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Thomas SK, Hoek KV, Ogoti T, Duong H, Angelovici R, Pires JC, Mendoza-Cozatl D, Washburn J, Schenck CA. Halophytes and heavy metals: A multi-omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima. AMERICAN JOURNAL OF BOTANY 2024:e16310. [PMID: 38600732 DOI: 10.1002/ajb2.16310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 04/12/2024]
Abstract
PREMISE The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we used Cakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole-genome triplication with closely related salt-sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy. METHODS Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response in C. maritima and identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium. RESULTS Cakile maritima is tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool in C. maritima and likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved in C. maritima abiotic stress tolerance. CONCLUSIONS These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.
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Affiliation(s)
- Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, 65211, MO, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, 65211, MO, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
| | - Kathryn Vanden Hoek
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| | - Tasha Ogoti
- Department of Computer Science, University of Missouri, Columbia, 65211, MO, USA
| | - Ha Duong
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, 65211, MO, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, Fort Collins, 80523-1170, CO, USA
| | - David Mendoza-Cozatl
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Division of Plant Sciences and Technology, University of Missouri, Columbia, 65211, MO, USA
| | - Jacob Washburn
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Plant Genetics Research Unit, USDA-ARS, Columbia, 65211, MO, USA
| | - Craig A Schenck
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
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2
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Sloan DB, Conover JL, Grover CE, Wendel JF, Sharbrough J. Polyploid plants take cytonuclear perturbations in stride. THE PLANT CELL 2024; 36:829-839. [PMID: 38267606 PMCID: PMC10980399 DOI: 10.1093/plcell/koae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/26/2024]
Abstract
Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between nuclear and organellar (mitochondrial and plastid) genomes by creating imbalances in the relative copy number of these genomes and producing genetic incompatibilities between maternally derived organellar genomes and the half of the allopolyploid nuclear genome from the paternal progenitor. Several evolutionary responses have been predicted to ameliorate these effects, including selection for changes in protein sequences that restore cytonuclear interactions; biased gene retention/expression/conversion favoring maternal nuclear gene copies; and fine-tuning of relative cytonuclear genome copy numbers and expression levels. Numerous recent studies, however, have found that evolutionary responses are inconsistent and rarely scale to genome-wide generalities. The apparent robustness of plant cytonuclear interactions to allopolyploidy may reflect features that are general to allopolyploids such as the lack of F2 hybrid breakdown under disomic inheritance, and others that are more plant-specific, including slow sequence divergence in organellar genomes and preexisting regulatory responses to changes in cell size and endopolyploidy during development. Thus, cytonuclear interactions may only rarely act as the main barrier to establishment of allopolyploid lineages, perhaps helping to explain why allopolyploidy is so pervasive in plant evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University,
Fort Collins, CO, USA
| | - Justin L Conover
- Department of Ecology and Evolutionary Biology, University of
Arizona, Tucson, AZ, USA
- Department of Molecular and Cellular Biology, University of
Arizona, Tucson, AZ, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA, USA
| | - Joel Sharbrough
- Department of Biology, New Mexico Institute of Mining and
Technology, Socorro, NM, USA
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3
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An H, Pires JC, Conant GC. Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. PLoS Comput Biol 2024; 20:e1011803. [PMID: 38227592 PMCID: PMC10817154 DOI: 10.1371/journal.pcbi.1011803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/26/2024] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
Hybridization coupled to polyploidy, or allopolyploidy, has dramatically shaped the evolution of flowering plants, teleost fishes, and other lineages. Studies of recently formed allopolyploid plants have shown that the two subgenomes that merged to form that new allopolyploid do not generally express their genes equally. Instead, one of the two subgenomes expresses its paralogs more highly on average. Meanwhile, older allopolyploidy events tend to show biases in duplicate losses, with one of the two subgenomes retaining more genes than the other. Since reduced expression is a pathway to duplicate loss, understanding the origins of expression biases may help explain the origins of biased losses. Because we expect gene expression levels to experience stabilizing selection, our conceptual frameworks for how allopolyploid organisms form tend to assume that the new allopolyploid will show balanced expression between its subgenomes. It is then necessary to invoke phenomena such as differences in the suppression of repetitive elements to explain the observed expression imbalances. Here we show that, even for phenotypically identical diploid progenitors, the inherent kinetics of gene expression give rise to biases between the expression levels of the progenitor genes in the hybrid. Some of these biases are expected to be gene-specific and not give rise to global differences in progenitor gene expression. However, particularly in the case of allopolyploids formed from progenitors with different genome sizes, global expression biases favoring one subgenome are expected immediately on formation. Hence, expression biases are arguably the expectation upon allopolyploid formation rather than a phenomenon needing explanation. In the future, a deeper understanding of the kinetics of allopolyploidy may allow us to better understand both biases in duplicate losses and hybrid vigor.
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Affiliation(s)
- Hong An
- MU Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America
| | - J. Chris Pires
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gavin C. Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
- Program in Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
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4
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Ebadi M, Bafort Q, Mizrachi E, Audenaert P, Simoens P, Van Montagu M, Bonte D, Van de Peer Y. The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil. Proc Natl Acad Sci U S A 2023; 120:e2307289120. [PMID: 37788315 PMCID: PMC10576144 DOI: 10.1073/pnas.2307289120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/07/2023] [Indexed: 10/05/2023] Open
Abstract
The importance of whole-genome duplication (WGD) for evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary dead end, there is growing evidence that polyploidization can help overcome environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete or outlive nonpolyploids at times of environmental upheaval remain elusive, especially for autopolyploids, in which heterosis effects are limited. On the longer term, WGD might increase both mutational and environmental robustness due to redundancy and increased genetic variation, but on the short-or even immediate-term, selective advantages of WGDs are harder to explain. Here, by duplicating artificially generated Gene Regulatory Networks (GRNs), we show that duplicated GRNs-and thus duplicated genomes-show higher signal output variation than nonduplicated GRNs. This increased variation leads to niche expansion and can provide polyploid populations with substantial advantages to survive environmental turmoil. In contrast, under stable environments, GRNs might be maladaptive to changes, a phenomenon that is exacerbated in duplicated GRNs. We believe that these results provide insights into how genome duplication and (auto)polyploidy might help organisms to adapt quickly to novel conditions and to survive ecological uproar or even cataclysmic events.
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Affiliation(s)
- Mehrshad Ebadi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria0028, South Africa
| | - Pieter Audenaert
- Department of Information Technology–IDLab, Ghent University-IMEC, Gent9052, Belgium
| | - Pieter Simoens
- Department of Information Technology–IDLab, Ghent University-IMEC, Gent9052, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Dries Bonte
- Department of Biology, Terrestrial Ecology Unit, Ghent University, Ghent9000, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing210095, China
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5
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Phelps WA, Hurton MD, Ayers TN, Carlson AE, Rosenbaum JC, Lee MT. Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis. eLife 2023; 12:e83952. [PMID: 37787392 PMCID: PMC10569791 DOI: 10.7554/elife.83952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/02/2023] [Indexed: 10/04/2023] Open
Abstract
After fertilization, maternally contributed factors to the egg initiate the transition to pluripotency to give rise to embryonic stem cells, in large part by activating de novo transcription from the embryonic genome. Diverse mechanisms coordinate this transition across animals, suggesting that pervasive regulatory remodeling has shaped the earliest stages of development. Here, we show that maternal homologs of mammalian pluripotency reprogramming factors OCT4 and SOX2 divergently activate the two subgenomes of Xenopus laevis, an allotetraploid that arose from hybridization of two diploid species ~18 million years ago. Although most genes have been retained as two homeologous copies, we find that a majority of them undergo asymmetric activation in the early embryo. Chromatin accessibility profiling and CUT&RUN for modified histones and transcription factor binding reveal extensive differences in predicted enhancer architecture between the subgenomes, which likely arose through genomic disruptions as a consequence of allotetraploidy. However, comparison with diploid X. tropicalis and zebrafish shows broad conservation of embryonic gene expression levels when divergent homeolog contributions are combined, implying strong selection to maintain dosage in the core vertebrate pluripotency transcriptional program, amid genomic instability following hybridization.
