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These interactions can lead to negative frequency-dependent selection, a form of balancing selection that is hypothesised to explain the high levels of polymorphism seen in many host immune and parasite antigen loci. Here, we sequence the genomes of several individuals of Heligmosomoides bakeri, a model parasite of house mice, and Heligmosomoides polygyrus, a closely related parasite of wood mice. Although H. bakeri is commonly referred to as H. polygyrus in the literature, their genomes show levels of divergence that are consistent with at least a million years of independent evolution. The genomes of both species contain hyper-divergent haplotypes that are enriched for proteins that interact with the host immune response. Many of these haplotypes originated prior to the divergence between H. bakeri and H. polygyrus, suggesting that they have been maintained by long-term balancing selection. Together, our results suggest that the selection pressures exerted by the host immune response have played a key role in shaping patterns of genetic diversity in the genomes of parasitic nematodes.
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Affiliation(s)
- Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK.
| | - Isaac Martínez-Ugalde
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Erna King
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Martin Wagah
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | | | - Rowan Bancroft
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Jessica L Hall
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | | | - Sarah Pelan
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Elaine Robertson
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Amy B Pedersen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Amy H Buck
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK.
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4
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McLaughlin MS, Roy M, Abbasi PA, Carisse O, Yurgel SN, Ali S. Why Do We Need Alternative Methods for Fungal Disease Management in Plants? Plants (Basel) 2023; 12:3822. [PMID: 38005718 PMCID: PMC10675458 DOI: 10.3390/plants12223822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
Fungal pathogens pose a major threat to food production worldwide. Traditionally, chemical fungicides have been the primary means of controlling these pathogens, but many of these fungicides have recently come under increased scrutiny due to their negative effects on the health of humans, animals, and the environment. Furthermore, the use of chemical fungicides can result in the development of resistance in populations of phytopathogenic fungi. Therefore, new environmentally friendly alternatives that provide adequate levels of disease control are needed to replace chemical fungicides-if not completely, then at least partially. A number of alternatives to conventional chemical fungicides have been developed, including plant defence elicitors (PDEs); biological control agents (fungi, bacteria, and mycoviruses), either alone or as consortia; biochemical fungicides; natural products; RNA interference (RNAi) methods; and resistance breeding. This article reviews the conventional and alternative methods available to manage fungal pathogens, discusses their strengths and weaknesses, and identifies potential areas for future research.
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Affiliation(s)
- Michael S. McLaughlin
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 4H5, Canada
| | - Maria Roy
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | - Pervaiz A. Abbasi
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
| | - Odile Carisse
- Saint-Jean-sur-Richelieu Research Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 7B5, Canada;
| | - Svetlana N. Yurgel
- United States Department of Agriculture (USDA), Agricultural Research Service, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA;
| | - Shawkat Ali
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
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5
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Kapoor B, Jenkins J, Schmutz J, Zhebentyayeva T, Kuelheim C, Coggeshall M, Heim C, Lasky JR, Leites L, Islam-Faridi N, Romero-Severson J, DeLeo VL, Lucas SM, Lazic D, Gailing O, Carlson J, Staton M. A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species. G3 (Bethesda) 2023; 13:jkad209. [PMID: 37708394 PMCID: PMC10627279 DOI: 10.1093/g3journal/jkad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023]
Abstract
Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Quercus robur. Phylogenetic analysis also identified 4 subfamilies of the IGT/LAZY gene family in Q. rubra important for plant structure. Single major QTL regions were identified for vegetative bud break and marcescence, which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and 8 tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomic community, which will expedite comparative genomics and biological studies in Quercus species.
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Affiliation(s)
- Beant Kapoor
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Tatyana Zhebentyayeva
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40506, USA
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Carsten Kuelheim
- College of Forest Resources and Environmental Science, Michigan Tech University, Houghton, MI 49931, USA
| | - Mark Coggeshall
- College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Chris Heim
- Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Leites
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Nurul Islam-Faridi
- Forest Tree Molecular Cytogenetics Laboratory, USDA-FS, SRS-4160, Department of Ecology & Conservation Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Victoria L DeLeo
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M Lucas
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Desanka Lazic
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - John Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
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6
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Le Naour—Vernet M, Charriat F, Gracy J, Cros-Arteil S, Ravel S, Veillet F, Meusnier I, Padilla A, Kroj T, Cesari S, Gladieux P. Adaptive evolution in virulence effectors of the rice blast fungus Pyricularia oryzae. PLoS Pathog 2023; 19:e1011294. [PMID: 37695773 PMCID: PMC10513199 DOI: 10.1371/journal.ppat.1011294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/21/2023] [Accepted: 08/09/2023] [Indexed: 09/13/2023] Open
Abstract
Plant pathogens secrete proteins called effectors that target host cellular processes to promote disease. Recently, structural genomics has identified several families of fungal effectors that share a similar three-dimensional structure despite remarkably variable amino-acid sequences and surface properties. To explore the selective forces that underlie the sequence variability of structurally-analogous effectors, we focused on MAX effectors, a structural family of effectors that are major determinants of virulence in the rice blast fungus Pyricularia oryzae. Using structure-informed gene annotation, we identified 58 to 78 MAX effector genes per genome in a set of 120 isolates representing seven host-associated lineages. The expression of MAX effector genes was primarily restricted to the early biotrophic phase of infection and strongly influenced by the host plant. Pangenome analyses of MAX effectors demonstrated extensive presence/absence polymorphism and identified gene loss events possibly involved in host range adaptation. However, gene knock-in experiments did not reveal a strong effect on virulence phenotypes suggesting that other evolutionary mechanisms are the main drivers of MAX effector losses. MAX effectors displayed high levels of standing variation and high rates of non-synonymous substitutions, pointing to widespread positive selection shaping the molecular diversity of MAX effectors. The combination of these analyses with structural data revealed that positive selection acts mostly on residues located in particular structural elements and at specific positions. By providing a comprehensive catalog of amino acid polymorphism, and by identifying the structural determinants of the sequence diversity, our work will inform future studies aimed at elucidating the function and mode of action of MAX effectors.
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Affiliation(s)
- Marie Le Naour—Vernet
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Florian Charriat
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Jérôme Gracy
- Centre de Biologie Structurale (CBS), Univ Montpellier, INSERM, CNRS, Montpellier, France
| | - Sandrine Cros-Arteil
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sébastien Ravel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Florian Veillet
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Isabelle Meusnier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - André Padilla
- Centre de Biologie Structurale (CBS), Univ Montpellier, INSERM, CNRS, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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7
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Li J, Lee CR. The role of gene presence-absence variations on genetic incompatibility in Asian rice. New Phytol 2023; 239:778-791. [PMID: 37194454 PMCID: PMC7615310 DOI: 10.1111/nph.18969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/18/2023] [Indexed: 05/18/2023]
Abstract
Genetic incompatibilities are widespread between species. However, it remains unclear whether they all originated after population divergence as suggested by the Bateson-Dobzhansky-Muller model, and if not, what is their prevalence and distribution within populations. The gene presence-absence variations (PAVs) provide an opportunity for investigating gene-gene incompatibility. Here, we searched for the repulsion of coexistence between gene PAVs to identify the negative interaction of gene functions separately in two Oryza sativa subspecies. Many PAVs are involved in subspecies-specific negative epistasis and segregate at low-to-intermediate frequencies in focal subspecies but at low or high frequencies in the other subspecies. Incompatible PAVs are enriched in two functional groups, defense response and protein phosphorylation, which are associated with plant immunity and consistent with autoimmunity being a known mechanism of hybrid incompatibility in plants. Genes in the two enriched functional groups are older and seldom directly interact with each other. Instead, they interact with other younger gene PAVs with diverse functions. Our results illustrate the landscape of genetic incompatibility at gene PAVs in rice, where many incompatible pairs have already segregated as polymorphisms within subspecies, and many are novel negative interactions between older defense-related genes and younger genes with diverse functions.
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Affiliation(s)
- Juan Li
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 106319, Taiwan
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Swiss Institute for Bioinformatics, 1015 Lausanne, Switzerland
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 106319, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei 106319, Taiwan
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8
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Gupta S, Harkess A, Soble A, Van Etten M, Leebens-Mack J, Baucom RS. Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance. New Phytol 2023; 238:1263-1277. [PMID: 36721257 DOI: 10.1111/nph.18782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by-product of genetic hitchhiking.
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Affiliation(s)
- Sonal Gupta
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Alex Harkess
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Anah Soble
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
| | - Megan Van Etten
- Biology Department, Pennsylvania State University, Dunmore, PA, 18512, USA
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
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9
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Gu H, Wang L, Lv X, Yang W, Zhang L, Zhang Z, Zhu T, Jia Y, Chen Y, Qu L. Domestication affects sex-biased gene expression evolution in the duck. R Soc Open Sci 2023; 10:221313. [PMID: 37035296 PMCID: PMC10073915 DOI: 10.1098/rsos.221313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Genes with sex-biased expression are thought to underlie sexually dimorphic phenotypes and are therefore subject to different selection pressures in males and females. Many authors have proposed that sexual conflict leads to the evolution of sex-biased expression, which allows males and females to reach separate phenotypic and fitness optima. The selection pressures associated with domestication may cause changes in population architectures and mating systems, which in turn can alter their direction and strength. We compared sex-biased expression and genetic signatures in wild and domestic ducks (Anas platyrhynchos), and observed changes of sexual selection and identified the genomic divergence affected by selection forces. The extent of sex-biased expression in both sexes is positively correlated with the level of both d N /d S and nucleotide diversity. This observed changing pattern may mainly be owing to relaxed genetic constraints. We also demonstrate a clear link between domestication and sex-biased evolutionary rate in a comparative framework. Decreased polymorphism and evolutionary rate in domesticated populations generally matched life-history phenotypes known to experience artificial selection. Taken together, our work suggests the important implications of domestication in sex-biased evolution and the roles of artificial selection and sexual selection for shaping the diversity and evolutionary rate of the genome.
