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Winkelmüller TM, Entila F, Anver S, Piasecka A, Song B, Dahms E, Sakakibara H, Gan X, Kułak K, Sawikowska A, Krajewski P, Tsiantis M, Garrido-Oter R, Fukushima K, Schulze-Lefert P, Laurent S, Bednarek P, Tsuda K. Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species. THE PLANT CELL 2021; 33:1863-1887. [PMID: 33751107 PMCID: PMC8290292 DOI: 10.1093/plcell/koab073] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/24/2021] [Indexed: 05/20/2023]
Abstract
Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, by employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species to investigate PTI responses, we identified a set of genes that commonly respond to the MAMP flg22 and genes that exhibit species-specific expression signatures. Variation in flg22-triggered transcriptome responses across Brassicaceae species was incongruent with their phylogeny, while expression changes were strongly conserved within A. thaliana. We found the enrichment of WRKY transcription factor binding sites in the 5'-regulatory regions of conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene expression patterns during PTI. Our findings advance our understanding of the evolution of the transcriptome during biotic stress.
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Affiliation(s)
- Thomas M Winkelmüller
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Frederickson Entila
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Shajahan Anver
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Present address: Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anna Piasecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Baoxing Song
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Present address: Institute for Genomic Diversity, Cornell University, Ithaca, New York
| | - Eik Dahms
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, 230-0045 Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Karolina Kułak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Present address: Department of Computational Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Aneta Sawikowska
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-628 Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany
| | - Paul Schulze-Lefert
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, 430070 Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, 430070 Wuhan, China
- Department of Plant–Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Author for correspondence:
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Go AC, Civetta A. Hybrid Incompatibilities and Transgressive Gene Expression Between Two Closely Related Subspecies of Drosophila. Front Genet 2020; 11:599292. [PMID: 33362859 PMCID: PMC7758320 DOI: 10.3389/fgene.2020.599292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Abstract
Genome-wide assays of expression between species and their hybrids have identified genes that become either over- or underexpressed relative to the parental species (i.e., transgressive). Transgressive expression in hybrids is of interest because it highlights possible changes in gene regulation linked to hybrid dysfunction. Previous studies in Drosophila that used long-diverged species pairs with complete or nearly complete isolation (i.e., full sterility and partial inviability of hybrids) and high-levels of genome misregulation have found correlations between expression and coding sequence divergence. The work highlighted the possible effects of directional selection driving sequence divergence and transgressive expression. Whether the same is true for taxa at early stages of divergence that have only achieved partial isolation remains untested. Here, we reanalyze previously published genome expression data and available genome sequence reads from a pair of partially isolated subspecies of Drosophila to compare expression and sequence divergence. We find a significant correlation in rates of expression and sequence evolution, but no support for directional selection driving transgressive expression in hybrids. We find that most transgressive genes in hybrids show no differential expression between parental subspecies and used SNP data to explore the role of stabilizing selection through compensatory mutations. We also examine possible misregulation through cascade effects that could be driven by interacting gene networks or co-option of off-target cis-regulatory elements.
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Affiliation(s)
- Alwyn C Go
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
| | - Alberto Civetta
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
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Pespeni MH, Ladner JT, Moczek AP. Signals of selection in conditionally expressed genes in the diversification of three horned beetle species. J Evol Biol 2017; 30:1644-1657. [PMID: 28379613 DOI: 10.1111/jeb.13079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 03/05/2017] [Indexed: 01/20/2023]
Abstract
Species radiations may be facilitated by phenotypic differences already present within populations, such as those arising through sex-specific development or developmental processes biased towards particular reproductive or trophic morphs. We sought to test this hypothesis by utilizing a comparative transcriptomic approach to contrast among- and within-species differentiation using three horned beetle species in the genus Onthophagus. These three species exhibit differences along three phenotypic axes reflective of much of the interspecific diversity present within the genus: horn location, polarity of sexual dimorphism and degree of nutritional sensitivity. Our approach combined de novo transcript assembly, assessment of amino acid substitutions (dN/dS) across orthologous gene pairs and integration of gene function and conditional gene expression data. We identified 17 genes across the three species pairs related to axis patterning, development and metabolism with dN/dS > 1 and detected elevated dN/dS in genes related to metabolism and biosynthesis in the most closely related species pair, which is characterized by a loss of nutritional polyphenism and a reversal of sexual dimorphism. Further, we found that genes that are conditionally expressed (i.e. as a function of sex, nutrition or body region) within one of our focal species also showed significantly stronger signals of positive or relaxed purifying selection between species divergent along the same morphological axis (i.e. polarity of sexual dimorphism, degree of nutritional sensitivity or location of horns). Our findings thus reveal a positive relationship between intraspecific differentiation due to condition-specific development and genetic divergences among species.
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Affiliation(s)
- M H Pespeni
- Department of Biology, Indiana University, Bloomington, IN, USA.,Department of Biology, University of Vermont, Burlington, VT, USA
| | - J T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - A P Moczek
- Department of Biology, Indiana University, Bloomington, IN, USA
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Idnurm A, Hood ME, Johannesson H, Giraud T. Contrasted patterns in mating-type chromosomes in fungi: hotspots versus coldspots of recombination. FUNGAL BIOL REV 2015; 29:220-229. [PMID: 26688691 PMCID: PMC4680991 DOI: 10.1016/j.fbr.2015.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
It is striking that, while central to sexual reproduction, the genomic regions determining sex or mating-types are often characterized by suppressed recombination that leads to a decrease in the efficiency of selection, shelters genetic load, and inevitably contributes to their genic degeneration. Research on model and lesser-explored fungi has revealed similarities in recombination suppression of the genomic regions involved in mating compatibility across eukaryotes, but fungi also provide opposite examples of enhanced recombination in the genomic regions that determine their mating types. These contrasted patterns of genetic recombination (sensu lato, including gene conversion and ectopic recombination) in regions of the genome involved in mating compatibility point to important yet complex processes occurring in their evolution. A number of pieces in this puzzle remain to be solved, in particular on the unclear selective forces that may cause the patterns of recombination, prompting theoretical developments and experimental studies. This review thus points to fungi as a fascinating group for studying the various evolutionary forces at play in the genomic regions involved in mating compatibility.
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Affiliation(s)
- Alexander Idnurm
- School of BioSciences, University of Melbourne, VIC 3010, Australia
| | - Michael E. Hood
- Department of Biology, Amherst College, Amherst, Massachusetts 01002 USA
| | - Hanna Johannesson
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution, UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360, Université Paris-Sud, 91405 Orsay cedex, France
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