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Affiliation(s)
- Wesley A Phelps
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Matthew D Hurton
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Taylor N Ayers
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Anne E Carlson
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Joel C Rosenbaum
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Miler T Lee
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
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6
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Xia HX, Li Q, Cushman SA, Yuan WJ, Li Y. Expression dosage effects of a small number of genes after the artificial doubling of weeping forsythia. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107945. [PMID: 37562202 DOI: 10.1016/j.plaphy.2023.107945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/04/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
Whole genome doubling (WGD) plays a critical role in plant evolution, yet the mechanisms underlying the maintenance of overall equilibrium following an artificial doubling event, as well as its impact on phenotype and adaptability, remain unclear. By comparing the gene expression of naturally occurring weeping forsythia diploids and colchicine-induced autotetraploids under normal growth conditions and cold stress, we identified gene expression dosage responses resulting from ploidy change. Only a small proportion of effectively expressed genes showed dosage effect, and most genes did not exhibit significant expression differences. However, the genes that showed expression dosage effect were largely random. The autotetraploids had slower overall growth rates, possibly resulting from negative gene dosage effects on zeatin synthesis and multiple metabolic delays caused by other negative dosage genes. Our comparative analysis of cold response genes in diploids and autotetraploids revealed that genes related to "response to abscisic acid" and "cold acclimation" were key factors contributing to greater cold tolerance in the autotetraploids. In particular, gene expression related to "cold acclimation" might mitigate the effects of cold stress. Taken together, our findings suggested that overall gene expression equilibrium following WGD of weeping forsythia autotetraploids was achieved through the inactivation of the majority of duplicated genes. Our research provides new insights into the mechanisms regulating expression dosage balance following polyploidization events.
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Affiliation(s)
- He-Xiao Xia
- College of Life Science and Technology, Inner Mongolia Normal University, Huhehaote, China; College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Qian Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Samuel A Cushman
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Wang-Jun Yuan
- School of Pharmacy, Henan University, Kaifeng, China
| | - Yong Li
- College of Life Science and Technology, Inner Mongolia Normal University, Huhehaote, China; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
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7
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Bird KA, Pires JC, VanBuren R, Xiong Z, Edger PP. Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus. Genetics 2023; 225:iyad114. [PMID: 37338008 PMCID: PMC10471226 DOI: 10.1093/genetics/iyad114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/10/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023] Open
Abstract
The gene balance hypothesis proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions of networks, pathways, and protein complexes to maintain balanced stoichiometry of interacting proteins, because perturbations to stoichiometric balance can result in reduced fitness. This selection has been called dosage balance selection. Dosage balance selection is also hypothesized to constrain expression responses to dosage changes, making dosage-sensitive genes (those encoding members of interacting proteins) experience more similar expression changes. In allopolyploids, where whole-genome duplication involves hybridization of diverged lineages, organisms often experience homoeologous exchanges that recombine, duplicate, and delete homoeologous regions of the genome and alter the expression of homoeologous gene pairs. Although the gene balance hypothesis makes predictions about the expression response to homoeologous exchanges, they have not been empirically tested. We used genomic and transcriptomic data from 6 resynthesized, isogenic Brassica napus lines over 10 generations to identify homoeologous exchanges, analyzed expression responses, and tested for patterns of genomic imbalance. Groups of dosage-sensitive genes had less variable expression responses to homoeologous exchanges than dosage-insensitive genes, a sign that their relative dosage is constrained. This difference was absent for homoeologous pairs whose expression was biased toward the B. napus A subgenome. Finally, the expression response to homoeologous exchanges was more variable than the response to whole-genome duplication, suggesting homoeologous exchanges create genomic imbalance. These findings expand our knowledge of the impact of dosage balance selection on genome evolution and potentially connect patterns in polyploid genomes over time, from homoeolog expression bias to duplicate gene retention.
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Affiliation(s)
- Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Inner Mongolia University, Hohhot, Inner Mongolia 010070, China
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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8
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Guo H, Zhang G, Zhou M, Wan M, Zhu B, Yang Z, Zeng D, Zeng Z. Whole genome doubling-induced the enrichment of H3K27me3 in genes carrying specific TEs in Aegilops tauschii. Front Genet 2023; 14:1241201. [PMID: 37560386 PMCID: PMC10407559 DOI: 10.3389/fgene.2023.1241201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023] Open
Abstract
Polyploidization plays important roles in the evolution and breeding of the common wheat. Aegilops tauschii, the D-genome progenitor of the common wheat, provides a valuable pool of resistance genes to multiple diseases. Extensive studies focus on the exploration of these genes for wheat improvement. However, few studies have unveiled alternations on genome-wide expression pattern and histone modifications induced by whole-genome doubling (WGD) process. In this study, we conducted transcriptome analysis for the diploid and tetraploid Ae. taushcii lines using the leaf and root tissues. Both lines tend to display similar tissue-specific pattern. Interestingly, we found that TEs located in genic regions were depleted of the repressive histone mark H3K27me3, whereas their adjacent chromatin was enriched with H3K27me3. The tetraploid line exhibited higher levels of H3K27me3 in those regions than the diploid line, particularly for genic regions associated with TEs of the long interspersed nuclear elements (LINEs), CACTA, PIF/Harbinger, Tc1/Mariner and unclassed DNA transposon. Surprisingly, the expression levels of these TEs cognate genes were negatively associated with the levels of H3K27me3 between the tetraploid and diploid lines, suggesting the five types of TEs located within genic regions might be involved in the regulation of the ploidy-related gene expression, possibly through differential enrichment of H3K27me3 in the genic regions. These findings will help to understand the potential role of specific types of TEs on transcription in response to WGD.