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Affiliation(s)
- Hongchang Gu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Li Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
| | - Zebin Zhang
- Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tao Zhu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing, People's Republic of China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
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10
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Taliadoros D, Stukenbrock EH. The use of evolutionary analyses to predict functionally relevant traits in filamentous plant pathogens. Curr Opin Microbiol 2023; 73:102244. [PMID: 36889024 DOI: 10.1016/j.mib.2022.102244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 03/08/2023]
Abstract
Identifying traits involved in plant-pathogen interactions is one of the major objectives in molecular plant pathology. Evolutionary analyses may assist in the identification of genes encoding traits that are involved in virulence and local adaptation, including adaptation to agricultural intervention strategies. In the past decades, the number of available genome sequences of fungal plant pathogens has rapidly increased, providing a rich source for the discovery of functionally important genes as well as inference of species histories. Positive selection in the form of diversifying or directional selection leaves particular signatures in genome alignments and can be identified with statistical genetics methods. This review summarises the concepts and approaches used in evolutionary genomics and lists major discoveries related to plant-pathogen adaptative evolution. We underline the significant contribution of evolutionary genomics in discovering virulence-related traits and the study of plant-pathogen ecology and adaptive evolution.
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11
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Roux F, Frachon L. A Genome-Wide Association study in Arabidopsis thaliana to decipher the adaptive genetics of quantitative disease resistance in a native heterogeneous environment. PLoS One 2022; 17:e0274561. [PMID: 36190949 DOI: 10.1371/journal.pone.0274561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/31/2022] [Indexed: 11/05/2022] Open
Abstract
Pathogens are often the main selective agents acting in plant communities, thereby influencing the distribution of polymorphism at loci affecting resistance within and among natural plant populations. In addition, the outcome of plant-pathogen interactions can be drastically affected by abiotic and biotic factors at different spatial and temporal grains. The characterization of the adaptive genetic architecture of disease resistance in native heterogeneous environments is however still missing. In this study, we conducted an in situ Genome-Wide Association study in the spatially heterogeneous native habitat of a highly genetically polymorphic local mapping population of Arabidopsis thaliana, to unravel the adaptive genetic architecture of quantitative disease resistance. Disease resistance largely differed among three native soils and was affected by the presence of the grass Poa annua. The observation of strong crossing reactions norms among the 195 A. thaliana genotypes for disease resistance among micro-habitats, combined with a negative fecundity-disease resistance relationship in each micro-habitat, suggest that alternative local genotypes of A. thaliana are favored under contrasting environmental conditions at the scale of few meters. A complex genetic architecture was detected for disease resistance and fecundity. However, only few QTLs were common between these two traits. Heterogeneous selection in this local population should therefore promote the maintenance of polymorphism at only few candidate resistance genes.
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12
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Xie P, Liu J, Lu R, Zhang Y, Sun X. Molecular evolution of the Pi-d2 gene conferring resistance to rice blast in Oryza. Front Genet 2022; 13:991900. [PMID: 36147495 PMCID: PMC9486079 DOI: 10.3389/fgene.2022.991900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/10/2022] [Indexed: 11/15/2022] Open
Abstract
The exploitation of plant disease resistance (R) genes in breeding programs is an effective strategy for coping with pathogens. An understanding of R gene variation is the basis for this strategy. Rice blast disease, caused by the Magnaporthe oryzae fungus, is a destructive disease of rice. The rice blast resistance gene Pi-d2 represents a new class of plant R gene because of its novel extracellular domain. We investigated the nucleotide polymorphism, phylogenetic topology and evolution patterns of the Pi-d2 gene among 67 cultivated and wild rice relatives. The Pi-d2 gene originated early in the basal Poales and has remained as a single gene without expansion. The striking finding is that susceptible Pi-d2 alleles might be derived from a single nucleotide substitution of the resistant alleles after the split of Oryza subspecies. Functional pleiotropy and linkage effects are proposed for the evolution and retention of the disease-susceptible alleles in rice populations. One set of DNA primers was developed from the polymorphic position to detect the functional nucleotide polymorphism for disease resistance of the Pi-d2 gene based on conventional Polymerase Chain Reaction. The nucleotide diversity level varied between different domains of the Pi-d2 gene, which might be related to distinct functions of each domain in the disease defense response. Directional (or purifying) selection appears dominant in the molecular evolution of the Pi-d2 gene and has shaped its conserved variation pattern.
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Affiliation(s)
| | | | | | | | - Xiaoqin Sun
- *Correspondence: Yanmei Zhang, ; Xiaoqin Sun,
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13
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Azar B. Profile of Joy M. Bergelson. Proc Natl Acad Sci U S A 2022; 119:e2212768119. [PMID: 35994635 DOI: 10.1073/pnas.2212768119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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14
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Abstract
Bacteria and lytic viruses (phages) engage in highly dynamic coevolutionary interactions over time, yet we have little idea of how transient selection by phages might shape the future evolutionary trajectories of their host populations. To explore this question, we generated genetically diverse phage-resistant mutants of the bacterium Pseudomonas syringae. We subjected the panel of mutants to prolonged experimental evolution in the absence of phages. Some populations re-evolved phage sensitivity, whereas others acquired compensatory mutations that reduced the costs of resistance without altering resistance levels. To ask whether these outcomes were driven by the initial genetic mechanisms of resistance, we next evolved independent replicates of each individual mutant in the absence of phages. We found a strong signature of historical contingency: some mutations were highly reversible across replicate populations, whereas others were highly entrenched. Through whole-genome sequencing of bacteria over time, we also found that populations with the same resistance gene acquired more parallel sets of mutations than populations with different resistance genes, suggesting that compensatory adaptation is also contingent on how resistance initially evolved. Our study identifies an evolutionary ratchet in bacteria–phage coevolution and may explain previous observations that resistance persists over time in some bacterial populations but is lost in others. We add to a growing body of work describing the key role of phages in the ecological and evolutionary dynamics of their host communities. Beyond this specific trait, our study provides a new insight into the genetic architecture of historical contingency, a crucial component of interpreting and predicting evolution.
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Affiliation(s)
- Reena Debray
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nina De Luna
- Department of Immunology, Pennsylvania State University, State College, PA, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.,Chan Zuckerberg BioHub, San Francisco, CA, USA
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15
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Drabeck DH, Rucavado A, Hingst-Zaher E, Dean A, Jansa SA. Ancestrally reconstructed Von Willebrand Factor (vWF) reveals evidence for trench warfare coevolution between opossums and pit vipers. Mol Biol Evol 2022; 39:6611844. [PMID: 35723968 PMCID: PMC9255381 DOI: 10.1093/molbev/msac140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Opossums in the tribe Didelphini are resistant to pit viper venoms and are hypothesized to be coevolving with venomous snakes. Specifically, a protein involved in blood clotting (von Willebrand factor [vWF] which is targeted by snake venom C-type lectins [CTLs]) has been found to undergo rapid adaptive evolution in Didelphini. Several unique amino acid changes in vWF could explain their resistance; however, experimental evidence that these changes disrupt binding to venom CTLs was lacking. Furthermore, without explicit testing of ancestral phenotypes to reveal the mode of evolution, the assertion that this system represents an example of coevolution rather than noncoevolutionary adaptation remains unsupported. Using expressed vWF proteins and purified venom CTLs, we quantified binding affinity for vWF proteins from all resistant taxa, their venom-sensitive relatives, and their ancestors. We show that CTL-resistant vWF is present in opossums outside clade Didelphini and likely across a wider swath of opossums (family Didelphidae) than previously thought. Ancestral reconstruction and in vitro testing of vWF phenotypes in a clade of rapidly evolving opossums reveal a pattern consistent with trench warfare coevolution between opossums and their venomous snake prey.
