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Gerstner BP, Laport RG, Rudgers JA, Whitney KD. Plant-soil microbe feedbacks depend on distance and ploidy in a mixed cytotype population of Larrea tridentata. AMERICAN JOURNAL OF BOTANY 2024; 111:e16298. [PMID: 38433501 DOI: 10.1002/ajb2.16298] [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: 09/16/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 03/05/2024]
Abstract
PREMISE Theory predicts that mixed ploidy populations should be short-lived due to strong fitness disadvantages for the rare ploidy. However, mixed ploidy populations are common, suggesting that the fitness costs for rare ploidies are counterbalanced by ecological benefits that emerge when rare. We investigated whether differences in ecological interactions with soil microbes help to maintain a tetraploid-hexaploid population of Larrea tridentata (creosote bush) in the Sonoran Desert, California, United States, where prior work documented ploidy-specific root-associated microbes. METHODS We used a plant-soil feedback (PSF) experiment to test whether host-specific soil microbes can alter the outcomes of intraploidy vs. interploidy competition. Host-specific soil microbes can build up over time; thus, distance from a host plant can affect the fitness of nearby plants. RESULTS Seedlings grown in soils from near plants of a different ploidy produced greater biomass relative to seedlings grown in soils from near plants of the same ploidy. Moreover, seedlings grown in soils from near plants of a different ploidy produced more biomass than those grown in soils that were farther from plants of a different ploidy. These results suggest that the ecological consequences of PSF may facilitate the persistence of mixed ploidy populations. CONCLUSIONS This is the first evidence, to our knowledge, that is consistent with plant-soil microbe feedback as a viable mechanism to maintain the coexistence of multiple ploidy levels in a single population.
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Affiliation(s)
- Benjamin P Gerstner
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Robert G Laport
- Department of Biology, The College of Idaho, Caldwell, ID, 83605, USA
| | - Jennifer A Rudgers
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
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2
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You L, Sheng J, Jiang G, Chen H, Yuan Y, Gong S, Yan M, Hu J, Xiang G, Duan R, Chen Y, Liu X. Molecular characterization and expression patterns of MTP genes under heavy metal stress in mustard (Brassica juncea L.). Sci Rep 2024; 14:17857. [PMID: 39090207 PMCID: PMC11294466 DOI: 10.1038/s41598-024-68877-8] [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: 04/20/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
Members of the Metal Tolerance Protein (MTP) family are critical in mediating the transport and tolerance of divalent metal cations. Despite their significance, the understanding of MTP genes in mustard (Brassica juncea) remains limited, especially regarding their response to heavy metal (HM) stress. In our study, we identified MTP gene sets in Brassica rapa (17 genes), Brassica nigra (18 genes), and B. juncea (33 genes) using the HMMER (Cation_efflux; PF01545) and BLAST analysis. For the 33 BjMTPs, a comprehensive bioinformatics analysis covering the physicochemical properties, phylogenetic relationships, conserved motifs, protein structures, collinearity, spatiotemporal RNA-seq expression, GO enrichment, and expression profiling under six HM stresses (Mn2+, Fe2+, Zn2+, Cd2+, Sb3+, and Pb2+) were carried out. According to the findings of physicochemical characteristics, phylogenetic tree, and collinearity, the allopolyploid B. juncea's MTP genes were inherited from its progenitors, B. rapa and B. nigra, with minimal gene loss during polyploidization. Members of the BjMTP family exhibited conserved motifs, promoter elements, and expression patterns across subgroups, consistent with the seven evolutionary branches (G1, G4-G9, and G12) of the MTPs. Further, spatiotemporal expression profiling under HM stresses successfully identified specific genes and crucial cis-regulatory elements associated with the response of BjMTPs to HM stresses. These findings may contribute to the genetic improvement of B. juncea for enhanced HM tolerance, facilitating the remediation of HM-contaminated areas.
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Affiliation(s)
- Liang You
- College of Agriculture and Biology, Key Laboratory of Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan of College of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, Hunan, China
| | - Jialin Sheng
- College of Agriculture and Biology, Key Laboratory of Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan of College of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, Hunan, China
| | - Guoxiang Jiang
- College of Agriculture and Biology, Key Laboratory of Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan of College of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, Hunan, China
| | - Hao Chen
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yuhui Yuan
- College of Agriculture and Biology, Key Laboratory of Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan of College of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, Hunan, China
| | - Sha Gong
- College of Agriculture and Biology, Key Laboratory of Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan of College of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, Hunan, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Junhe Hu
- College of Agriculture and Biology, Key Laboratory of Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan of College of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, Hunan, China
| | - Guohong Xiang
- College of Agriculture and Biology, Key Laboratory of Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan of College of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, Hunan, China
| | - Renyan Duan
- College of Agriculture and Biology, Key Laboratory of Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan of College of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, Hunan, China
| | - Yong Chen
- College of Agriculture and Biology, Key Laboratory of Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan of College of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, Hunan, China.
| | - Xianjun Liu
- College of Agriculture and Biology, Key Laboratory of Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan of College of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, Hunan, China.