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Affiliation(s)
- Hongwei Guo
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Guoyan Zhang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Min Zhou
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Min Wan
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Bo Zhu
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Deying Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
| | - Zixian Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
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9
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Guo H, Zhou M, Zhang G, He L, Yan C, Wan M, Hu J, He W, Zeng D, Zhu B, Zeng Z. Development of homozygous tetraploid potato and whole genome doubling-induced the enrichment of H3K27ac and potentially enhanced resistance to cold-induced sweetening in tubers. HORTICULTURE RESEARCH 2023; 10:uhad017. [PMID: 36968186 PMCID: PMC10031744 DOI: 10.1093/hr/uhad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Polyploid plants typically display advantages on some agronomically important traits over their diploid counterparts. Extensive studies have shown genetic, transcriptomic, and epigenetic dynamics upon polyploidization in multiple plant species. However, few studies have unveiled those alternations imposed only by ploidy level, without any interference from heterozygosity. Cultivated potato is highly heterozygous. Thus, in this study, we developed two homozygous autotetraploid lines and one homozygous diploid line in parallel from a homozygous diploid potato. We confirmed their ploidy levels using chloroplast counting and karyotyping. Oligo-FISH and genome re-sequencing validated that these potato lines are nearly homozygous. We investigated variations in phenotypes, transcription, and histone modifications between two ploidies. Both autotetraploid lines produced larger but fewer tubers than the diploid line. Interestingly, each autotetraploid line displayed ploidy-related differential expression for various genes. We also discovered a genome-wide enrichment of H3K27ac in genic regions upon whole-genome doubling (WGD). However, such enrichment was not associated with the differential gene expression between two ploidies. The tetraploid lines may exhibit better resistance to cold-induced sweetening (CIS) than the diploid line in tubers, potentially regulated through the expression of CIS-related key genes, which seems to be associated with the levels of H3K4me3 in cold-stored tubers. These findings will help to understand the impacts of autotetraploidization on dynamics of phenotypes, transcription, and histone modifications, as well as on CIS-related genes in response to cold storage.
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Affiliation(s)
| | | | | | | | - Caihong Yan
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu 610101, Sichuan, China
| | - Min Wan
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu 610101, Sichuan, China
| | - Jianjun Hu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Wei He
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Deying Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu 610101, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu 610101, Sichuan, China
| | - Bo Zhu
- Corresponding authors. E-mails: ;
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10
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Chen S, Yu Y, Wang X, Wang S, Zhang T, Zhou Y, He R, Meng N, Wang Y, Liu W, Liu Z, Liu J, Guo Q, Huang H, Sederoff RR, Wang G, Qu G, Chen S. Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'. Mol Ecol Resour 2023. [PMID: 36789493 DOI: 10.1111/1755-0998.13770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/16/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
Many recent studies have provided significant insights into polyploid breeding, but limited research has been carried out on trees. The genomic information needed to understand growth and response to abiotic stress in polyploidy trees is largely unknown, but has become critical due to the threats to forests imposed by climate change. Populus alba 'Berolinensis,' also known "Yinzhong poplar," is a triploid poplar from northeast China. This hybrid triploid poplar is widely used as a landscape ornamental and in urban forestry owing to its adaptation to adverse environments and faster growth than its parental diploid. It is an artificially synthesized male allotriploid hybrid, with three haploid genomes of P. alba 'Berolinensis' originating from different poplar species, so it is attractive for studying polyploidy genomic mechanisms in heterosis. In this study, we focused on the allelic genomic interactions in P. alba 'Berolinensis,' and generated a high-quality chromosome-level genome assembly consisting of 19 allelic chromosomes. Its three haploid chromosome sets are polymorphic with an average of 25.73 nucleotide polymorphism sites per kilobase. We found that some stress-related genes such as RD22 and LEA7 exhibited sequence differences between different haploid genomes. The genome assembly has been deposited in our polyploid genome online analysis website TreeGenomes (https://www.treegenomes.com). These polyploid genome-related resources will provide a critical foundation for the molecular breeding of P. alba 'Berolinensis' and help us uncover the allopolyploidization effects of heterosis and abiotic stress resistance and traits of polyploidy species in the future.
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Affiliation(s)
- Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yue Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinyu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Sui Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Tianjiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yan Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ruihan He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Nan Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yiran Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wenxuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhijie Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jinwen Liu
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, China
| | - Qiwen Guo
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Haijiao Huang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R Sederoff
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Guohua Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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11
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Coate JE. Beyond Transcript Concentrations: Quantifying Polyploid Expression Responses per Biomass, per Genome, and per Cell with RNA-Seq. Methods Mol Biol 2023; 2545:227-250. [PMID: 36720816 DOI: 10.1007/978-1-0716-2561-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
RNA-seq has been used extensively to study expression responses to polyploidy. Most current methods for normalizing RNA-seq data yield estimates of transcript concentrations (transcripts per transcriptome). The implicit assumption of these normalization methods is that transcriptome size is equivalent between the samples being compared such that transcript concentrations are equivalent to transcripts per cell. In recent years, however, evidence has mounted that transcriptome size can vary dramatically in response to a range of factors including polyploidy and that such variation is ubiquitous. Where such variation exists, transcript concentration is often a poor or even misleading proxy for expression responses at other biologically relevant scales (e.g., expression per cell). Thus, it is important that transcriptomic studies of polyploids move beyond simply comparing transcript concentrations if we are to gain a complete understanding of how genome multiplication affects gene expression. I discuss this issue in more detail and summarize a suite of approaches that can leverage RNA-seq to quantify expression responses per genome, per cell, and per unit of biomass.
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12
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Zhang XX, Ren XL, Qi XT, Yang ZM, Feng XL, Zhang T, Wang HJ, Liang P, Jiang QY, Yang WJ, Fu Y, Chen M, Fu ZX, Xu B. Evolution of the CBL and CIPK gene families in Medicago: genome-wide characterization, pervasive duplication, and expression pattern under salt and drought stress. BMC PLANT BIOLOGY 2022; 22:512. [PMID: 36324083 PMCID: PMC9632064 DOI: 10.1186/s12870-022-03884-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/17/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Calcineurin B-like proteins (CBLs) are ubiquitous Ca2+ sensors that mediate plant responses to various stress and developmental processes by interacting with CBL-interacting protein kinases (CIPKs). CBLs and CIPKs play essential roles in acclimatization of crop plants. However, evolution of these two gene families in the genus Medicago is poorly understood. RESULTS A total of 68 CBL and 135 CIPK genes have been identified in five genomes from Medicago. Among these genomes, the gene number of CBLs and CIPKs shows no significant difference at the haploid genome level. Phylogenetic and comprehensive characteristic analyses reveal that CBLs and CIPKs are classified into four clades respectively, which is validated by distribution of conserved motifs. The synteny analysis indicates that the whole genome duplication events (WGDs) have contributed to the expansion of both families. Expression analysis demonstrates that two MsCBLs and three MsCIPKs are specifically expressed in roots, mature leaves, developing flowers and nitrogen fixing nodules of Medicago sativa spp. sativa, the widely grown tetraploid species. In particular, the expression of these five genes was highly up-regulated in roots when exposed to salt and drought stress, indicating crucial roles in stress responses. CONCLUSIONS Our study leads to a comprehensive understanding of evolution of CBL and CIPK gene families in Medicago, but also provides a rich resource to further address the functions of CBL-CIPK complexes in cultivated species and their closely related wild relatives.