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Affiliation(s)
- Danielle H Drabeck
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave., St Paul, MN 55108, USA.,Bell Museum, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Alexandra Rucavado
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Erika Hingst-Zaher
- Museu Biológico, Instituto Butantan, CEP 05503-900, São Paulo, SP, Brasil
| | - Antony Dean
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave., St Paul, MN 55108, USA
| | - Sharon A Jansa
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave., St Paul, MN 55108, USA.,Bell Museum, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA
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16
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Hou Z, Li A. Genomic Differentiation and Demographic Histories of Two Closely Related Salicaceae Species. Front Plant Sci 2022; 13:911467. [PMID: 35747877 PMCID: PMC9210983 DOI: 10.3389/fpls.2022.911467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Populus alba (P. alba) and Populus davidiana (P. davidiana) are important plant species for answering a variety of issues on species evolution due to their wide distribution and ability to adapt to a variety of environments and climates. Even though P. alba and P. davidiana belong to ecologically and economically important forest trees in the Northern Hemisphere, little is known about their genomic landscape and genome divergence during speciation. We re-sequenced 20 and 19 members of P. davidiana and P. alba, respectively, and found that the Dxy value between P. alba and P. davidiana was 0.2658, whereas the F ST values were 0.2988, indicating that the genetic divergence was fairly clear. Populus davidiana and P. alba diverged from the ancestor in the middle Pleistocene, c. 0.80 Ma (95% HPD: 0.79-0.81 Ma). The population sizes of P. davidiana increased ~20,000 years ago after a considerable long-term decline following divergence. However, after differentiation, the effective population size of P. alba expanded slightly before experiencing a long-term bottleneck effect. According to the expectation of allopatric speciation, we found a significant number of genomic differentiation sites in both species' speciation events, and the majority of these genomic differentiation regions can be attributed to neutral evolutionary processes. Nevertheless, the regions with extreme divergence exist in abundance, indicating that natural selection has had an impact. Positive selection can be found in highly differentiated regions, while long-term balancing selection traits can be easily observed in low differentiated regions. According to these findings, climate differences over the Quaternary, as well as variance in linked selection and recombination, all contributed significantly to genomic divergence during allopatric speciation of the two aspens.
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17
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Cantila AY, Neik TX, Tirnaz S, Thomas WJW, Bayer PE, Edwards D, Batley J. Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana. Biology 2022; 11:821. [PMID: 35741342 PMCID: PMC9220128 DOI: 10.3390/biology11060821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary Developing cultivars with resistance genes (R genes) is an effective strategy to support high yield and quality in Brassica crops. The availability of clone R gene and genomic sequences in Brassica species and Arabidopsis thaliana provide the opportunity to compare genomic regions and survey R genes across genomic databases. In this paper, we aim to identify genes related to cloned genes through sequence identity, providing a repertoire of species-wide related R genes in Brassica crops. The comprehensive list of candidate R genes can be used as a reference for functional analysis. Abstract Various diseases severely affect Brassica crops, leading to significant global yield losses and a reduction in crop quality. In this study, we used the complete protein sequences of 49 cloned resistance genes (R genes) that confer resistance to fungal and bacterial diseases known to impact species in the Brassicaceae family. Homology searches were carried out across Brassica napus, B. rapa, B. oleracea, B. nigra, B. juncea, B. carinata and Arabidopsis thaliana genomes. In total, 660 cloned disease R gene homologs (CDRHs) were identified across the seven species, including 431 resistance gene analogs (RGAs) (248 nucleotide binding site-leucine rich repeats (NLRs), 150 receptor-like protein kinases (RLKs) and 33 receptor-like proteins (RLPs)) and 229 non-RGAs. Based on the position and distribution of specific homologs in each of the species, we observed a total of 87 CDRH clusters composed of 36 NLR, 16 RLK and 3 RLP homogeneous clusters and 32 heterogeneous clusters. The CDRHs detected consistently across the seven species are candidates that can be investigated for broad-spectrum resistance, potentially providing resistance to multiple pathogens. The R genes identified in this study provide a novel resource for the future functional analysis and gene cloning of Brassicaceae R genes towards crop improvement.
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18
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Märkle H, Saur IML, Stam R. Evolution of resistance (R) gene specificity. Essays Biochem 2022:EBC20210077. [PMID: 35612398 DOI: 10.1042/EBC20210077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022]
Abstract
Plant resistance (R) genes are members of large gene families with significant within and between species variation. It has been hypothesised that a variety of processes have shaped R gene evolution and the evolution of R gene specificity. In this review, we illustrate the main mechanisms that generate R gene diversity and provide examples of how they can change R gene specificity. Next, we explain which evolutionary mechanisms are at play and how they determine the fate of new R gene alleles and R genes. Finally, we place this in a larger context by comparing the diversity and evolution of R gene specificity within and between species scales.
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19
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Songsomboon K, Crawford R, Crawford J, Hansen J, Cummings J, Mattson N, Bergstrom GC, Viands DR. Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum L.). Plants 2022; 11:plants11101362. [PMID: 35631787 PMCID: PMC9144872 DOI: 10.3390/plants11101362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022]
Abstract
Switchgrass (Panicum virgatum L.), a northern native perennial grass, suffers from yield reduction from Bipolaris leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoemaker. This study aimed to determine the resistant populations via multiple phenotyping approaches and identify potential resistance genes from genome-wide association studies (GWAS) in the switchgrass northern association panel. The disease resistance was evaluated from both natural (field evaluations in Ithaca, New York and Phillipsburg, Philadelphia) and artificial inoculations (detached leaf and leaf disk assays). The most resistant populations based on a combination of three phenotyping approaches—detached leaf, leaf disk, and mean from two locations—were ‘SW788’, ‘SW806’, ‘SW802’, ‘SW793’, ‘SW781’, ‘SW797’, ‘SW798’, ‘SW803’, ‘SW795’, ‘SW805’. The GWAS from the association panel showed 27 significant SNPs on 12 chromosomes: 1K, 2K, 2N, 3K, 3N, 4N, 5K, 5N, 6N, 7K, 7N, and 9N. These markers accumulatively explained the phenotypic variance of the resistance ranging from 3.28 to 26.52%. Within linkage disequilibrium of 20 kb, these SNP markers linked with the potential resistance genes included the genes encoding for NBS-LRR, PPR, cell-wall related proteins, homeostatic proteins, anti-apoptotic proteins, and ABC transporter.
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Affiliation(s)
- Kittikun Songsomboon
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
- Correspondence:
| | - Ryan Crawford
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
| | - Jamie Crawford
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
| | - Julie Hansen
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
| | | | - Neil Mattson
- Section of Horticulture, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA;
| | - Gary C. Bergstrom
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA;
| | - Donald R. Viands
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
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20
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Naung MT, Martin E, Munro J, Mehra S, Guy AJ, Laman M, Harrison GLA, Tavul L, Hetzel M, Kwiatkowski D, Mueller I, Bahlo M, Barry AE. Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens. PLoS Comput Biol 2022; 18:e1009801. [PMID: 35108259 DOI: 10.1371/journal.pcbi.1009801] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/14/2022] [Accepted: 01/03/2022] [Indexed: 12/30/2022] Open
Abstract
Investigation of the diversity of malaria parasite antigens can help prioritize and validate them as vaccine candidates and identify the most common variants for inclusion in vaccine formulations. Studies of vaccine candidates of the most virulent human malaria parasite, Plasmodium falciparum, have focused on a handful of well-known antigens, while several others have never been studied. Here we examine the global diversity and population structure of leading vaccine candidate antigens of P. falciparum using the MalariaGEN Pf3K (version 5.1) resource, comprising more than 2600 genomes from 15 malaria endemic countries. A stringent variant calling pipeline was used to extract high quality antigen gene 'haplotypes' from the global dataset and a new R-package named VaxPack was used to streamline population genetic analyses. In addition, a newly developed algorithm that enables spatial averaging of selection pressure on 3D protein structures was applied to the dataset. We analysed the genes encoding 23 leading and novel candidate malaria vaccine antigens including csp, trap, eba175, ama1, rh5, and CelTOS. Our analysis shows that current malaria vaccine formulations are based on rare haplotypes and thus may have limited efficacy against natural parasite populations. High levels of diversity with evidence of balancing selection was detected for most of the erythrocytic and pre-erythrocytic antigens. Measures of natural selection were then mapped to 3D protein structures to predict targets of functional antibodies. For some antigens, geographical variation in the intensity and distribution of these signals on the 3D structure suggests adaptation to different human host or mosquito vector populations. This study provides an essential framework for the diversity of P. falciparum antigens to be considered in the design of the next generation of malaria vaccines.
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21
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Abstract
Host and parasite evolution are closely intertwined, with selection for adaptations and counter‐adaptations forming a coevolutionary feedback loop. Coevolutionary dynamics are often difficult to intuit due to these feedbacks and are hard to demonstrate empirically in most systems. Theoretical models have therefore played a crucial role in shaping our understanding of host–parasite coevolution. Theoretical models vary widely in their assumptions, approaches and aims, and such variety makes it difficult, especially for non‐theoreticians and those new to the field, to: (1) understand how model approaches relate to one another; (2) identify key modelling assumptions; (3) determine how model assumptions relate to biological systems; and (4) reconcile the results of different models with contrasting assumptions. In this review, we identify important model features, highlight key results and predictions and describe how these pertain to model assumptions. We carry out a literature survey of theoretical studies published since the 1950s (n = 219 papers) to support our analysis. We identify two particularly important features of models that tend to have a significant qualitative impact on the outcome of host–parasite coevolution: population dynamics and the genetic basis of infection. We also highlight the importance of other modelling features, such as stochasticity and whether time proceeds continuously or in discrete steps, that have received less attention but can drastically alter coevolutionary dynamics. We finish by summarizing recent developments in the field, specifically the trend towards greater model complexity, and discuss likely future directions for research.