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3
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Barker MS, Jiao Y, Glennon KL. Doubling down on polyploid discoveries: Global advances in genomics and ecological impacts of polyploidy. AMERICAN JOURNAL OF BOTANY 2024; 111:e16395. [PMID: 39164922 DOI: 10.1002/ajb2.16395] [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: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024]
Abstract
All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants.
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Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, 85721, AZ, USA
| | - Yuannian Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Kelsey L Glennon
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
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4
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Hagen ER, Vasconcelos T, Boyko JD, Beaulieu JM. Investigating historical drivers of latitudinal gradients in polyploid plant biogeography: A multiclade perspective. AMERICAN JOURNAL OF BOTANY 2024; 111:e16356. [PMID: 38867412 DOI: 10.1002/ajb2.16356] [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: 05/06/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024]
Abstract
PREMISE The proportion of polyploid plants in a community increases with latitude, and different hypotheses have been proposed about which factors drive this pattern. Here, we aimed to understand the historical causes of the latitudinal polyploidy gradient using a combination of ancestral state reconstruction methods. Specifically, we assessed whether (1) polyploidization enables movement to higher latitudes (i.e., polyploidization precedes occurrences in higher latitudes) or (2) higher latitudes facilitate polyploidization (i.e., occurrence in higher latitudes precedes polyploidization). METHODS We reconstructed the ploidy states and ancestral niches of 1032 angiosperm species at four paleoclimatic time slices ranging from 3.3 million years ago to the present, comprising taxa from four well-represented clades: Onagraceae, Primulaceae, Solanum (Solanaceae), and Pooideae (Poaceae). We used ancestral niche reconstruction models alongside a customized discrete character evolution model to allow reconstruction of states at specific time slices. Patterns of latitudinal movement were reconstructed and compared in relation to inferred ploidy shifts. RESULTS No single hypothesis applied equally well across all analyzed clades. While significant differences in median latitudinal occurrence were detected in the largest clade, Poaceae, no significant differences were detected in latitudinal movement in any clade. CONCLUSIONS Our preliminary study is the first to attempt to connect ploidy changes to continuous latitudinal movement, but we cannot favor one hypothesis over another. Given that patterns seem to be clade-specific, more clades must be analyzed in future studies for generalities to be drawn.
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Affiliation(s)
- Eric R Hagen
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, ON, Canada
| | - Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - James D Boyko
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, 72701, AR, USA
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5
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Anneberg TJ, Cullen NP, O'Neill EM, Wei N, Ashman TL. Neopolyploidy has variable effects on the diversity and composition of the wild strawberry microbiome. AMERICAN JOURNAL OF BOTANY 2024; 111:e16287. [PMID: 38366679 DOI: 10.1002/ajb2.16287] [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: 07/17/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 02/18/2024]
Abstract
PREMISE Whole-genome duplication (neopolyploidy) can instantly differentiate the phenotype of neopolyploids from their diploid progenitors. These phenotypic shifts in organs such as roots and leaves could also differentiate the way neopolyploids interact with microbial species. While some studies have addressed how specific microbial interactions are affected by neopolyploidy, we lack an understanding of how genome duplication affects the diversity and composition of microbial communities. METHODS We performed a common garden experiment with multiple clones of artificially synthesized autotetraploids and their ancestral diploids, derived from 13 genotypes of wild strawberry, Fragaria vesca. We sequenced epiphytic bacteria and fungi from roots and leaves and characterized microbial communities and leaf functional traits. RESULTS Autotetraploidy had no effect on bacterial alpha diversity of either organ, but it did have a genotype-dependent effect on the diversity of fungi on leaves. In contrast, autotetraploidy restructured the community composition of leaf bacteria and had a genotype-dependent effect on fungal community composition in both organs. The most differentially abundant bacterial taxon on leaves belonged to the Sphingomonas, while a member of the Trichoderma was the most differentially abundant fungal taxon on roots. Ploidy-induced change in leaf size was strongly correlated with a change in bacterial but not fungal leaf communities. CONCLUSIONS Genome duplication can immediately alter aspects of the plant microbiome, but this effect varies by host genotype and bacterial and fungal community. Expanding these studies to wild settings where plants are exposed continuously to microbes are needed to confirm the patterns observed here.