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Affiliation(s)
- Xiao-Xia Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiao-Long Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Tong Qi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Min Yang
- Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, 075000, China
| | - Xiao-Lei Feng
- Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, 075000, China
| | - Tian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui-Jie Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Liang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi-Ying Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Jun Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Zhi-Xi Fu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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13
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A temporal gradient of cytonuclear coordination of chaperonins and chaperones during RuBisCo biogenesis in allopolyploid plants. Proc Natl Acad Sci U S A 2022; 119:e2200106119. [PMID: 35969751 PMCID: PMC9407610 DOI: 10.1073/pnas.2200106119] [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] [Indexed: 11/18/2022] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo), consisting of subunits encoded by nuclear and cytoplasmic genes, is a model for cytonuclear evolution in plant allopolyploids. To date, coordinated cytonuclear evolutionary responses of auxiliary cofactors involved in RuBisCo biogenesis remain unexplored. This study characterized and compared genomic and transcriptional cytonuclear coevolutionary responses of chaperonin/chaperones in RuBisCo folding and assembly processes across different allopolyploids. We discovered significant cytonuclear evolutionary responses in folding cofactors, with diminishing or attenuated responses later during assembly. Our results have general significance for understanding the unrecognized cytonuclear evolution of chaperonin/chaperone genes, structural and functional features of intermediate complexes, and the functioning stage of the Raf2 cofactor. Generally, the results reveal a hitherto unexplored dimension of allopolyploidy in plants. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo) has long been studied from many perspectives. As a multisubunit (large subunits [LSUs] and small subunits[SSUs]) protein encoded by genes residing in the chloroplast (rbcL) and nuclear (rbcS) genomes, RuBisCo also is a model for cytonuclear coevolution following allopolyploid speciation in plants. Here, we studied the genomic and transcriptional cytonuclear coordination of auxiliary chaperonin and chaperones that facilitate RuBisCo biogenesis across multiple natural and artificially synthesized plant allopolyploids. We found similar genomic and transcriptional cytonuclear responses, including respective paternal-to-maternal conversions and maternal homeologous biased expression, in chaperonin/chaperon-assisted folding and assembly of RuBisCo in different allopolyploids. One observation is about the temporally attenuated genomic and transcriptional cytonuclear evolutionary responses during early folding and later assembly process of RuBisCo biogenesis, which were established by long-term evolution and immediate onset of allopolyploidy, respectively. Our study not only points to the potential widespread and hitherto unrecognized features of cytonuclear evolution but also bears implications for the structural interaction interface between LSU and Cpn60 chaperonin and the functioning stage of the Raf2 chaperone.
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14
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Montgomery SA, Hisanaga T, Wang N, Axelsson E, Akimcheva S, Sramek M, Liu C, Berger F. Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia. eLife 2022; 11:79258. [PMID: 35996955 PMCID: PMC9402228 DOI: 10.7554/elife.79258] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/18/2022] [Indexed: 02/06/2023] Open
Abstract
Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.
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Affiliation(s)
- Sean Akira Montgomery
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Nan Wang
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Milos Sramek
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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15
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Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis. Curr Biol 2022; 32:2719-2729.e5. [DOI: 10.1016/j.cub.2022.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/14/2022] [Accepted: 05/06/2022] [Indexed: 01/04/2023]
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16
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Sharbrough J, Conover JL, Gyorfy MF, Grover CE, Miller ER, Wendel JF, Sloan DB. Global Patterns of subgenome evolution in organelle-targeted genes of six allotetraploid angiosperms. Mol Biol Evol 2022; 39:6564157. [PMID: 35383845 PMCID: PMC9040051 DOI: 10.1093/molbev/msac074] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary “mismatches” between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.
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Affiliation(s)
- Joel Sharbrough
- Biology Department, Colorado State University, Fort Collins, CO, USA.,Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Emma R Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B Sloan
- Biology Department, Colorado State University, Fort Collins, CO, USA
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17
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Dimos B, Emery M, Beavers K, MacKnight N, Brandt M, Demuth J, Mydlarz L. Adaptive Variation in Homolog Number Within Transcript Families Promotes Expression Divergence in Reef-Building Coral. Mol Ecol 2022; 31:2594-2610. [PMID: 35229964 DOI: 10.1111/mec.16414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 02/10/2022] [Accepted: 02/22/2022] [Indexed: 11/30/2022]
Abstract
Gene expression, especially in multi-species experiments, is used to gain insight into the genetic basis of how organisms adapt and respond to changing environments. However, evolutionary processes which can influence gene expression patterns between species such as the presence of paralogs which arise from gene duplication events are rarely accounted for. Paralogous transcripts can alter the transcriptional output of a gene and thus exclusion of these transcripts can obscure important biological differences between species. To address this issue, we investigated how differences in transcript family size is associated with divergent gene expression patterns in five species of Caribbean reef-building corals. We demonstrate that transcript families that are rapidly evolving in terms of size have increased levels of expression divergence. Additionally, these rapidly evolving transcript families are enriched for multiple biological processes, with genes involved in the coral innate immune system demonstrating pronounced variation in homolog number between species. Overall, this investigation demonstrates the importance of incorporating paralogous transcripts when comparing gene expression across species by influencing both transcriptional output and the number of transcripts within biological processes. As this investigation was based on transcriptome assemblies, additional insights into the relationship between gene duplications and expression patterns will likely emergence once more genome assemblies are available for study.
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Affiliation(s)
- Bradford Dimos
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Madison Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Kelsey Beavers
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Nicholas MacKnight
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Marilyn Brandt
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, US Virgin Islands, 00802, USA
| | - Jeffery Demuth
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Laura Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
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18
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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:2115570119. [PMID: 35027454 PMCID: PMC8784105 DOI: 10.1073/pnas.2115570119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the tissue-specific defects correlate with residual ATXR6 expression. We also determined that ATXR5/6 function is essential for female germline development. Furthermore, we provide a comprehensive analysis of H3K27me1 changes in relation to other epigenetic marks. We also determined that some previously reported suppressors of atxr5/6 may act by restoring the levels of H3K27me1, such as through up-regulation of the ATXR6 transcript in the atxr6 hypomorphic promoter allele. ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements (TEs), chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. How loss of ATXR5/6 and H3K27me1 leads to these phenotypes remains unclear. Here we provide extensive characterization of the atxr5/6 hypomorphic mutant by comprehensively examining gene expression and epigenetic changes in the mutant. We found that the tissue-specific phenotypes of TE derepression and excessive DNA in this atxr5/6 mutant correlated with residual ATXR6 expression from the hypomorphic ATXR6 allele. However, up-regulation of DNA damage genes occurred regardless of ATXR6 levels and thus appears to be a separable process. We also isolated an atxr6-null allele which showed that ATXR5 and ATXR6 are required for female germline development. Finally, we characterize three previously reported suppressors of the hypomorphic atxr5/6 mutant and show that these rescue atxr5/6 via distinct mechanisms, two of which involve increasing H3K27me1 levels.