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Affiliation(s)
- Lydia J Buckingham
- Department of Mathematical Sciences, University of Bath, Bath, UK, BA2 7AY.,Milner Centre for Evolution, University of Bath, Bath, UK, BA2 7AY
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, Bath, UK, BA2 7AY.,Milner Centre for Evolution, University of Bath, Bath, UK, BA2 7AY
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22
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Abstract
Bacterial defenses against phage, which include CRISPR-mediated immunity and other mechanisms, can carry substantial growth rate costs and can be rapidly lost when pathogens are eliminated. How bacteria preserve their molecular defenses despite their costs, in the face of variable pathogen levels and inter-strain competition, remains a major unsolved problem in evolutionary biology. Here, we present a multilevel model that incorporates biophysics of molecular binding, host-pathogen population dynamics, and ecological dynamics across a large number of independent territories. Using techniques of game theory and non-linear dynamical systems, we show that by maintaining a non-zero failure rate of defenses, hosts sustain sufficient levels of pathogen within an ecology to select against loss of the defense. This resistance switching strategy is evolutionarily stable, and provides a powerful evolutionary mechanism that maintains host-pathogen interactions, selects against cheater strains that avoid the costs of immunity, and enables co-evolutionary dynamics in a wide range of systems.
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Affiliation(s)
- Antun Skanata
- Department of Biology & Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Edo Kussell
- Department of Biology & Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA.
- Department of Physics, New York University, New York, NY, 10003, USA.
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23
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Roberts Kingman GA, Lee D, Jones FC, Desmet D, Bell MA, Kingsley DM. Longer or shorter spines: Reciprocal trait evolution in stickleback via triallelic regulatory changes in Stanniocalcin2a. Proc Natl Acad Sci U S A 2021; 118:e2100694118. [PMID: 34321354 PMCID: PMC8346906 DOI: 10.1073/pnas.2100694118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Vertebrates have repeatedly modified skeletal structures to adapt to their environments. The threespine stickleback is an excellent system for studying skeletal modifications, as different wild populations have either increased or decreased the lengths of their prominent dorsal and pelvic spines in different freshwater environments. Here we identify a regulatory locus that has a major morphological effect on the length of stickleback dorsal and pelvic spines, which we term Maser (major spine enhancer). Maser maps in a closely linked supergene complex that controls multiple armor, feeding, and behavioral traits on chromosome IV. Natural alleles in Maser are differentiated between marine and freshwater sticklebacks; however, alleles found among freshwater populations are also differentiated, with distinct alleles found in short- and long-spined freshwater populations. The distinct freshwater alleles either increase or decrease expression of the bone growth inhibitor gene Stanniocalcin2a in developing spines, providing a simple genetic mechanism for either increasing or decreasing spine lengths in natural populations. Genomic surveys suggest many recurrently differentiated loci in sticklebacks are similarly specialized into three or more distinct alleles, providing multiple ancient standing variants in particular genes that may contribute to a range of phenotypes in different environments.
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Affiliation(s)
| | - David Lee
- Stanford University School of Humanities and Sciences, Stanford University, Stanford, CA 94305
| | - Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Danielle Desmet
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA 94720
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305;
- HHMI, Stanford University School of Medicine, Stanford, CA 94305
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24
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Märkle H, John S, Cornille A, Fields PD, Tellier A. Novel genomic approaches to study antagonistic coevolution between hosts and parasites. Mol Ecol 2021; 30:3660-3676. [PMID: 34038012 DOI: 10.1111/mec.16001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
Host-parasite coevolution is ubiquitous, shaping genetic and phenotypic diversity and the evolutionary trajectory of interacting species. With the advances of high throughput sequencing technologies applicable to model and non-model organisms alike, it is now feasible to study in greater detail (a) the genetic underpinnings of coevolution, (b) the speed and type of dynamics at coevolving loci, and (c) the genomic consequences of coevolution. This review focuses on three recently developed approaches that leverage information from host and parasite full genome data simultaneously to pinpoint coevolving loci and draw inference on the coevolutionary history. First, co-genome-wide association study (co-GWAS) methods allow pinpointing the loci underlying host-parasite interactions. These methods focus on detecting associations between genetic variants and the outcome of experimental infection tests or on correlations between genomes of naturally infected hosts and their infecting parasites. Second, extensions to population genomics methods can detect genes under coevolution and infer the coevolutionary history, such as fitness costs. Third, correlations between host and parasite population size in time are indicative of coevolution, and polymorphism levels across independent spatially distributed populations of hosts and parasites can reveal coevolutionary loci and infer coevolutionary history. We describe the principles of these three approaches and discuss their advantages and limitations based on coevolutionary theory. We present recommendations for their application to various host (prokaryotes, fungi, plants, and animals) and parasite (viruses, bacteria, fungi, and macroparasites) species. We conclude by pointing out methodological and theoretical gaps to be filled to extract maximum information from full genome data and thereby to shed light on the molecular underpinnings of coevolution.
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Affiliation(s)
- Hanna Märkle
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Sona John
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Amandine Cornille
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Peter D Fields
- Department of Environmental Sciences, University of Basel, Zoology, Basel, Switzerland
| | - Aurélien Tellier
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
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25
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Abstract
Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, and especially the intracellular nucleotide-binding site leucine-rich repeat receptors, also known as NOD-like receptors (NLRs), are highly diversified, both among family members in the same genome, and between individuals in the same species. While this diversity has long been appreciated, its true extent has remained unknown. With pan-genome and pan-NLRome studies becoming more and more comprehensive, our knowledge of NLR sequence diversity is growing rapidly, and pan-NLRomes provide powerful platforms for assigning function to NLRs. These efforts are an important step toward the goal of comprehensively predicting from sequence alone whether an NLR provides disease resistance, and if so, to which pathogens.
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Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Calvo-Baltanás V, Wang J, Chae E. Hybrid Incompatibility of the Plant Immune System: An Opposite Force to Heterosis Equilibrating Hybrid Performances. Front Plant Sci 2021; 11:576796. [PMID: 33717206 PMCID: PMC7953517 DOI: 10.3389/fpls.2020.576796] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Hybridization is a core element in modern rice breeding as beneficial combinations of two parental genomes often result in the expression of heterosis. On the contrary, genetic incompatibility between parents can manifest as hybrid necrosis, which leads to tissue necrosis accompanied by compromised growth and/or reduced reproductive success. Genetic and molecular studies of hybrid necrosis in numerous plant species revealed that such self-destructing symptoms in most cases are attributed to autoimmunity: plant immune responses are inadvertently activated in the absence of pathogenic invasion. Autoimmunity in hybrids predominantly occurs due to a conflict involving a member of the major plant immune receptor family, the nucleotide-binding domain and leucine-rich repeat containing protein (NLR; formerly known as NBS-LRR). NLR genes are associated with disease resistance traits, and recent population datasets reveal tremendous diversity in this class of immune receptors. Cases of hybrid necrosis involving highly polymorphic NLRs as major causes suggest that diversified R gene repertoires found in different lineages would require a compatible immune match for hybridization, which is a prerequisite to ensure increased fitness in the resulting hybrids. In this review, we overview recent genetic and molecular findings on hybrid necrosis in multiple plant species to provide an insight on how the trade-off between growth and immunity is equilibrated to affect hybrid performances. We also revisit the cases of hybrid weakness in which immune system components are found or implicated to play a causative role. Based on our understanding on the trade-off, we propose that the immune system incompatibility in plants might play an opposite force to restrict the expression of heterosis in hybrids. The antagonism is illustrated under the plant fitness equilibrium, in which the two extremes lead to either hybrid necrosis or heterosis. Practical proposition from the equilibrium model is that breeding efforts for combining enhanced disease resistance and high yield shall be achieved by balancing the two forces. Reverse breeding toward utilizing genomic data centered on immune components is proposed as a strategy to generate elite hybrids with balanced immunity and growth.
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Barragan AC, Collenberg M, Wang J, Lee RRQ, Cher WY, Rabanal FA, Ashkenazy H, Weigel D, Chae E. A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana. Mol Biol Evol 2021; 38:557-574. [PMID: 32966577 PMCID: PMC7826191 DOI: 10.1093/molbev/msaa245] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies 3 weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR (nucleotide-binding site leucine-rich repeat) disease-resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11). There are multiple DM10 allelic variants in the global A. thaliana population, several of which have premature stop codons. One of these, which has a truncated LRR-PL (leucine-rich repeat [LRR]-post-LRR) region, corresponds to the DM10 risk allele. The DM10 locus and the adjacent genomic region in the risk allele carriers are highly differentiated from those in the nonrisk carriers in the global A. thaliana population, suggesting that this allele became geographically widespread only relatively recently. The DM11 risk allele is much rarer and found only in two accessions from southwestern Spain-a region from which the DM10 risk haplotype is absent-indicating that the ranges of DM10 and DM11 risk alleles may be nonoverlapping.
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Affiliation(s)
- Ana Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jinge Wang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rachelle R Q Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Wei Yuan Cher
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Fernando A Rabanal
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Haim Ashkenazy
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Biological Sciences, National University of Singapore, Singapore
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28
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Abstract
Males and females of the same species share the majority of their genomes, yet they are frequently exposed to conflicting selection pressures. Gene regulation is widely assumed to resolve these conflicting sex-specific selection pressures, and although there has been considerable focus on elucidating the role of gene expression level in sex-specific adaptation, other regulatory mechanisms have been overlooked. Alternative splicing enables different transcripts to be generated from the same gene, meaning that exons which have sex-specific beneficial effects can in theory be retained in the gene product, whereas exons with detrimental effects can be skipped. However, at present, little is known about how sex-specific selection acts on broad patterns of alternative splicing. Here, we investigate alternative splicing across males and females of multiple bird species. We identify hundreds of genes that have sex-specific patterns of splicing and establish that sex differences in splicing are correlated with phenotypic sex differences. Additionally, we find that alternatively spliced genes have evolved rapidly as a result of sex-specific selection and suggest that sex differences in splicing offer another route to sex-specific adaptation when gene expression level changes are limited by functional constraints. Overall, our results shed light on how a diverse transcriptional framework can give rise to the evolution of phenotypic sexual dimorphism.