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Affiliation(s)
- Thomas J Anneberg
- Department of Biological Sciences, University of Pittsburgh, PA, USA
| | - Nevin P Cullen
- Department of Biological Sciences, University of Pittsburgh, PA, USA
| | | | - Na Wei
- Department of Biological Sciences, University of Pittsburgh, PA, USA
- Holden Arboretum, OH, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, PA, USA
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6
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Dougan KE, Bellantuono AJ, Kahlke T, Abbriano RM, Chen Y, Shah S, Granados-Cifuentes C, van Oppen MJH, Bhattacharya D, Suggett DJ, Rodriguez-Lanetty M, Chan CX. Whole-genome duplication in an algal symbiont bolsters coral heat tolerance. SCIENCE ADVANCES 2024; 10:eadn2218. [PMID: 39028812 PMCID: PMC11259175 DOI: 10.1126/sciadv.adn2218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/14/2024] [Indexed: 07/21/2024]
Abstract
The algal endosymbiont Durusdinium trenchii enhances the resilience of coral reefs under thermal stress. D. trenchii can live freely or in endosymbiosis, and the analysis of genetic markers suggests that this species has undergone whole-genome duplication (WGD). However, the evolutionary mechanisms that underpin the thermotolerance of this species are largely unknown. Here, we present genome assemblies for two D. trenchii isolates, confirm WGD in these taxa, and examine how selection has shaped the duplicated genome regions using gene expression data. We assess how the free-living versus endosymbiotic lifestyles have contributed to the retention and divergence of duplicated genes, and how these processes have enhanced the thermotolerance of D. trenchii. Our combined results suggest that lifestyle is the driver of post-WGD evolution in D. trenchii, with the free-living phase being the most important, followed by endosymbiosis. Adaptations to both lifestyles likely enabled D. trenchii to provide enhanced thermal stress protection to the host coral.
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Affiliation(s)
- Katherine E. Dougan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Yibi Chen
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sarah Shah
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Camila Granados-Cifuentes
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Madeleine J. H. van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - David J. Suggett
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
- KAUST Reefscape Restoration Initiative (KRRI) and Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Mauricio Rodriguez-Lanetty
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
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7
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Valdés-Florido A, González-Toral C, Maguilla E, Cires E, Díaz-Lifante Z, Andrés-Camacho C, Nieto Feliner G, Arroyo J, Escudero M. Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae). ANNALS OF BOTANY 2024; 134:247-262. [PMID: 38687133 PMCID: PMC11232519 DOI: 10.1093/aob/mcae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND AND AIMS Polyploidy is considered one of the main mechanisms of plant evolution and speciation. In the Mediterranean Basin, polyploidy has contributed to making this region a biodiversity hotspot, along with its geological and climatic history and other ecological and biogeographical factors. The Mediterranean genus Centaurium (Gentianaceae) comprises ~25 species, of which 60 % are polyploids, including tetraploids and hexaploids. To date, the evolutionary history of centauries has been studied using Sanger sequencing phylogenies, which have been insufficient to fully understand the phylogenetic relationships in this lineage. The goal of this study is to gain a better understanding of the evolutionary history of Centaurium by exploring the mechanisms that have driven its diversification, specifically hybridization and polyploidy. We aim to identify the parentage of hybrid species, at the species or clade level, as well as assessing whether morphological traits are associated with particular ploidy levels. METHODS We sequenced RADseq markers from 42 samples of 28 Centaurium taxa, and performed phylogenomic analyses using maximum likelihood, summary coalescent SVDquartets and Neighbor-Net approaches. To identify hybrid taxa, we used PhyloNetworks and the fastSTRUCTURE algorithm. To infer the putative parental species of the allopolyploids, we employed genomic analyses (SNIPloid). The association between different traits and particular ploidy levels was explored with non-metric multidimensional scaling. KEY RESULTS Our phylogenetic analyses confirmed the long-suspected occurrence of recurrent hybridization. The allopolyploid origin of the tetraploid C. serpentinicola and the hexaploids C. mairei, C. malzacianum and C. centaurioides was also confirmed, unlike that of C. discolor. We inferred additional signatures of hybridization events within the genus and identified morphological traits differentially distributed in different ploidy levels. CONCLUSIONS This study highlights the important role that hybridization has played in the evolution of a Mediterranean genus such as Centaurium, leading to a polyploid complex, which facilitated its diversification and may exemplify that of other Mediterranean groups.
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Affiliation(s)
- Ana Valdés-Florido
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | | | - Enrique Maguilla
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, 41013, Spain
| | - Eduardo Cires
- Department of Organisms and Systems Biology, University of Oviedo, Oviedo, 33071, Spain
- Institute of Natural Resources and Territorial Planning (INDUROT), Campus de Mieres, Mieres, 33600, Spain
| | - Zoila Díaz-Lifante
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | - Cristina Andrés-Camacho
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | | | - Juan Arroyo
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | - Marcial Escudero
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
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8
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Pungaršek Š, Frajman B. Influence of polyploidy on morphology and distribution of the Cypress Spurge (Euphorbia cyparissias, Euphorbiaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2024. [PMID: 38979801 DOI: 10.1111/plb.13685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/26/2024] [Indexed: 07/10/2024]
Abstract
Polyploidy can cause differences in phenotypic and physiological traits among different cytotypes of the same species. Polyploids may have larger organs or occupy different ecological niches than their diploid counterparts, therefore they are hypothesized to have larger distributions or prosper in stressful environments, such as higher elevations. The Cypress spurge (Euphorbia cyparissias L.; Euphorbiaceae) is a widespread European heteroploid species including di- (2x), tetra- (4x) and hexaploid (6x) cytotypes. We tested the hypotheses that polyploids are more widespread and more abundant at higher elevations and have larger organs than their diploid ancestors in the case of E. cyparissias. We also analysed whether genome downsizing had occurred after polyploidisation. We conducted a comprehensive geographic sampling of 617 populations of E. cyparissias throughout Europe. We estimated their relative genome size using flow cytometry and inferred ploidy level of each population. We scored 13 morphological traits of vegetative and seed characters and performed statistical analyses. The study indicates that polyploidisation facilitated colonisation of new areas in E. cyparissias, where the tetraploids are most widespread, whereas the diploids are limited to putative Pleistocene refugia, mostly in southern Europe. On the other hand, the three ploidies do not differ in their elevational distribution. Although some quantitative morphological traits exhibited an increasing trend with increasing ploidy, most traits did not differ significantly among the three ploidies, and there was no overall phenotypic differentiation among them. Given that individuals of different ploidies thrive in similar habitats across the same elevations, we suggest that ecological segregation following polyploidisation is a more important trigger for morphological differentiation than polyploidisation itself in autopolyploid plants. The study demonstrates that polyploidisation can be crucial for the colonisation of new areas and for range expansion, but it does not necessarily influence elevational distribution nor confer a different phenotype.