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19
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Mottes F, Villa C, Osella M, Caselle M. The impact of whole genome duplications on the human gene regulatory networks. PLoS Comput Biol 2021; 17:e1009638. [PMID: 34871317 PMCID: PMC8675932 DOI: 10.1371/journal.pcbi.1009638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/16/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
This work studies the effects of the two rounds of Whole Genome Duplication (WGD) at the origin of the vertebrate lineage on the architecture of the human gene regulatory networks. We integrate information on transcriptional regulation, miRNA regulation, and protein-protein interactions to comparatively analyse the role of WGD and Small Scale Duplications (SSD) in the structural properties of the resulting multilayer network. We show that complex network motifs, such as combinations of feed-forward loops and bifan arrays, deriving from WGD events are specifically enriched in the network. Pairs of WGD-derived proteins display a strong tendency to interact both with each other and with common partners and WGD-derived transcription factors play a prominent role in the retention of a strong regulatory redundancy. Combinatorial regulation and synergy between different regulatory layers are in general enhanced by duplication events, but the two types of duplications contribute in different ways. Overall, our findings suggest that the two WGD events played a substantial role in increasing the multi-layer complexity of the vertebrate regulatory network by enhancing its combinatorial organization, with potential consequences on its overall robustness and ability to perform high-level functions like signal integration and noise control. Lastly, we discuss in detail the RAR/RXR pathway as an illustrative example of the evolutionary impact of WGD duplications in human. Gene duplication is one of the main mechanisms driving genome evolution. The duplication of a genomic segment can be the result of a local event, involving only a small portion of the genome, or of a dramatic duplication of the whole genome, which is however only rarely retained. All vertebrates descend from two rounds of Whole-Genome Duplication (WGD) that occurred approximately 500 Mya. We show that these events influenced in unique ways the evolution of different human gene regulatory networks, with sizeable effects on their current structure. We find that WGDs statistically increased the presence of specific classes of simple genetic circuits, considered to be fundamental building blocks of more sophisticated circuitry and commonly associated to complex functions. Our findings support the hypothesis that these rare, large-scale events have played a substantial role in the emergence of complex traits in vertebrates.
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Affiliation(s)
| | - Chiara Villa
- School of Mathematics and Statistics, University of St Andrews, Mathematical Institute, North Haugh, St Andrews, United Kingdom
| | - Matteo Osella
- Department of Physics, University of Turin & INFN, Turin, Italy
| | - Michele Caselle
- Department of Physics, University of Turin & INFN, Turin, Italy
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20
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Williams JH. Consequences of whole genome duplication for 2n pollen performance. PLANT REPRODUCTION 2021; 34:321-334. [PMID: 34302535 DOI: 10.1007/s00497-021-00426-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
The vegetative cell of the angiosperm male gametophyte (pollen) functions as a free-living, single-celled organism that both produces and transports sperm to egg. Whole-genome duplication (WGD) should have strong effects on pollen because of the haploid to diploid transition and because of both genetic and epigenetic effects on cell-level phenotypes. To disentangle historical effects of WGD on pollen performance, studies can compare 1n pollen from diploids to neo-2n pollen from diploids and synthetic autotetraploids to older 2n pollen from established neo-autotetraploids. WGD doubles both gene number and bulk nuclear DNA mass, and a substantial proportion of diploid and autotetraploid heterozygosity can be transmitted to 2n pollen. Relative to 1n pollen, 2n pollen can exhibit heterosis due to higher gene dosage, higher heterozygosity and new allelic interactions. Doubled genome size also has consequences for gene regulation and expression as well as epigenetic effects on cell architecture. Pollen volume doubling is a universal effect of WGD, whereas an increase in aperture number is common among taxa with simultaneous microsporogenesis and pored apertures, mostly eudicots. WGD instantly affects numerous evolved compromises among mature pollen functional traits and these are rapidly shaped by highly diverse tissue interactions and pollen competitive environments in the early post-WGD generations. 2n pollen phenotypes generally incur higher performance costs, and the degree to which these are met or evolve by scaling up provisioning and metabolic vigor needs further study.
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Affiliation(s)
- Joseph H Williams
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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21
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Hawkins C, Ginzburg D, Zhao K, Dwyer W, Xue B, Xu A, Rice S, Cole B, Paley S, Karp P, Rhee SY. Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1888-1905. [PMID: 34403192 DOI: 10.1111/jipb.13163] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/14/2021] [Indexed: 05/18/2023]
Abstract
To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.
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Affiliation(s)
- Charles Hawkins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Daniel Ginzburg
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - William Dwyer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Bo Xue
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Angela Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Selena Rice
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley Laboratory, Berkeley, California, 94720, USA
| | - Suzanne Paley
- SRI International, Menlo Park, California, 94025, USA
| | - Peter Karp
- SRI International, Menlo Park, California, 94025, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
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22
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Miao Z, Zhang T, Xie B, Qi Y, Ma C. Evolutionary implications of the RNA N6-methyladenosine methylome in plants. Mol Biol Evol 2021; 39:6388042. [PMID: 34633447 PMCID: PMC8763109 DOI: 10.1093/molbev/msab299] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Epigenetic modifications play important roles in genome evolution and innovation. However, most analyses have focused on the evolutionary role of DNA modifications, and little is understood about the influence of post-transcriptional RNA modifications on genome evolution. To explore the evolutionary significance of RNA modifications, we generated transcriptome-wide profiles of N6-methyladenosine (m6A), the most prevalent internal modification of mRNA, for 13 representative plant species spanning over half a billion years of evolution. These data reveal the evolutionary conservation and divergence of m6A methylomes in plants, uncover the preference of m6A modifications on ancient orthologous genes, and demonstrate less m6A divergence between orthologous gene pairs with earlier evolutionary origins. Further investigation revealed that the evolutionary divergence of m6A modifications is related to sequence variation between homologs from whole genome duplication and gene family expansion from local genome duplication. Unexpectedly, a significant negative correlation was found between the retention ratio of m6A modifications and the number of family members. Moreover, the divergence of m6A modifications is accompanied by variation in the expression level and translation efficiency of duplicated genes from whole and local genome duplication. Our work reveals new insights into evolutionary patterns of m6A methylomes in plant species and their implications, and provides a resource of plant m6A profiles for further studies of m6A regulation and function in an evolutionary context.
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Affiliation(s)
- Zhenyan Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Shaanxi, Yangling, 712100, China.,Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, 712100, China
| | - Ting Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Shaanxi, Yangling, 712100, China
| | - Bin Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Shaanxi, Yangling, 712100, China
| | - Yuhong Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Shaanxi, Yangling, 712100, China
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Shaanxi, Yangling, 712100, China.,Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, 712100, China
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23
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Fernandes Gyorfy M, Miller ER, Conover JL, Grover CE, Wendel JF, Sloan DB, Sharbrough J. Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:219-230. [PMID: 34309123 DOI: 10.1111/tpj.15436] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication (WGD) events in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follows WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated the organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.
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Affiliation(s)
| | - Emma R Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B Sloan
- Biology Department, Colorado State University, Fort Collins, CO, USA
| | - Joel Sharbrough
- Biology Department, Colorado State University, Fort Collins, CO, USA
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
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Wang H, Dang J, Wu D, Xie Z, Yan S, Luo J, Guo Q, Liang G. Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica). PLANT METHODS 2021; 17:93. [PMID: 34479588 PMCID: PMC8418031 DOI: 10.1186/s13007-021-00792-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/24/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND Ploidy manipulation is effective in seedless loquat breeding, in which flesh color is a key agronomic and economic trait. Few techniques are currently available for detecting the genotypes of polyploids in plants, but this ability is essential for most genetic research and molecular breeding. RESULTS We developed a system for genotyping by quantitative PCR (qPCR) that allowed flesh color genotyping in multiple tetraploid and triploid loquat varieties (lines). The analysis of 13 different ratios of DNA mixtures between two homozygous diploids (AA and aa) showed that the proportion of allele A has a high correlation (R2 = 0.9992) with parameter b [b = a1/(a1 + a2)], which is derived from the two normalized allele signals (a1 and a2) provided by qPCR. Cluster analysis and variance analysis from simulating triploid and tetraploid hybrids provided completely correct allelic configurations. Four genotypes (AAA, AAa, Aaa, aaa) were found in triploid loquats, and four (AAAA, AAAa, AAaa, Aaaa; absence of aaaa homozygotes) were found in tetraploid loquats. DNA markers analysis showed that the segregation of flesh color in all F1 hybrids conformed to Mendel's law. When tetraploid B431 was the female parent, more white-fleshed triploids occurred among the progeny. CONCLUSIONS qPCR can detect the flesh color genotypes of loquat polyploids and provides an alternative method for analyzing polyploid genotype and breeding, dose effects and allele-specific expression.