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Affiliation(s)
- Thea F Rogers
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Daniela H Palmer
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Alison E Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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Md Hatta MA, Ghosh S, Athiyannan N, Richardson T, Steuernagel B, Yu G, Rouse MN, Ayliffe M, Lagudah ES, Radhakrishnan GV, Periyannan SK, Wulff BBH. Extensive Genetic Variation at the Sr22 Wheat Stem Rust Resistance Gene Locus in the Grasses Revealed Through Evolutionary Genomics and Functional Analyses. Mol Plant Microbe Interact 2020; 33:1286-1298. [PMID: 32779520 DOI: 10.1094/mpmi-01-20-0018-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In the last 20 years, severe wheat stem rust outbreaks have been recorded in Africa, Europe, and Central Asia. This previously well controlled disease, caused by the fungus Puccinia graminis f. sp. tritici, has reemerged as a major threat to wheat cultivation. The stem rust (Sr) resistance gene Sr22 encodes a nucleotide-binding and leucine-rich repeat receptor which confers resistance to the highly virulent African stem rust isolate Ug99. Here, we show that the Sr22 gene is conserved among grasses in the Triticeae and Poeae lineages. Triticeae species contain syntenic loci with single-copy orthologs of Sr22 on chromosome 7, except Hordeum vulgare, which has experienced major expansions and rearrangements at the locus. We also describe 14 Sr22 sequence variants obtained from both Triticum boeoticum and the domesticated form of this species, T. monococcum, which have been postulated to encode both functional and nonfunctional Sr22 alleles. The nucleotide sequence analysis of these alleles identified historical sequence exchange resulting from recombination or gene conversion, including breakpoints within codons, which expanded the coding potential at these positions by introduction of nonsynonymous substitutions. Three Sr22 alleles were transformed into wheat cultivar Fielder and two postulated resistant alleles from Schomburgk (hexaploid wheat introgressed with T. boeoticum segment carrying Sr22) and T. monococcum accession PI190945, respectively, conferred resistance to P. graminis f. sp. tritici race TTKSK, thereby unequivocally confirming Sr22 effectiveness against Ug99. The third allele from accession PI573523, previously believed to confer susceptibility, was confirmed as nonfunctional against Australian P. graminis f. sp. tritici race 98-1,2,3,5,6.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- M Asyraf Md Hatta
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Naveenkumar Athiyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Terese Richardson
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
| | | | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Matthew N Rouse
- United States Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
| | - Evans S Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
| | | | - Sambasivam K Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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Nilusmas S, Mercat M, Perrot T, Djian‐Caporalino C, Castagnone‐Sereno P, Touzeau S, Calcagno V, Mailleret L. Multi-seasonal modelling of plant-nematode interactions reveals efficient plant resistance deployment strategies. Evol Appl 2020; 13:2206-2221. [PMID: 33005219 PMCID: PMC7513734 DOI: 10.1111/eva.12989] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023] Open
Abstract
Root-knot nematodes, Meloidogyne spp., are soil-borne polyphagous pests with major impact on crop yield worldwide. Resistant crops efficiently control avirulent root-knot nematodes, but favour the emergence of virulent forms. Since virulence is associated with fitness costs, susceptible crops counter-select virulent root-knot nematodes. In this study, we identify optimal rotation strategies between susceptible and resistant crops to control root-knot nematodes and maximize crop yield. We developed an epidemiological model describing the within-season dynamics of avirulent and virulent root-knot nematodes on susceptible or resistant plant root-systems, and their between-season survival. The model was fitted to experimental data and used to predict yield-maximizing rotation strategies, with special attention to the impact of epidemic severity and genetic parameters. Crop rotations were found to be efficient under realistic parameter ranges. They were characterized by low ratios of resistant plants and were robust to parameter uncertainty. Rotations provide significant gain over resistant-only strategies, especially under intermediate fitness costs and severe epidemic contexts. Switching from the current general deployment of resistant crops to custom rotation strategies could not only maintain or increase crop yield, but also preserve the few and valuable R-genes available.
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Affiliation(s)
- Samuel Nilusmas
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
| | - Mathilde Mercat
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
| | - Thomas Perrot
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
| | | | | | - Suzanne Touzeau
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
| | | | - Ludovic Mailleret
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
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31
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Tennessen JA, Bollmann SR, Peremyslova E, Kronmiller BA, Sergi C, Hamali B, Blouin MS. Clusters of polymorphic transmembrane genes control resistance to schistosomes in snail vectors. eLife 2020; 9:59395. [PMID: 32845238 PMCID: PMC7494358 DOI: 10.7554/elife.59395] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
Schistosomiasis is a debilitating parasitic disease infecting hundreds of millions of people. Schistosomes use aquatic snails as intermediate hosts. A promising avenue for disease control involves leveraging innate host mechanisms to reduce snail vectorial capacity. In a genome-wide association study of Biomphalaria glabrata snails, we identify genomic region PTC2 which exhibits the largest known correlation with susceptibility to parasite infection (>15 fold effect). Using new genome assemblies with substantially higher contiguity than the Biomphalaria reference genome, we show that PTC2 haplotypes are exceptionally divergent in structure and sequence. This variation includes multi-kilobase indels containing entire genes, and orthologs for which most amino acid residues are polymorphic. RNA-Seq annotation reveals that most of these genes encode single-pass transmembrane proteins, as seen in another resistance region in the same species. Such groups of hyperdiverse snail proteins may mediate host-parasite interaction at the cell surface, offering promising targets for blocking the transmission of schistosomiasis.
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Affiliation(s)
- Jacob A Tennessen
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Stephanie R Bollmann
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Ekaterina Peremyslova
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Brent A Kronmiller
- Department of Integrative Biology, Oregon State University, Corvallis, United States.,Center for Genome Research and Biocomputing, Oregon State University, Corvallis, United States
| | - Clint Sergi
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Bulut Hamali
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Michael Scott Blouin
- Department of Integrative Biology, Oregon State University, Corvallis, United States
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32
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Abstract
Cooperation has been essential to the evolution of biological complexity, but many societies struggle to overcome internal conflicts and divisions. Dictyostelium discoideum, or the social amoeba, has been a useful model system for exploring these conflicts and how they can be resolved. When starved, these cells communicate, gather into groups, and build themselves into a multicellular fruiting body. Some cells altruistically die to form the rigid stalk, while the remainder sit atop the stalk, become spores, and disperse. Evolutionary theory predicts that conflict will arise over which cells die to form the stalk and which cells become spores and survive. The power of the social amoeba lies in the ability to explore how cooperation and conflict work across multiple levels, ranging from proximate mechanisms (how does it work?) to ultimate evolutionary answers (why does it work?). Recent studies point to solutions to the problem of ensuring fairness, such as the ability to suppress selfishness and to recognize and avoid unrelated individuals. This work confirms a central role for kin selection, but also suggests new explanations for how social amoebae might enforce cooperation. New approaches based on genomics are also enabling researchers to decipher for the first time the evolutionary history of cooperation and conflict and to determine its role in shaping the biology of multicellular organisms.
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Affiliation(s)
- Elizabeth A Ostrowski
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand.
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Zmienko A, Marszalek-Zenczak M, Wojciechowski P, Samelak-Czajka A, Luczak M, Kozlowski P, Karlowski WM, Figlerowicz M. AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. Plant Cell 2020; 32:1797-1819. [PMID: 32265262 PMCID: PMC7268809 DOI: 10.1105/tpc.19.00640] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 03/09/2020] [Accepted: 03/30/2020] [Indexed: 05/13/2023]
Abstract
Copy number variations (CNVs) greatly contribute to intraspecies genetic polymorphism and phenotypic diversity. Recent analyses of sequencing data for >1000 Arabidopsis (Arabidopsis thaliana) accessions focused on small variations and did not include CNVs. Here, we performed genome-wide analysis and identified large indels (50 to 499 bp) and CNVs (500 bp and larger) in these accessions. The CNVs fully overlap with 18.3% of protein-coding genes, with enrichment for evolutionarily young genes and genes involved in stress and defense. By combining analysis of both genes and transposable elements (TEs) affected by CNVs, we revealed that the variation statuses of genes and TEs are tightly linked and jointly contribute to the unequal distribution of these elements in the genome. We also determined the gene copy numbers in a set of 1060 accessions and experimentally validated the accuracy of our predictions by multiplex ligation-dependent probe amplification assays. We then successfully used the CNVs as markers to analyze population structure and migration patterns. Finally, we examined the impact of gene dosage variation triggered by a CNV spanning the SEC10 gene on SEC10 expression at both the transcript and protein levels. The catalog of CNVs, CNV-overlapping genes, and their genotypes in a top model dicot will stimulate the exploration of the genetic basis of phenotypic variation.