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Affiliation(s)
- Š Pungaršek
- Department of Botany, University of Innsbruck, Innsbruck, Austria
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | - B Frajman
- Department of Botany, University of Innsbruck, Innsbruck, Austria
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9
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Zhang H, Liu H, Han X. Traits-based approach: leveraging genome size in plant-microbe interactions. Trends Microbiol 2024; 32:333-341. [PMID: 37925351 DOI: 10.1016/j.tim.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
Trait-based approaches have gained growing interest in studying plant-microbe interactions. However, current traits normally considered (e.g., morphological, physiological, or chemical traits) are biased towards those showing large intraspecific variations, necessitating the identification of fewer plastic traits that differ between species. Here, we propose using genome size (the amount of DNA in the nucleus of a cell) as a suitable trait for studying plant-microbiome interactions due to its relatively stable nature, minimally affected by external environmental variations. Emerging evidence suggests that plant genome size affects the plant-associated microbial community, and tissue-specific environments select microbes based on their genome size. These findings pinpoint environmental selection in genome size as an emerging driver of plant-microbiome interactions, potentially impacting ecosystem functions and productivity.
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Affiliation(s)
- Haiyang Zhang
- College of Life Sciences, Hebei University, Baoding, China.
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2753, Australia
| | - Xingguo Han
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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10
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Anneberg TJ, Turcotte MM, Ashman TL. Plant neopolyploidy and genetic background differentiate the microbiome of duckweed across a variety of natural freshwater sources. Mol Ecol 2023; 32:5849-5863. [PMID: 37750335 DOI: 10.1111/mec.17142] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/06/2023] [Indexed: 09/27/2023]
Abstract
Whole-genome duplication has long been appreciated for its role in driving phenotypic novelty in plants, often altering the way organisms interface with the abiotic environment. Only recently, however, have we begun to investigate how polyploidy influences interactions of plants with other species, despite the biotic niche being predicted as one of the main determinants of polyploid establishment. Nevertheless, we lack information about how polyploidy affects the diversity and composition of the microbial taxa that colonize plants, and whether this is genotype-dependent and repeatable across natural environments. This information is a first step towards understanding whether the microbiome contributes to polyploid establishment. We, thus, tested the immediate effect of polyploidy on the diversity and composition of the bacterial microbiome of the aquatic plant Spirodela polyrhiza using four pairs of diploids and synthetic autotetraploids. Under controlled conditions, axenic plants were inoculated with pond waters collected from 10 field sites across a broad environmental gradient. Autotetraploids hosted 4%-11% greater bacterial taxonomic and phylogenetic diversity than their diploid progenitors. Polyploidy, along with its interactions with the inoculum source and genetic lineage, collectively explained 7% of the total variation in microbiome composition. Furthermore, polyploidy broadened the core microbiome, with autotetraploids having 15 unique bacterial taxa in addition to the 55 they shared with diploids. Our results show that whole-genome duplication directly leads to novelty in the plant microbiome and importantly that the effect is dependent on the genetic ancestry of the polyploid and generalizable over many environmental contexts.
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Affiliation(s)
- Thomas J Anneberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Martin M Turcotte
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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11
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Wolfe TM, Balao F, Trucchi E, Bachmann G, Gu W, Baar J, Hedrén M, Weckwerth W, Leitch AR, Paun O. Recurrent allopolyploidizations diversify ecophysiological traits in marsh orchids (Dactylorhiza majalis s.l.). Mol Ecol 2023; 32:4777-4790. [PMID: 37452724 PMCID: PMC10947288 DOI: 10.1111/mec.17070] [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: 01/03/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Whole-genome duplication has shaped the evolution of angiosperms and other organisms, and is important for many crops. Structural reorganization of chromosomes and repatterning of gene expression are frequently observed in allopolyploids, with physiological and ecological consequences. Recurrent origins from different parental populations are widespread among polyploids, resulting in an array of lineages that provide excellent models to uncover mechanisms of adaptation to divergent environments in early phases of polyploid evolution. We integrate here transcriptomic and ecophysiological comparative studies to show that sibling allopolyploid marsh orchid species (Dactylorhiza, Orchidaceae) occur in different habitats (low nutrient fens vs. meadows with mesic soils) and are characterized by a complex suite of intertwined, pronounced ecophysiological differences between them. We uncover distinct features in leaf elemental chemistry, light-harvesting, photoprotection, nutrient transport and stomata activity of the two sibling allopolyploids, which appear to match their specific ecologies, in particular soil chemistry differences at their native sites. We argue that the phenotypic divergence between the sibling allopolyploids has a clear genetic basis, generating ecological barriers that maintain distinct, independent lineages, despite pervasive interspecific gene flow. This suggests that recurrent origins of polyploids bring about a long-term potential to trigger and maintain functional and ecological diversity in marsh orchids and other groups.
