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Behling AH, Winter DJ, Ganley ARD, Cox MP. Cross-kingdom transcriptomic trends in the evolution of hybrid gene expression. J Evol Biol 2022; 35:1126-1137. [PMID: 35830478 PMCID: PMC9546207 DOI: 10.1111/jeb.14059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/13/2022] [Indexed: 11/29/2022]
Abstract
Hybridization is a route to speciation that occurs widely across the eukaryote tree of life. The success of allopolyploids (hybrid species with increased ploidy) and homoploid hybrids (with unchanged ploidy) is well documented. However, their formation and establishment is not straightforward, with a suite of near‐instantaneous and longer term biological repercussions faced by the new species. Central to these challenges is the rewiring of gene regulatory networks following the merger of distinct genomes inherited from both parental species. Research on the evolution of hybrid gene expression has largely involved studies on a single hybrid species or a few gene families. Here, we present the first standardized transcriptome‐wide study exploring the fates of genes following hybridization across three kingdoms: animals, plants and fungi. Within each kingdom, we pair an allopolyploid system with a closely related homoploid hybrid to decouple the influence of increased ploidy from genome merger. Genome merger, not changes in ploidy, has the greatest effect on posthybridization expression patterns across all study systems. Strikingly, we find that differentially expressed genes in parent species preferentially switch to more similar expression in hybrids across all kingdoms, likely as a consequence of regulatory trans‐acting cross‐talk within the hybrid nucleus. We also highlight the prevalence of gene loss or silencing among extremely differentially expressed genes in hybrid species across all kingdoms. These shared patterns suggest that the evolutionary process of hybridization leads to common high‐level expression outcomes, regardless of the particular species or kingdom.
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Affiliation(s)
- Anna H Behling
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - David J Winter
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
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Jia KH, Liu H, Zhang RG, Xu J, Zhou SS, Jiao SQ, Yan XM, Tian XC, Shi TL, Luo H, Li ZC, Bao YT, Nie S, Guo JF, Porth I, El-Kassaby YA, Wang XR, Chen C, Van de Peer Y, Zhao W, Mao JF. Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. HORTICULTURE RESEARCH 2021; 8:177. [PMID: 34465761 PMCID: PMC8408255 DOI: 10.1038/s41438-021-00614-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 05/11/2023]
Abstract
Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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Affiliation(s)
- Kai-Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hui Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, 261000, Shandong, China
| | - Jie Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shan-Shan Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Mei Yan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Chan Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Tian-Le Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hang Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhi-Chao Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yu-Tao Bao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jing-Fang Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xiao-Ru Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden.
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Hovhannisyan H, Saus E, Ksiezopolska E, Hinks Roberts AJ, Louis EJ, Gabaldón T. Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization. Front Genet 2020; 11:404. [PMID: 32457798 PMCID: PMC7221068 DOI: 10.3389/fgene.2020.00404] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/30/2020] [Indexed: 12/30/2022] Open
Abstract
The formation of interspecific hybrids results in the coexistence of two diverged genomes within the same nucleus. It has been hypothesized that negative epistatic interactions and regulatory interferences between the two sub-genomes may elicit a so-called genomic shock involving, among other alterations, broad transcriptional changes. To assess the magnitude of this shock in hybrid yeasts, we investigated the transcriptomic differences between a newly formed Saccharomyces cerevisiae × Saccharomyces uvarum diploid hybrid and its diploid parentals, which diverged ∼20 mya. RNA sequencing (RNA-Seq) based allele-specific expression (ASE) analysis indicated that gene expression changes in the hybrid genome are limited, with only ∼1-2% of genes significantly altering their expression with respect to a non-hybrid context. In comparison, a thermal shock altered six times more genes. Furthermore, differences in the expression between orthologous genes in the two parental species tended to be diminished for the corresponding homeologous genes in the hybrid. Finally, and consistent with the RNA-Seq results, we show a limited impact of hybridization on chromatin accessibility patterns, as assessed with assay for transposase-accessible chromatin using sequencing (ATAC-Seq). Overall, our results suggest a limited genomic shock in a newly formed yeast hybrid, which may explain the high frequency of successful hybridization in these organisms.
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Affiliation(s)
- Hrant Hovhannisyan
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
| | - Ester Saus
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
| | - Ewa Ksiezopolska
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
| | - Alex J. Hinks Roberts
- Centre for Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | - Edward J. Louis
- Centre for Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | - Toni Gabaldón
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Health and Life Sciences. Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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