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Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | | | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
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Hall AR, Ashby B, Bascompte J, King KC. Measuring Coevolutionary Dynamics in Species-Rich Communities. Trends Ecol Evol 2020; 35:539-50. [DOI: 10.1016/j.tree.2020.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/24/2020] [Accepted: 02/03/2020] [Indexed: 12/18/2022]
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35
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Zhao C, Li T, Zhao Y, Zhang B, Li A, Zhao S, Hou L, Xia H, Fan S, Qiu J, Li P, Zhang Y, Guo B, Wang X. Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds. BMC Plant Biol 2020; 20:215. [PMID: 32404101 PMCID: PMC7222326 DOI: 10.1186/s12870-020-02426-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 04/30/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND MicroRNAs are important gene expression regulators in plants immune system. Aspergillus flavus is the most common causal agents of aflatoxin contamination in peanuts, but information on the function of miRNA in peanut-A. flavus interaction is lacking. In this study, the resistant cultivar (GT-C20) and susceptible cultivar (Tifrunner) were used to investigate regulatory roles of miRNAs in response to A. flavus growth. RESULTS A total of 30 miRNAs, 447 genes and 21 potential miRNA/mRNA pairs were differentially expressed significantly when treated with A. flavus. A total of 62 miRNAs, 451 genes and 44 potential miRNA/mRNA pairs exhibited differential expression profiles between two peanut varieties. Gene Ontology (GO) analysis showed that metabolic-process related GO terms were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses further supported the GO results, in which many enriched pathways were related with biosynthesis and metabolism, such as biosynthesis of secondary metabolites and metabolic pathways. Correlation analysis of small RNA, transcriptome and degradome indicated that miR156/SPL pairs might regulate the accumulation of flavonoids in resistant and susceptible genotypes. The miR482/2118 family might regulate NBS-LRR gene which had the higher expression level in resistant genotype. These results provided useful information for further understanding the roles of miR156/157/SPL and miR482/2118/NBS-LRR pairs. CONCLUSIONS Integration analysis of the transcriptome, miRNAome and degradome of resistant and susceptible peanut varieties were performed in this study. The knowledge gained will help to understand the roles of miRNAs of peanut in response to A. flavus.
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Affiliation(s)
- Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Tingting Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- Rizhao Experimental High School od Shandong, Rizhao, 276826 PR China
| | - Yuhan Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC USA
| | - Aiqin Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Shoujin Fan
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Jingjing Qiu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Ye Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, GA 31793 USA
- Department of Plant Pathology, University of Georgia, Tifton, GA USA
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
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36
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Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, Jones JDG, Dangl JL, Weigel D, Bemm F. A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell 2020; 178:1260-1272.e14. [PMID: 31442410 PMCID: PMC6709784 DOI: 10.1016/j.cell.2019.07.038] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/13/2019] [Accepted: 07/19/2019] [Indexed: 12/18/2022]
Abstract
Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes. Species-wide NLR diversity is high but not unlimited A large fraction of NLR diversity is recovered with 40–50 accessions Presence/absence variation in NLRs is widespread, resulting in a mosaic population A high diversity of NLR-integrated domains favor known virulence targets
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Affiliation(s)
- Anna-Lena Van de Weyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Freddy Monteiro
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Oliver J Furzer
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Marc T Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Milner Centre for Evolution & Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Jeffery L Dangl
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Klymiuk V, Fatiukha A, Raats D, Bocharova V, Huang L, Feng L, Jaiwar S, Pozniak C, Coaker G, Dubcovsky J, Fahima T. Three previously characterized resistances to yellow rust are encoded by a single locus Wtk1. J Exp Bot 2020; 71:2561-2572. [PMID: 31942623 PMCID: PMC7210774 DOI: 10.1093/jxb/eraa020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/12/2020] [Indexed: 05/21/2023]
Abstract
The wild emmer wheat (Triticum turgidum ssp. dicoccoides; WEW) yellow (stripe) rust resistance genes Yr15, YrG303, and YrH52 were discovered in natural populations from different geographic locations. They all localize to chromosome 1B but were thought to be non-allelic based on differences in resistance response. We recently cloned Yr15 as a Wheat Tandem Kinase 1 (WTK1) and show here that these three resistance loci co-segregate in fine-mapping populations and share an identical full-length genomic sequence of functional Wtk1. Independent ethyl methanesulfonate (EMS)-mutagenized susceptible yrG303 and yrH52 lines carried single nucleotide mutations in Wtk1 that disrupted function. A comparison of the mutations for yr15, yrG303, and yrH52 mutants showed that while key conserved residues were intact, other conserved regions in critical kinase subdomains were frequently affected. Thus, we concluded that Yr15-, YrG303-, and YrH52-mediated resistances to yellow rust are encoded by a single locus, Wtk1. Introgression of Wtk1 into multiple genetic backgrounds resulted in variable phenotypic responses, confirming that Wtk1-mediated resistance is part of a complex immune response network. WEW natural populations subjected to natural selection and adaptation have potential to serve as a good source for evolutionary studies of different traits and multifaceted gene networks.
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Affiliation(s)
- Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Andrii Fatiukha
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Dina Raats
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Valeria Bocharova
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Lin Huang
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Lihua Feng
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Samidha Jaiwar
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Gitta Coaker
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
- Correspondence:
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Brosseau C, Bolaji A, Roussin-Léveillée C, Zhao Z, Biga S, Moffett P. Natural variation in the Arabidopsis AGO2 gene is associated with susceptibility to potato virus X. New Phytol 2020; 226:866-878. [PMID: 31880814 DOI: 10.1111/nph.16397] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
RNA silencing functions as an anti-viral defence in plants through the action of DICER-like (DCL) and ARGONAUTE (AGO) proteins. Despite the importance of this mechanism, little is known about the functional consequences of variation in genes encoding RNA silencing components. The AGO2 protein has been shown to be important for defense against multiple viruses, and we investigated how naturally occurring differences in AGO2 between and within species affects its antiviral activities. We find that the AGO2 protein from Arabidopsis thaliana, but not Nicotiana benthamiana, effectively limits potato virus X (PVX). Consistent with this, we find that the A. thaliana AGO2 gene shows a high incidence of polymorphisms between accessions, with evidence of selective pressure. Using functional analyses, we identify polymorphisms that specifically affect AGO2 antiviral activity, without interfering with other AGO2-associated functions such as anti-bacterial resistance or DNA methylation. Our results suggest that viruses adapt to overcome RNA silencing in their hosts. Furthermore, they indicate that plant-virus interactions have influenced natural variation in RNA-silencing components and that the latter may be a source of genetically encoded virus resistance.
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Affiliation(s)
- Chantal Brosseau
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Ayooluwa Bolaji
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | | | - Zhenxing Zhao
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Sébastien Biga
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Peter Moffett
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
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Dehasque M, Ávila‐Arcos MC, Díez‐del‐Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas A, Marques‐Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD. Inference of natural selection from ancient DNA. Evol Lett 2020; 4:94-108. [PMID: 32313686 PMCID: PMC7156104 DOI: 10.1002/evl3.165] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/13/2020] [Accepted: 02/02/2020] [Indexed: 01/01/2023] Open
Abstract
Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.
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Affiliation(s)
- Marianne Dehasque
- Centre for Palaeogenetics10691StockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural History10405StockholmSweden
- Department of ZoologyStockholm University10691StockholmSweden
| | - María C. Ávila‐Arcos
- International Laboratory for Human Genome Research (LIIGH)UNAM JuriquillaQueretaro76230Mexico
| | - David Díez‐del‐Molino
- Centre for Palaeogenetics10691StockholmSweden
- Department of ZoologyStockholm University10691StockholmSweden
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park CampusImperial College LondonAscotSL5 7PYUnited Kingdom
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Science for Life LaboratoryUppsala University75236UppsalaSweden
| | | | - Anna‐Sapfo Malaspinas
- Department of Computational BiologyUniversity of Lausanne1015LausanneSwitzerland
- SIB Swiss Institute of Bioinformatics1015LausanneSwitzerland
| | - Tomas Marques‐Bonet
- Institut de Biologia Evolutiva(CSIC‐Universitat Pompeu Fabra), Parc de Recerca Biomèdica de BarcelonaBarcelonaSpain
- National Centre for Genomic Analysis—Centre for Genomic RegulationBarcelona Institute of Science and Technology08028BarcelonaSpain
- Institucio Catalana de Recerca i Estudis Avançats08010BarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Michael D. Martin
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Gemma G. R. Murray
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB2 1TNUnited Kingdom
| | - Alexander S. T. Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorLL57 2UWUnited Kingdom
| | | | - Daniel Wegmann
- Department of BiologyUniversité de Fribourg1700FribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| | - Love Dalén
- Centre for Palaeogenetics10691StockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural History10405StockholmSweden
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorLL57 2UWUnited Kingdom
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Hoseinzadeh P, Ruge-Wehling B, Schweizer P, Stein N, Pidon H. High Resolution Mapping of a Hordeum bulbosum-Derived Powdery Mildew Resistance Locus in Barley Using Distinct Homologous Introgression Lines. Front Plant Sci 2020; 11:225. [PMID: 32194602 PMCID: PMC7063055 DOI: 10.3389/fpls.2020.00225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/13/2020] [Indexed: 05/17/2023]
Abstract
Powdery mildew caused by Blumeria graminis f. sp. hordei (Bgh) is one of the main foliar diseases in barley (Hordeum vulgare L.; Hv). Naturally occurring resistance genes used in barley breeding are a cost effective and environmentally sustainable strategy to minimize the impact of pathogens, however, the primary gene pool of H. vulgare contains limited diversity owing to recent domestication bottlenecks. To ensure durable resistance against this pathogen, more genes are required that could be unraveled by investigation of secondary barley gene-pool. A large set of Hordeum bulbosum (Hb) introgression lines (ILs) harboring a diverse set of desirable resistance traits have been developed and are being routinely used as source of novel diversity in gene mapping studies. Nevertheless, this strategy is often compromised by a lack of recombination between the introgressed fragment and the orthologous chromosome of the barley genome. In this study, we fine-mapped a Hb gene conferring resistance to barley powdery mildew. The initial genotyping of two Hb ILs mapping populations with differently sized 2HS introgressions revealed severely reduced interspecific recombination in the region of the introgressed segment, preventing precise localization of the gene. To overcome this difficulty, we developed an alternative strategy, exploiting intraspecific recombination by crossing two Hv/Hb ILs with collinear Hb introgressions, one of which carries a powdery mildew resistance gene, while the other doesn't. The intraspecific recombination rate in the Hb-introgressed fragment of 2HS was approximately 20 times higher than it was in the initial simple ILs mapping populations. Using high-throughput genotyping-by-sequencing (GBS), we allocated the resistance gene to a 1.4 Mb interval, based on an estimate using the Hv genome as reference, in populations of only 103 and 146 individuals, respectively, similar to what is expected at this locus in barley. The most likely candidate resistance gene within this interval is part of the coiled-coil nucleotide-binding-site leucine-rich-repeat (CC-NBS-LLR) gene family, which is over-represented among genes conferring strong dominant resistance to pathogens. The reported strategy can be applied as a general strategic approach for identifying genes underlying traits of interest in crop wild relatives.