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Affiliation(s)
- Thomas M. Wolfe
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
- Department of Forest and Soil SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Francisco Balao
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Departamento de Biologia Vegetal y EcologiaUniversity of SevilleSevillaSpain
| | - Emiliano Trucchi
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Marche Polytechnic UniversityAnconaItaly
| | - Gert Bachmann
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS)University of ViennaViennaAustria
| | - Wenjia Gu
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Juliane Baar
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | | | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS)University of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Andrew R. Leitch
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
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12
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Yuan J, Song Q. Polyploidy and diploidization in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:51. [PMID: 37313224 PMCID: PMC10244302 DOI: 10.1007/s11032-023-01396-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023]
Abstract
Polyploidy is widespread and particularly common in angiosperms. The prevalence of polyploidy in the plant suggests it as a crucial driver of diversification and speciation. The paleopolyploid soybean (Glycine max) is one of the most important crops of plant protein and oil for humans and livestock. Soybean experienced two rounds of whole genome duplication around 13 and 59 million years ago. Due to the relatively slow process of post-polyploid diploidization, most genes are present in multiple copies across the soybean genome. Growing evidence suggests that polyploidization and diploidization could cause rapid and dramatic changes in genomic structure and epigenetic modifications, including gene loss, transposon amplification, and reorganization of chromatin architecture. This review is focused on recent progresses about genetic and epigenetic changes during polyploidization and diploidization of soybean and represents the challenges and potentials for application of polyploidy in soybean breeding.
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Affiliation(s)
- Jingya Yuan
- College of Life Sciences, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 Jiangsu China
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 Jiangsu China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 Jiangsu China
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13
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Shafir A, Halabi K, Escudero M, Mayrose I. A non-homogeneous model of chromosome-number evolution to reveal shifts in the transition patterns across the phylogeny. THE NEW PHYTOLOGIST 2023; 238:1733-1744. [PMID: 36759331 DOI: 10.1111/nph.18805] [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: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Changes in chromosome numbers, including polyploidy and dysploidy events, play a key role in eukaryote evolution as they could expediate reproductive isolation and have the potential to foster phenotypic diversification. Deciphering the pattern of chromosome-number change within a phylogeny currently relies on probabilistic evolutionary models. All currently available models assume time homogeneity, such that the transition rates are identical throughout the phylogeny. Here, we develop heterogeneous models of chromosome-number evolution that allow multiple transition regimes to operate in distinct parts of the phylogeny. The partition of the phylogeny to distinct transition regimes may be specified by the researcher or, alternatively, identified using a sequential testing approach. Once the number and locations of shifts in the transition pattern are determined, a second search phase identifies regimes with similar transition dynamics, which could indicate on convergent evolution. Using simulations, we study the performance of the developed model to detect shifts in patterns of chromosome-number evolution and demonstrate its applicability by analyzing the evolution of chromosome numbers within the Cyperaceae plant family. The developed model extends the capabilities of probabilistic models of chromosome-number evolution and should be particularly helpful for the analyses of large phylogenies that include multiple distinct subclades.
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Affiliation(s)
- Anat Shafir
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Keren Halabi
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Reina Mercedes, ES-41012, Seville, Spain
| | - Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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14
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Preston R, Rodil IF. Genetic characteristics influence the phenotype of marine macroalga Fucus vesiculosus (Phaeophyceae). Ecol Evol 2023; 13:e9788. [PMID: 36744077 PMCID: PMC9889845 DOI: 10.1002/ece3.9788] [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: 09/29/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Intraspecific variation is an important component of heterogeneity in biological systems that can manifest at the genotypic and phenotypic level. This study investigates the influence of genetic characteristics on the phenotype of free-living Fucus vesiculosus using traditional morphological measures and microsatellite genotyping. Two sympatric morphotypes were observed to be significantly genetically and morphologically differentiated despite experiencing analogous local environmental conditions; indicating a genetic element to F. vesiculosus morphology. Additionally, the observed intraclonal variation established divergent morphology within some genets. This demonstrated that clonal lineages have the ability to alter morphological traits by either a plastic response or somatic mutations. We provide support for the potential occurrence of the Gigas effect (cellular/organ enlargement through genome duplication) in the Fucus genus, with polyploidization appearing to correlate with a general increase in the size of morphological features. Phenotypic traits, as designated by morphology within the study, of F. vesiculosus are partially controlled by the genetic characteristics of the thalli. This study suggests that largely asexually reproducing algal populations may have the potential to adapt to changing environmental conditions through genome changes or phenotypic plasticity.