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Affiliation(s)
- Haiyan Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Di Wu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Zhongyi Xie
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Shuang Yan
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Jingnan Luo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China.
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China.
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25
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Veitia RA, Birchler JA. Gene-dosage issues: a recurrent theme in whole genome duplication events. Trends Genet 2021; 38:1-3. [PMID: 34215425 DOI: 10.1016/j.tig.2021.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 11/30/2022]
Abstract
Two recent studies have addressed the long-term consequences of whole genome duplications (WGD). Specifically, they analyzed transcriptomes of the plant Arabidopsis thaliana and of four salmonids to assess the impact of WGD on gene expression. These studies point to commonalities in gene expression adjustments after polyploidization that we outline and discuss below.
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Affiliation(s)
- Reiner A Veitia
- Université de Paris, F-75006, Paris, France; Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France; Université Paris-Saclay, Institut de Biologie F. Jacob, Commissariat à l'Energie Atomique, Fontenay aux Roses, France.
| | - James A Birchler
- University of Missouri, Division of Biological Sciences, Columbia, MO 65211, USA
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Shi X, Yang H, Chen C, Hou J, Hanson KM, Albert PS, Ji T, Cheng J, Birchler JA. Genomic imbalance determines positive and negative modulation of gene expression in diploid maize. THE PLANT CELL 2021; 33:917-939. [PMID: 33677584 PMCID: PMC8226301 DOI: 10.1093/plcell/koab030] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/25/2021] [Indexed: 05/20/2023]
Abstract
Genomic imbalance caused by changing the dosage of individual chromosomes (aneuploidy) has a more detrimental effect than varying the dosage of complete sets of chromosomes (ploidy). We examined the impact of both increased and decreased dosage of 15 distal and 1 interstitial chromosomal regions via RNA-seq of maize (Zea mays) mature leaf tissue to reveal new aspects of genomic imbalance. The results indicate that significant changes in gene expression in aneuploids occur both on the varied chromosome (cis) and the remainder of the genome (trans), with a wider spread of modulation compared with the whole-ploidy series of haploid to tetraploid. In general, cis genes in aneuploids range from a gene-dosage effect to dosage compensation, whereas for trans genes the most common effect is an inverse correlation in that expression is modulated toward the opposite direction of the varied chromosomal dosage, although positive modulations also occur. Furthermore, this analysis revealed the existence of increased and decreased effects in which the expression of many genes under genome imbalance are modulated toward the same direction regardless of increased or decreased chromosomal dosage, which is predicted from kinetic considerations of multicomponent molecular interactions. The findings provide novel insights into understanding mechanistic aspects of gene regulation.
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Affiliation(s)
- Xiaowen Shi
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri 65211, USA
| | - Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri 65211, USA
| | - Katherine M Hanson
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Patrice S Albert
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Tieming Ji
- Department of Statistics, University of Missouri, Columbia, Missouri 65211, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri 65211, USA
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27
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Yang H, Shi X, Chen C, Hou J, Ji T, Cheng J, Birchler JA. Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize. THE PLANT CELL 2021; 33:901-916. [PMID: 33656551 PMCID: PMC8226288 DOI: 10.1093/plcell/koab029] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/23/2021] [Indexed: 05/12/2023]
Abstract
The phenotypic consequences of the addition or subtraction of part of a chromosome is more severe than changing the dosage of the whole genome. By crossing diploid trisomies to a haploid inducer, we identified 17 distal segmental haploid disomies that cover ∼80% of the maize genome. Disomic haploids provide a level of genomic imbalance that is not ordinarily achievable in multicellular eukaryotes, allowing the impact to be stronger and more easily studied. Transcriptome size estimates revealed that a few disomies inversely modulate most of the transcriptome. Based on RNA sequencing, the expression levels of genes located on the varied chromosome arms (cis) in disomies ranged from being proportional to chromosomal dosage (dosage effect) to showing dosage compensation with no expression change with dosage. For genes not located on the varied chromosome arm (trans), an obvious trans-acting effect can be observed, with the majority showing a decreased modulation (inverse effect). The extent of dosage compensation of varied cis genes correlates with the extent of trans inverse effects across the 17 genomic regions studied. The results also have implications for the role of stoichiometry in gene expression, the control of quantitative traits, and the evolution of dosage-sensitive genes.
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Affiliation(s)
- Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Xiaowen Shi
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri 65211, USA
| | - Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri 65211, USA
| | - Tieming Ji
- Department of Statistics, University of Missouri, Columbia, Missouri 65211, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri 65211, USA
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28
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Bastiaanse H, Henry IM, Tsai H, Lieberman M, Canning C, Comai L, Groover A. A systems genetics approach to deciphering the effect of dosage variation on leaf morphology in Populus. THE PLANT CELL 2021; 33:940-960. [PMID: 33793772 PMCID: PMC8226299 DOI: 10.1093/plcell/koaa016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/30/2020] [Indexed: 05/05/2023]
Abstract
Gene copy number variation is frequent in plant genomes of various species, but the impact of such gene dosage variation on morphological traits is poorly understood. We used a large population of Populus carrying genomically characterized insertions and deletions across the genome to systematically assay the effect of gene dosage variation on a suite of leaf morphology traits. A systems genetics approach was used to integrate insertion and deletion locations, leaf morphology phenotypes, gene expression, and transcriptional network data, to provide an overview of how gene dosage influences morphology. Dosage-sensitive genomic regions were identified that influenced individual or pleiotropic morphological traits. We also identified cis-expression quantitative trait loci (QTL) within these dosage QTL regions, a subset of which modulated trans-expression QTL as well. Integration of data types within a gene co-expression framework identified co-expressed gene modules that are dosage sensitive, enriched for dosage expression QTL, and associated with morphological traits. Functional description of these modules linked dosage-sensitive morphological variation to specific cellular processes, as well as candidate regulatory genes. Together, these results show that gene dosage variation can influence morphological variation through complex changes in gene expression, and suggest that frequently occurring gene dosage variation has the potential to likewise influence quantitative traits in nature.
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Affiliation(s)
- Héloïse Bastiaanse
- Present address: VIB Center for Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
| | - Isabelle M Henry
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
| | - Helen Tsai
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
| | - Meric Lieberman
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
| | - Courtney Canning
- Pacific Southwest Research Station, US Forest Service, Davis, California 95618
| | - Luca Comai
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
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29
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Garcia-Lozano M, Natarajan P, Levi A, Katam R, Lopez-Ortiz C, Nimmakayala P, Reddy UK. Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:588-600. [PMID: 33788333 DOI: 10.1111/tpj.15256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Polyploidy has played a crucial role in plant evolution, development and function. Synthetic autopolyploid represents an ideal system to investigate the effects of polyploidization on transcriptional regulation. In this study, we deciphered the impact of genome duplication at phenotypic and molecular levels in watermelon. Overall, 88% of the genes in tetraploid watermelon followed a >1:1 dosage effect, and accordingly, differentially expressed genes were largely upregulated. In addition, a great number of hypomethylated regions (1688) were identified in an isogenic tetraploid watermelon. These differentially methylated regions were localized in promoters and intergenic regions and near transcriptional start sites of the identified upregulated genes, which enhances the importance of methylation in gene regulation. These changes were reflected in sophisticated higher-order chromatin structures. The genome doubling caused switching of 108 A and 626 B compartments that harbored genes associated with growth, development and stress responses.