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Affiliation(s)
- Parastoo Hoseinzadeh
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Brigitte Ruge-Wehling
- Institute for Breeding Research on Agricultural Crops, Julius Kühn Institute (JKI), Sanitz, Germany
| | - Patrick Schweizer
- Pathogen-Stress Genomics, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Hélène Pidon
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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41
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Märkle H, Tellier A. Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments. PLoS Comput Biol 2020; 16:e1007668. [PMID: 32203545 PMCID: PMC7156111 DOI: 10.1371/journal.pcbi.1007668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 04/14/2020] [Accepted: 01/19/2020] [Indexed: 01/27/2023] Open
Abstract
There is a long-standing interest in understanding host-parasite coevolutionary dynamics and associated fitness effects. Increasing amounts of genomic data for both interacting species offer a promising source to identify candidate loci and to infer the main parameters of the past coevolutionary history. However, so far no method exists to perform the latter. By coupling a gene-for-gene model with coalescent simulations, we first show that three types of biological costs, namely, resistance, infectivity and infection, define the allele frequencies at the internal equilibrium point of the coevolution model. These in return determine the strength of selective signatures at the coevolving host and parasite loci. We apply an Approximate Bayesian Computation (ABC) approach on simulated datasets to infer these costs by jointly integrating host and parasite polymorphism data at the coevolving loci. To control for the effect of genetic drift on coevolutionary dynamics, we assume that 10 or 30 repetitions are available from controlled experiments or several natural populations. We study two scenarios: 1) the cost of infection and population sizes (host and parasite) are unknown while costs of infectivity and resistance are known, and 2) all three costs are unknown while populations sizes are known. Using the ABC model choice procedure, we show that for both scenarios, we can distinguish with high accuracy pairs of coevolving host and parasite loci from pairs of neutrally evolving loci, though the statistical power decreases with higher cost of infection. The accuracy of parameter inference is high under both scenarios especially when using both host and parasite data because parasite polymorphism data do inform on costs applying to the host and vice-versa. As the false positive rate to detect pairs of genes under coevolution is small, we suggest that our method complements recently developed methods to identify host and parasite candidate loci for functional studies.
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Affiliation(s)
- Hanna Märkle
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Aurélien Tellier
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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Bellis ES, Kelly EA, Lorts CM, Gao H, DeLeo VL, Rouhan G, Budden A, Bhaskara GB, Hu Z, Muscarella R, Timko MP, Nebie B, Runo SM, Chilcoat ND, Juenger TE, Morris GP, dePamphilis CW, Lasky JR. Genomics of sorghum local adaptation to a parasitic plant. Proc Natl Acad Sci U S A 2020; 117:4243-4251. [PMID: 32047036 PMCID: PMC7049153 DOI: 10.1073/pnas.1908707117] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Host-parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR-Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.
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Affiliation(s)
- Emily S Bellis
- Department of Biology, The Pennsylvania State University, University Park, PA 16802;
- Arkansas Biosciences Institute, Arkansas State University, State University, AR 72467
- Department of Computer Science, Arkansas State University, State University, AR 72467
| | - Elizabeth A Kelly
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Intercollege Graduate Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802
| | - Claire M Lorts
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Huirong Gao
- Applied Science and Technology, Corteva Agriscience, Johnston, IA 50131
| | - Victoria L DeLeo
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Intercollege Graduate Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802
| | - Germinal Rouhan
- Institut Systématique Evolution Biodiversité, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, École Pratique des Hautes Études, CP39, 75005 Paris, France
| | - Andrew Budden
- Identification & Naming, Royal Botanic Gardens, Kew, TW9 3AB Richmond, United Kingdom
| | - Govinal B Bhaskara
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Robert Muscarella
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, SE-75236 Uppsala, Sweden
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904
| | - Baloua Nebie
- West and Central Africa Regional Program, International Crops Research Institute for the Semi-Arid Tropics, BP 320 Bamako, Mali
| | - Steven M Runo
- Department of Biochemistry and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - N Doane Chilcoat
- Applied Science and Technology, Corteva Agriscience, Johnston, IA 50131
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Geoffrey P Morris
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Jesse R Lasky
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
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Mizuno H, Katagiri S, Kanamori H, Mukai Y, Sasaki T, Matsumoto T, Wu J. Evolutionary dynamics and impacts of chromosome regions carrying R-gene clusters in rice. Sci Rep 2020; 10:872. [PMID: 31964985 PMCID: PMC6972905 DOI: 10.1038/s41598-020-57729-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/06/2020] [Indexed: 11/17/2022] Open
Abstract
To elucidate R-gene evolution, we compared the genomic compositions and structures of chromosome regions carrying R-gene clusters among cultivated and wild rice species. Map-based sequencing and gene annotation of orthologous genomic regions (1.2 to 1.9 Mb) close to the terminal end of the long arm of rice chromosome 11 revealed R-gene clusters within six cultivated and ancestral wild rice accessions. NBS-LRR R-genes were much more abundant in Asian cultivated rice (O. sativa L.) than in its ancestors, indicating that homologs of functional genes involved in the same pathway likely increase in number because of tandem duplication of chromosomal segments and were selected during cultivation. Phylogenetic analysis using amino acid sequences indicated that homologs of paired Pikm1–Pikm2 (NBS-LRR) genes conferring rice-blast resistance were likely conserved among all cultivated and wild rice species we examined, and the homolog of Xa3/Xa26 (LRR-RLK) conferring bacterial blight resistance was lacking only in Kasalath.
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Affiliation(s)
- Hiroshi Mizuno
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 1-2, Ohwashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Satoshi Katagiri
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 1-2, Ohwashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 1-2, Ohwashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Yoshiyuki Mukai
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 1-2, Ohwashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Takuji Sasaki
- Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-0054, Japan
| | - Takashi Matsumoto
- Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-0054, Japan
| | - Jianzhong Wu
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 1-2, Ohwashi, Tsukuba, Ibaraki, 305-8634, Japan.