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Affiliation(s)
- Roxana Preston
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland,Tvärminne Zoological StationUniversity of HelsinkiHankoFinland
| | - Iván F. Rodil
- Tvärminne Zoological StationUniversity of HelsinkiHankoFinland,Department of Biology, INMARUniversity of Cadiz, International Campus of Excellence of the Sea (CEIMAR)CádizSpain
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15
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Kapoor B, Kumar P, Verma V, Irfan M, Sharma R, Bhargava B. How plants conquered land: evolution of terrestrial adaptation. J Evol Biol 2023; 36:5-14. [PMID: 36083189 DOI: 10.1111/jeb.14062] [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: 11/15/2021] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023]
Abstract
The transition of plants from water to land is considered one of the most significant events in the evolution of life on Earth. The colonization of land by plants, accompanied by their morphological, physiological and developmental changes, resulted in plant biodiversity. Besides significantly influencing oxygen levels in the air and on land, plants manufacture organic matter from CO2 and water with the help of sunlight, paving the way for the diversification of nonplant lineages ranging from microscopic organisms to animals. Land plants regulate the climate by adjusting total biomass and energy flow. At the genetic level, these innovations are achieved through the rearrangement of pre-existing genetic information. Advances in genome sequencing technology are revamping our understanding of plant evolution. This study highlights the morphological and genomic innovations that allow plants to integrate life on Earth.
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Affiliation(s)
- Bhuvnesh Kapoor
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Vipasha Verma
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, USA
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Bhavya Bhargava
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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16
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Becker FW, Oberlander KC, Trávníček P, Dreyer LL. Inconsistent expression of the gigas effect in polyploid Oxalis. AMERICAN JOURNAL OF BOTANY 2022; 109:1607-1621. [PMID: 36193941 DOI: 10.1002/ajb2.16077] [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: 03/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
PREMISE It is well-known that whole genome duplication (WGD) has played a significant role in the evolution of plants. The best-known phenotypic effect of WGD is the gigas effect, or the enlargement of polyploid plant traits. WGD is often linked with increased weediness, which could be a result of fitness advantages conferred by the gigas effect. As a result, the gigas effect could potentially explain polyploid persistence and abundance. We test whether a gigas effect is present in the polyploid-rich geophyte Oxalis, at both organ and cellular scales. METHODS We measured traits in conspecific diploid and polyploid accessions of 24 species across the genus. In addition, we measured the same and additional traits in 20 populations of the weedy and highly ploidy-variable species Oxalis purpurea L., including measures of clonality and selfing as a proxy for weediness. Ploidy level was determined using flow cytometry. RESULTS We found substantial variation and no consistent ploidy-related size difference, both between and within species, and across traits. Oxalis purpurea polyploids did, however, produce significantly more underground biomass and more bulbils than diploids, consistent with a potential role of WGD in the weediness of this species. CONCLUSIONS Our results suggest a more nuanced role for the gigas effect, at least in Oxalis. It may be temporary, short-lived, and inconsistently expressed and retained on evolutionary time scales, but in the short term can contribute to lineage success via increased vegetative reproduction.
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Affiliation(s)
- Frederik W Becker
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Kenneth C Oberlander
- H. G. W. J. Schweickerdt Herbarium, Department of Plant and Soil Sciences, Plant Sciences Complex, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Pavel Trávníček
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic, and Department of Botany, Charles University, Praha, Czech Republic
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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17
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Moraes AP, Engel TBJ, Forni-Martins ER, de Barros F, Felix LP, Cabral JS. Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids. ANNALS OF BOTANY 2022; 130:11-25. [PMID: 35143612 PMCID: PMC9295925 DOI: 10.1093/aob/mcac021] [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: 11/18/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS The entangled relationship of chromosome number and genome size with species distribution has been the subject of study for almost a century, but remains an open question due to previous ecological and phylogenetic knowledge constraints. To better address this subject, we used the clade Maxillariinae, a widely distributed and karyotypically known orchid group, as a model system to infer such relationships in a robust methodological framework. METHODS Based on the literature and new data, we gathered the chromosome number and genome size for 93 and 64 species, respectively. We built a phylogenetic hypothesis and assessed the best macroevolutionary model for both genomic traits. Additionally, we collected together ecological data (preferences for bioclimatic variables, elevation and habit) used as explanatory variables in multivariate phylogenetic models explaining genomic traits. Finally, the impact of polyploidy was estimated by running the analyses with and without polyploids in the sample. KEY RESULTS The association between genomic and ecological data varied depending on whether polyploids were considered or not. Without polyploids, chromosome number failed to present consistent associations with ecological variables. With polyploids, there was a tendency to waive epiphytism and colonize new habitats outside humid forests. The genome size showed association with ecological variables: without polyploids, genome increase was associated with flexible habits, with higher elevation and with drier summers; with polyploids, genome size increase was associated with colonizing drier environments. CONCLUSIONS The chromosome number and genome size variations, essential but neglected traits in the ecological niche, are shaped in the Maxillariinae by both neutral and adaptive evolution. Both genomic traits are partially correlated to bioclimatic variables and elevation, even when controlling for phylogenetic constraints. While polyploidy was associated with shifts in the environmental niche, the genome size emerges as a central trait in orchid evolution by the association between small genome size and epiphytism, a key innovation to Neotropical orchid diversification.