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Affiliation(s)
- Marleny Garcia-Lozano
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Amnon Levi
- USDA, ARS, U.S. Vegetable Lab, Charleston, SC, USA
| | - Ramesh Katam
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL, USA
| | - Carlos Lopez-Ortiz
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
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30
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Zhang H, Xie J, Wang W, Wang J. Comparison of Brassica Genomes reveals asymmetrical gene retention between functional groups of genes in recurrent polyploidizations. PLANT MOLECULAR BIOLOGY 2021; 106:193-206. [PMID: 33742369 DOI: 10.1007/s11103-021-01137-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
We provided a study on homeologous gene evolution of homeologous genes by comparing Brassica genomes. Polyploidy has played fundamental roles during the evolution of plants. Following polyploidization, many duplicated genes are diversified or lost in a process termed diploidization. Understanding the retention and diversification of homeologs after polyploidization will help elucidate the process of diploidization. Here, we investigated the evolution of homeologous genes in Brassica genomes and observed similarly asymmetrical gene retention among different functional groups and consistent retention after recurrent polyploidizations. In the comparative analysis of Brassica diploid genomes, we found that preferentially retained genes show different patterns on sequence and expression divergence: genes with the function of 'biosynthetic process' and 'transport' were under much stronger purifying selection, while transcriptional regulatory genes diverged much faster than other genes. Duplicate pairs of the former two functional groups show conserved high expression patterns, while most of transcriptional regulatory genes are simultaneously lowly expressed. Furthermore, homeologs in diploids and allotetraploids showed similar loss and retention patterns: duplicates in progenitor genomes were more likely to be retained and accumulated fewer substitutions. However, transcriptional regulation is also enriched in the genes that do not have any non-synonymous mutations in the Brassica allotetraploids, indicating that some of these genes were under strong purifying selection. Overall, our study provided insight into the evolution of homeologs genes during diploidization process.
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Affiliation(s)
- Haorui Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiandan Xie
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Wenliang Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Jianbo Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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31
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Gillard GB, Grønvold L, Røsæg LL, Holen MM, Monsen Ø, Koop BF, Rondeau EB, Gundappa MK, Mendoza J, Macqueen DJ, Rohlfs RV, Sandve SR, Hvidsten TR. Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication. Genome Biol 2021; 22:103. [PMID: 33849620 PMCID: PMC8042706 DOI: 10.1186/s13059-021-02323-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80-100 million years ago. RESULTS We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of "toxic mutations". Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. CONCLUSIONS Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.
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Affiliation(s)
- Gareth B Gillard
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars Grønvold
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Line L Røsæg
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Matilde Mengkrog Holen
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Øystein Monsen
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, Canada
| | - Eric B Rondeau
- Department of Biology, University of Victoria, Victoria, Canada
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - John Mendoza
- Department of Computer Science, San Francisco State University, San Francisco, USA
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Rori V Rohlfs
- Department of Biology, San Francisco State University, San Francisco, USA
| | - Simen R Sandve
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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32
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Giraud D, Lima O, Rousseau-Gueutin M, Salmon A, Aïnouche M. Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae). Front Genet 2021; 12:589160. [PMID: 33841492 PMCID: PMC8027259 DOI: 10.3389/fgene.2021.589160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Gene expression dynamics is a key component of polyploid evolution, varying in nature, intensity, and temporal scales, most particularly in allopolyploids, where two or more sub-genomes from differentiated parental species and different repeat contents are merged. Here, we investigated transcriptome evolution at different evolutionary time scales among tetraploid, hexaploid, and neododecaploid Spartina species (Poaceae, Chloridoideae) that successively diverged in the last 6-10 my, at the origin of differential phenotypic and ecological traits. Of particular interest are the recent (19th century) hybridizations between the two hexaploids Spartina alterniflora (2n = 6x = 62) and S. maritima (2n = 6x = 60) that resulted in two sterile F1 hybrids: Spartina × townsendii (2n = 6x = 62) in England and Spartina × neyrautii (2n = 6x = 62) in France. Whole genome duplication of S. × townsendii gave rise to the invasive neo-allododecaploid species Spartina anglica (2n = 12x = 124). New transcriptome assemblies and annotations for tetraploids and the enrichment of previously published reference transcriptomes for hexaploids and the allododecaploid allowed identifying 42,423 clusters of orthologs and distinguishing 21 transcribed transposable element (TE) lineages across the seven investigated Spartina species. In 4x and 6x mesopolyploids, gene and TE expression changes were consistent with phylogenetic relationships and divergence, revealing weak expression differences in the tetraploid sister species Spartina bakeri and Spartina versicolor (<2 my divergence time) compared to marked transcriptome divergence between the hexaploids S. alterniflora and S. maritima that diverged 2-4 mya. Differentially expressed genes were involved in glycolysis, post-transcriptional protein modifications, epidermis development, biosynthesis of carotenoids. Most detected TE lineages (except SINE elements) were found more expressed in hexaploids than in tetraploids, in line with their abundance in the corresponding genomes. Comparatively, an astonishing (52%) expression repatterning and deviation from parental additivity were observed following recent reticulate evolution (involving the F1 hybrids and the neo-allododecaploid S. anglica), with various patterns of biased homoeologous gene expression, including genes involved in epigenetic regulation. Downregulation of TEs was observed in both hybrids and accentuated in the neo-allopolyploid. Our results reinforce the view that allopolyploidy represents springboards to new regulatory patterns, offering to worldwide invasive species, such as S. anglica, the opportunity to colonize stressful and fluctuating environments on saltmarshes.
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Affiliation(s)
- Delphine Giraud
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
| | - Oscar Lima
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
| | | | - Armel Salmon
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
| | - Malika Aïnouche
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
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33
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Van de Peer Y, Ashman TL, Soltis PS, Soltis DE. Polyploidy: an evolutionary and ecological force in stressful times. THE PLANT CELL 2021; 33:11-26. [PMID: 33751096 PMCID: PMC8136868 DOI: 10.1093/plcell/koaa015] [Citation(s) in RCA: 238] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
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Affiliation(s)
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
- Department of Biology, University of Florida, Gainesville, Florida 32611
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Huang B, Gan L, Chen D, Zhang Y, Zhang Y, Liu X, Chen S, Wei Z, Tong L, Song Z, Zhang X, Cai D, Zhang C, He Y. Integration of small RNA, degradome and proteome sequencing in Oryza sativa reveals a delayed senescence network in tetraploid rice seed. PLoS One 2020; 15:e0242260. [PMID: 33186373 PMCID: PMC7665819 DOI: 10.1371/journal.pone.0242260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Seed of rice is an important strategic resource for ensuring the security of China's staple food. Seed deterioration as a result of senescence is a major problem during seed storage, which can cause major economic losses. Screening among accessions in rice germplasm resources for traits such as slow senescence and increased seed longevity during storage is, therefore, of great significance. However, studies on delayed senescence in rice have been based mostly on diploid rice seed to date. Despite better tolerance have been verified by the artificial aging treatment for polyploid rice seed, the delayed senescence properties and delayed senescence related regulatory mechanisms of polyploid rice seed are rarely reported, due to the lack of polyploid rice materials with high seed set. High-throughput sequencing was applied to systematically investigate variations in small RNAs, the degradome, and the proteome between tetraploid and diploid rice seeds. Degradome sequencing analysis of microRNAs showed that expression of miR-164d, which regulates genes encoding antioxidant enzymes, was changed significantly, resulting in decreased miRNA-mediated cleavage of target genes in tetraploid rice. Comparisons of the expression levels of small RNAs (sRNAs) in the tetraploid and diploid libraries revealed that 12 sRNAs changed significantly, consistent with the findings from degradome sequencing. Furthermore, proteomics also showed that antioxidant enzymes were up-regulated in tetraploid rice seeds, relative to diploids.