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Mitri C, Bischoff E, Eiglmeier K, Holm I, Dieme C, Brito-Fravallo E, Raz A, Zakeri S, Nejad MIK, Djadid ND, Vernick KD, Riehle MM. Gene copy number and function of the APL1 immune factor changed during Anopheles evolution. Parasit Vectors 2020; 13:18. [PMID: 31931885 PMCID: PMC6958605 DOI: 10.1186/s13071-019-3868-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background The recent reference genome assembly and annotation of the Asian malaria vector Anopheles stephensi detected only one gene encoding the leucine-rich repeat immune factor APL1, while in the Anopheles gambiae and sibling Anopheles coluzzii, APL1 factors are encoded by a family of three paralogs. The phylogeny and biological function of the unique APL1 gene in An. stephensi have not yet been specifically examined. Methods The APL1 locus was manually annotated to confirm the computationally predicted single APL1 gene in An. stephensi. APL1 evolution within Anopheles was explored by phylogenomic analysis. The single or paralogous APL1 genes were silenced in An. stephensi and An. coluzzii, respectively, followed by mosquito survival analysis, experimental infection with Plasmodium and expression analysis. Results APL1 is present as a single ancestral gene in most Anopheles including An. stephensi but has expanded to three paralogs in an African lineage that includes only the Anopheles gambiae species complex and Anopheles christyi. Silencing of the unique APL1 copy in An. stephensi results in significant mosquito mortality. Elevated mortality of APL1-depleted An. stephensi is rescued by antibiotic treatment, suggesting that pathology due to bacteria is the cause of mortality, and indicating that the unique APL1 gene is essential for host survival. Successful Plasmodium development in An. stephensi depends upon APL1 activity for protection from high host mortality due to bacteria. In contrast, silencing of all three APL1 paralogs in An. coluzzii does not result in elevated mortality, either with or without Plasmodium infection. Expression of the single An. stephensi APL1 gene is regulated by both the Imd and Toll immune pathways, while the two signaling pathways regulate different APL1 paralogs in the expanded APL1 locus. Conclusions APL1 underwent loss and gain of functions concomitant with expansion from a single ancestral gene to three paralogs in one lineage of African Anopheles. We infer that activity of the unique APL1 gene promotes longevity in An. stephensi by conferring protection from or tolerance to an effect of bacterial pathology. The evolution of an expanded APL1 gene family could be a factor contributing to the exceptional levels of malaria transmission mediated by human-feeding members of the An. gambiae species complex in Africa.![]()
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Affiliation(s)
- Christian Mitri
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France
| | - Emmanuel Bischoff
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France
| | - Karin Eiglmeier
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France
| | - Inge Holm
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France
| | - Constentin Dieme
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France.,Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA
| | - Emma Brito-Fravallo
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France
| | - Abbasali Raz
- Malaria and Vector Research Group, Biotechnology Research Center, Institut Pasteur of Iran, Tehran, Iran
| | - Sedigheh Zakeri
- Malaria and Vector Research Group, Biotechnology Research Center, Institut Pasteur of Iran, Tehran, Iran
| | - Mahdokht I K Nejad
- Malaria and Vector Research Group, Biotechnology Research Center, Institut Pasteur of Iran, Tehran, Iran
| | - Navid D Djadid
- Malaria and Vector Research Group, Biotechnology Research Center, Institut Pasteur of Iran, Tehran, Iran
| | - Kenneth D Vernick
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France. .,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France.
| | - Michelle M Riehle
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.
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Martel A, Laflamme B, Seto D, Bastedo DP, Dillon MM, Almeida RND, Guttman DS, Desveaux D. Immunodiversity of the Arabidopsis ZAR1 NLR Is Conveyed by Receptor-Like Cytoplasmic Kinase Sensors. Front Plant Sci 2020; 11:1290. [PMID: 32983191 PMCID: PMC7475706 DOI: 10.3389/fpls.2020.01290] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/07/2020] [Indexed: 05/06/2023]
Abstract
The Arabidopsis nucleotide-binding leucine-rich repeat protein ZAR1 can recognize at least six distinct families of pathogenic effector proteins to mount an effector-triggered immune response. This remarkable immunodiversity appears to be conveyed by receptor-like cytoplasmic kinase (RLCK) complexes, which associate with ZAR1 to sense several effector-induced kinase perturbations. Here we show that the recently identified ZAR1-mediated immune responses against the HopX1, HopO1, and HopBA1 effector families of Pseudomonas syringae rely on an expanded diversity of RLCK sensors. We show that individual sensors can recognize distinct effector families, thereby contributing to the expanded surveillance potential of ZAR1 and supporting its role as a guardian of the plant kinome.
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Affiliation(s)
- Alexandre Martel
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Bradley Laflamme
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Derek Seto
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - D. Patrick Bastedo
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Marcus M. Dillon
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Renan N. D. Almeida
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
- *Correspondence: David S. Guttman, ; Darrell Desveaux,
| | - Darrell Desveaux
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
- *Correspondence: David S. Guttman, ; Darrell Desveaux,
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Abstract
Background Coevolution is a selective process of reciprocal adaptation in hosts and parasites or in mutualistic symbionts. Classic population genetics theory predicts the signatures of selection at the interacting loci of both species, but not the neutral genome-wide polymorphism patterns. To bridge this gap, we build an eco-evolutionary model, where neutral genomic changes over time are driven by a single selected locus in hosts and parasites via a simple biallelic gene-for-gene or matching-allele interaction. This coevolutionary process may lead to cyclic changes in the sizes of the interacting populations. Results We investigate if and when these changes can be observed in the site frequency spectrum of neutral polymorphisms from host and parasite full genome data. We show that changes of the host population size are too smooth to be observable in its polymorphism pattern over the course of time. Conversely, the parasite population may undergo a series of strong bottlenecks occurring on a slower relative time scale, which may lead to observable changes in a time series sample. We also extend our results to cases with 1) several parasites per host accelerating relative time, and 2) multiple parasite generations per host generation slowing down rescaled time. Conclusions Our results show that time series sampling of host and parasite populations with full genome data are crucial to understand if and how coevolution occurs. This model provides therefore a framework to interpret and draw inference from genome-wide polymorphism data of interacting species.
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Affiliation(s)
- Daniel Živković
- Section of Population Genetics, Technical University of Munich, Freising, Germany.
| | - Sona John
- Section of Population Genetics, Technical University of Munich, Freising, Germany
| | - Mélissa Verin
- Section of Population Genetics, Technical University of Munich, Freising, Germany.,Department of Mathematics and Statistics, Queen's University, Kingston, Ontario, Canada
| | - Wolfgang Stephan
- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Aurélien Tellier
- Section of Population Genetics, Technical University of Munich, Freising, Germany.
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47
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Stam R, Silva-Arias GA, Tellier A. Subsets of NLR genes show differential signatures of adaptation during colonization of new habitats. New Phytol 2019; 224:367-379. [PMID: 31230368 DOI: 10.1111/nph.16017] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
Nucleotide binding site, leucine-rich repeat receptors (NLRs) are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonization of novel habitats in a model tomato species, Solanum chilense. We used R-gene enrichment sequencing to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonization by resequencing whole genomes from three S. chilense plants from three key populations and performing approximate Bayesian computation using data from the 14 populations. Using these parameters, we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution and identified small subsets of outlier NLRs exhibiting signatures of selection across populations. NLRs under selection between habitats are more often helper genes, whereas those showing signatures of adaptation in single populations are more often sensor-NLRs. Thus, centrality in the NLR network does not constrain NLR evolvability, and new mutations in central genes in the network are key for R-gene adaptation during colonization of different habitats.
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Affiliation(s)
- Remco Stam
- Phytopathology, Technical University Munich, 85354, Freising, Germany
- Population Genetics, Technical University Munich, 85354, Freising, Germany
| | | | - Aurelien Tellier
- Population Genetics, Technical University Munich, 85354, Freising, Germany
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48
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Gupta MK, Vadde R. Genetic Basis of Adaptation and Maladaptation via Balancing Selection. ZOOLOGY 2019; 136:125693. [PMID: 31513936 DOI: 10.1016/j.zool.2019.125693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022]
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49
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MacQueen A, Tian D, Chang W, Holub E, Kreitman M, Bergelson J. Population Genetics of the Highly Polymorphic RPP8 Gene Family. Genes (Basel) 2019; 10:genes10090691. [PMID: 31500388 PMCID: PMC6771003 DOI: 10.3390/genes10090691] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/31/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023] Open
Abstract
Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb distant. We sequenced 48 RPP8 alleles from 37 accessions of A. thaliana and 12 RPP8 alleles from Arabidopsis lyrata to investigate the patterns of interlocus shared variation. The tandem duplicates display fixed differences and share less variation with each other than either shares with the distant paralog. A high level of shared polymorphism among alleles at one of the tandem duplicates, the single-copy locus and the distal locus, must involve both classical crossing over and intergenic gene conversion. Despite these polymorphism-enhancing mechanisms, the observed nucleotide diversity could not be replicated under neutral forward-in-time simulations. Only by adding balancing selection to the simulations do they approach the level of polymorphism observed at RPP8. In this NLR gene triad, genetic architecture, gene function and selection all combine to generate diversity.
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Affiliation(s)
- Alice MacQueen
- Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210008, China.
| | - Wenhan Chang
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
| | - Eric Holub
- School of Life Sciences, Wellesbourne Innovation Campus, University of Warwick, Wellesbourne CV359EF, UK.
| | - Martin Kreitman
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
| | - Joy Bergelson
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
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50
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Hernandez CA, Koskella B. Phage resistance evolution in vitro is not reflective of in vivo outcome in a plant-bacteria-phage system. Evolution 2019; 73:2461-2475. [PMID: 31433508 DOI: 10.1111/evo.13833] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022]
Abstract
The evolution of resistance to parasites is fundamentally important to disease ecology, yet we remain unable to predict when and how resistance will evolve. This is largely due to the context-dependent nature of host-parasite interactions, as the benefit of resistance will depend on the abiotic and biotic environment. Through experimental evolution of the plant pathogenic bacterium Pseudomonas syringae and two lytic bacteriophages across two different environments (high-nutrient media and the tomato leaf apoplast), we demonstrate that de novo evolution of resistance is negligible in planta despite high levels of resistance evolution in vitro. We find no evidence supporting the evolution of phage-selected resistance in planta despite multiple passaging experiments, multiple assays for resistance, and high multiplicities of infection. Additionally, we find that phage-resistant mutants (evolved in vitro) did not realize a fitness benefit over phage-sensitive cells when grown in planta in the presence of phage, despite reduced growth of sensitive cells, evidence of phage replication in planta, and a large fitness benefit in the presence of phage observed in vitro. Thus, this context-dependent benefit of phage resistance led to different evolutionary outcomes across environments. These results underscore the importance of studying the evolution of parasite resistance in ecologically relevant environments.
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Affiliation(s)
- Catherine A Hernandez
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
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