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Affiliation(s)
| | - Thaissa Brogliato Junqueira Engel
- Universidade de Campinas – UNICAMP, Instituto de Biologia, Departamento de Biologia Vegetal, Programa de Pós Graduação em Biologia Vegetal, Campinas, 13083-970, São Paulo, Brazil
| | - Eliana R Forni-Martins
- Universidade de Campinas – UNICAMP, Instituto de Biologia, Departamento de Biologia Vegetal, Programa de Pós Graduação em Biologia Vegetal, Campinas, 13083-970, São Paulo, Brazil
| | - Fábio de Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquidário do Estado, São Paulo, 04045-972, São Paulo, Brazil
| | - Leonardo P Felix
- Universidade Federal da Paraíba – UFPB, Campus II, Departamento de Ciências Biológicas, Areia, 58397-000, Paraíba, Brazil
| | - Juliano Sarmento Cabral
- University of Würzburg, Ecosystem Modeling, Center for Computational and Theoretical Biology (CCTB), Klara-Oppenheimer-Weg 32, D-97074, Würzburg, Germany
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18
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Van Drunen WE, Johnson MTJ. Polyploidy in urban environments. Trends Ecol Evol 2022; 37:507-516. [PMID: 35246321 DOI: 10.1016/j.tree.2022.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
Abstract
Polyploidy is a major driver of evolutionary change in plants, but many aspects of polyploidy in natural systems remain enigmatic. We argue that urban landscapes present an unprecedented opportunity to observe polyploidy in action. Integrating polyploid biology and urban evolutionary ecology, we discuss multiple factors expected to promote polyploid formation, establishment, and persistence in urban systems. We develop a predictive framework for the contemporary ecology and evolution of polyploid plants in cities, and through this novel perspective propose that studying polyploidy in an urban context could lead to breakthroughs in understanding fundamental processes in polyploid evolution. We conclude by highlighting the potential consequences of polyploidy in urban environments, and outline a roadmap for research into this currently unexplored field.
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Affiliation(s)
- Wendy E Van Drunen
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada; Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
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19
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Li M, Wang F, Ma J, Liu H, Ye H, Zhao P, Wang J. Comprehensive Evolutionary Analysis of CPP Genes in Brassica napus L. and Its Two Diploid Progenitors Revealing the Potential Molecular Basis of Allopolyploid Adaptive Advantage Under Salt Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:873071. [PMID: 35548281 PMCID: PMC9085292 DOI: 10.3389/fpls.2022.873071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Allopolyploids exist widely in nature and have strong environmental adaptability. The typical allopolyploid Brassica napus L. is a widely cultivated crop, but whether it is superior to its diploid progenitors in abiotic stress resistance and the key genes that may be involved are not fully understood. Cystein-rich polycomb-like protein (CPP) genes encode critical transcription factors involved in the response of abiotic stress, including salt stress. To explore the potential molecular basis of allopolyploid adaptation to salt stress, we comprehensively analyzed the characteristics and salt stress response of the CPP genes in B. napus and its two diploid progenitors in this study. We found some molecular basis that might be associated with the adaptability of B. napus, including the expansion of the CPP gene family, the acquisition of introns by some BnCPPs, and abundant cis-acting elements upstream of BnCPPs. We found two duplication modes (whole genome duplication and transposed duplication) might be the main reasons for the expansion of CPP gene family in B. napus during allopolyploidization. CPP gene expression levels and several physiological indexes were changed in B. napus and its diploid progenitors after salt stress, suggesting that CPP genes might play important roles in the response of salt stress. We found that some BnCPPs might undergo new functionalization or subfunctionalization, and some BnCPPs also show biased expression, which might contribute to the adaptation of B. napus under saline environment. Compared with diploid progenitors, B. napus showed stronger physiological responses, and BnCPP gene expression also showed higher changes after salt stress, indicating that the allopolyploid B. napus had an adaptive advantage under salt stress. This study could provide evidence for the adaptability of polyploid and provide important clues for the study of the molecular mechanism of salt stress resistance in B. napus.