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Affiliation(s)
- Baosheng Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- Shandong Provincial Key Laboratory of Storage and Transportation Technology of Agricultural Products, Jinan, China
| | - Lu Gan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Dongjie Chen
- Shandong Provincial Key Laboratory of Storage and Transportation Technology of Agricultural Products, Jinan, China
| | - Yachun Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Yujie Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Xiangli Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Si Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhisong Wei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Liqi Tong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhaojian Song
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- Wuhan Polyploid Biology Technology Co. Ltd, Wuhan, China
| | - Xianhua Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- Wuhan Polyploid Biology Technology Co. Ltd, Wuhan, China
| | - Detian Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- Wuhan Polyploid Biology Technology Co. Ltd, Wuhan, China
| | - Changfeng Zhang
- Shandong Provincial Key Laboratory of Storage and Transportation Technology of Agricultural Products, Jinan, China
- * E-mail: (YH); (CZ)
| | - Yuchi He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- Wuhan Polyploid Biology Technology Co. Ltd, Wuhan, China
- * E-mail: (YH); (CZ)
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Coate JE, Farmer AD, Schiefelbein JW, Doyle JJ. Expression Partitioning of Duplicate Genes at Single Cell Resolution in Arabidopsis Roots. Front Genet 2020; 11:596150. [PMID: 33240334 PMCID: PMC7670048 DOI: 10.3389/fgene.2020.596150] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/12/2020] [Indexed: 01/11/2023] Open
Abstract
Gene duplication is a key evolutionary phenomenon, prevalent in all organisms but particularly so in plants, where whole genome duplication (WGD; polyploidy) is a major force in genome evolution. Much effort has been expended in attempting to understand the evolution of duplicate genes, addressing such questions as why some paralog pairs rapidly return to single copy status whereas, in other pairs, both paralogs are retained and may diverge in expression pattern or function. The effect of a gene - its site of expression and thus the initial locus of its function - occurs at the level of a cell comprising a single cell type at a given state of the cell's development. Using Arabidopsis thaliana single cell transcriptomic data we categorized patterns of expression for 11,470 duplicate gene pairs across 36 cell clusters comprising nine cell types and their developmental states. Among these 11,470 pairs, 10,187 (88.8%) had at least one copy expressed in at least one of the 36 cell clusters. Pairs produced by WGD more often had both paralogs expressed in root cells than did pairs produced by small scale duplications. Three quarters of gene pairs expressed in the 36 cell clusters (7,608/10,187) showed extreme expression bias in at least one cluster, including 352 cases of reciprocal bias, a pattern consistent with expression subfunctionalization. More than twice as many pairs showed reciprocal expression bias between cell states than between cell types or between roots and leaves. A group of 33 gene pairs with reciprocal expression bias showed evidence of concerted divergence of gene networks in stele vs. epidermis. Pairs with both paralogs expressed without bias were less likely to have paralogs with divergent mutant phenotypes; such bias-free pairs showed evidence of preservation by maintenance of dosage balance. Overall, we found considerable evidence of shifts in gene expression following duplication, including in >80% of pairs encoding 7,653 genes expressed ubiquitously in all root cell types and states for which we inferred the polarity of change.
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Affiliation(s)
- Jeremy E. Coate
- Department of Biology, Reed College, Portland, OR, United States
| | - Andrew D. Farmer
- National Center for Genome Resources, Santa Fe, NM, United States
| | - John W. Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Jeff J. Doyle
- School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, United States
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Doyle JJ, Coate JE. Autopolyploidy: an epigenetic macromutation. AMERICAN JOURNAL OF BOTANY 2020; 107:1097-1100. [PMID: 32737992 DOI: 10.1002/ajb2.1513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/05/2020] [Indexed: 05/28/2023]
Affiliation(s)
- Jeff J Doyle
- School of Integrative Plant Science, Plant Breeding & Genetics and Plant Biology Sections, Cornell University, Ithaca, NY, 14853, USA
| | - Jeremy E Coate
- Department of Biology, Reed College, Portland, OR, 97202, USA
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37
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Raju SKK. Gene Dosage Balance Immediately following Whole-Genome Duplication in Arabidopsis. THE PLANT CELL 2020; 32:1344-1345. [PMID: 32184348 PMCID: PMC7203935 DOI: 10.1105/tpc.20.00205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
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Coate JE, Schreyer WM, Kum D, Doyle JJ. Robust Cytonuclear Coordination of Transcription in Nascent Arabidopsis thaliana Autopolyploids. Genes (Basel) 2020; 11:E134. [PMID: 32012851 PMCID: PMC7074348 DOI: 10.3390/genes11020134] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
Polyploidy is hypothesized to cause dosage imbalances between the nucleus and the other genome-containing organelles (mitochondria and plastids), but the evidence for this is limited. We performed RNA-seq on Arabidopsis thaliana diploids and their derived autopolyploids to quantify the degree of inter-genome coordination of transcriptional responses to nuclear whole genome duplication in two different organs (sepals and rosette leaves). We show that nuclear and organellar genomes exhibit highly coordinated responses in both organs. First, organelle genome copy number increased in response to nuclear whole genome duplication (WGD), at least partially compensating for altered nuclear genome dosage. Second, transcriptional output of the different cellular compartments is tuned to maintain diploid-like levels of relative expression among interacting genes. In particular, plastid genes and nuclear genes whose products are plastid-targeted show coordinated down-regulation, such that their expression levels relative to each other remain constant across ploidy levels. Conversely, mitochondrial genes and nuclear genes with mitochondrial targeting show either constant or coordinated up-regulation of expression relative to other nuclear genes. Thus, cytonuclear coordination is robust to changes in nuclear ploidy level, with diploid-like balance in transcript abundances achieved within three generations after nuclear whole genome duplication.
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Affiliation(s)
- Jeremy E. Coate
- Department of Biology, Reed College, Portland, OR 97202, USA; (W.M.S.); (D.K.)
| | - W. Max Schreyer
- Department of Biology, Reed College, Portland, OR 97202, USA; (W.M.S.); (D.K.)
| | - David Kum
- Department of Biology, Reed College, Portland, OR 97202, USA; (W.M.S.); (D.K.)
| | - Jeff J. Doyle
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA;
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