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Affiliation(s)
- Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fan Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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20
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Ponsford JCB, Hubbard CJ, Harrison JG, Maignien L, Buerkle CA, Weinig C. Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities. mSystems 2022; 7:e0097321. [PMID: 35014873 PMCID: PMC8751390 DOI: 10.1128/msystems.00973-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/15/2021] [Indexed: 01/04/2023] Open
Abstract
The composition of microbial communities found in association with plants is influenced by host phenotype and genotype. However, the ways in which specific genetic architectures of host plants shape microbiomes are unknown. Genome duplication events are common in the evolutionary history of plants and influence many important plant traits, and thus, they may affect associated microbial communities. Using experimentally induced whole-genome duplication (WGD), we tested the effect of WGD on rhizosphere bacterial communities in Arabidopsis thaliana. We performed 16S rRNA amplicon sequencing to characterize differences between microbiomes associated with specific host genetic backgrounds (Columbia versus Landsberg) and ploidy levels (diploid versus tetraploid). We modeled relative abundances of bacterial taxa using a hierarchical Bayesian approach. We found that host genetic background and ploidy level affected rhizosphere community composition. We then tested to what extent microbiomes derived from a specific genetic background or ploidy level affected plant performance by inoculating sterile seedlings with microbial communities harvested from a prior generation. We found a negative effect of the tetraploid Columbia microbiome on growth of all four plant genetic backgrounds. These findings suggest an interplay between host genetic background and ploidy level and bacterial community assembly with potential ramifications for host fitness. Given the prevalence of ploidy-level variation in both wild and managed plant populations, the effects on microbiomes of this aspect of host genetic architecture could be a widespread driver of differences in plant microbiomes. IMPORTANCE Plants influence the composition of their associated microbial communities, yet the underlying host-associated genetic determinants are typically unknown. Genome duplication events are common in the evolutionary history of plants and affect many plant traits. Using Arabidopsis thaliana, we characterized how whole-genome duplication affected the composition of rhizosphere bacterial communities and how bacterial communities associated with two host plant genetic backgrounds and ploidy levels affected subsequent plant growth. We observed an interaction between ploidy level and genetic background that affected both bacterial community composition and function. This research reveals how genome duplication, a widespread genetic feature of both wild and crop plant species, influences bacterial assemblages and affects plant growth.
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Affiliation(s)
| | - Charley J. Hubbard
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
| | | | - Lois Maignien
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Massachusetts, USA
- Laboratory of Microbiology of Extreme Environments, UMR 6197, Institut Européen de la Mer, Université de Bretagne Occidentale, Plouzane, France
| | - C. Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
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21
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Lv J, Chen B, Ma C, Qiao K, Fan S, Ma Q. Identification and characterization of the AINV genes in five Gossypium species with potential functions of GhAINVs under abiotic stress. PHYSIOLOGIA PLANTARUM 2021; 173:2091-2102. [PMID: 34537974 DOI: 10.1111/ppl.13559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/26/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
Acid invertase (AINV) is a kind of sucrose hydrolase with an important role in plants. Currently, the AINV genes have not been systematically studied in cotton. In this study, a total of 92 AINV genes were identified in five cotton species. The phylogenetic analysis revealed that the AINV proteins were divided into two subgroups in cotton: vacuolar invertase (VINV) and cell wall invertase (CWINV). The analysis of gene structures, conserved motifs, and three-dimensional protein structures suggested that GhAINVs were significantly conserved. The synteny analysis showed that whole-genome duplication was the main force promoting the expansion of the AINV gene family. The cis-element, transcriptome, and quantitative real time-polymerase chain reaction (qRT-PCR) showed that some GhAINVs were possibly associated with stress response. GhCWINV4, highly expressed in PEG treatment, was cloned, and subsequent virus-induced gene silencing assay confirmed that this gene was involved in the drought stress response. Overall, this study might be helpful for further analyzing the biological function of AINVs and provide clues for improving the resistance of cotton to stress.
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Affiliation(s)
- Jiaoyan Lv
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, Henan, China
| | - Baizhi Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, Henan, China
| | - Changkai Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, Henan, China
| | - Kaikai Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, Henan, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, Henan, China
| | - Qifeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, Henan, China
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22
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Clo J, Kolář F. Short- and long-term consequences of genome doubling: a meta-analysis. AMERICAN JOURNAL OF BOTANY 2021; 108:2315-2322. [PMID: 34618350 DOI: 10.1002/ajb2.1759] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Whole-genome duplication (WGD) is ubiquitous in plants. Recent reviews and meta-analyses, aiming to understand how such phenotypic transition could facilitate neopolyploid establishment, demonstrated multifarious immediate effects of WGD on fitness and reproductive traits. Yet, little is known about how short-term modifications evolve through time. Such a comparison among new and established polyploid lineages is crucial to understand which effects of WGD promote or impede polyploid survival. METHODS We performed a meta-analysis to determine how WGD affects morphological, cellular, and fitness traits in autotetraploid individuals compared to their diploid progenitors. We studied how established tetraploids differed from diploids compared to neotetraploids, to further learn about the fate of WGD-associated phenotypic effects during polyploid establishment. RESULTS The short-term effects of WGD were an increase in size of morphological traits and cells, accompanied by a decrease in fitness and the number of cells. After establishment, the morphological effect persisted, but cellular and fitness components reverted back to the values observed in the diploid ancestors. CONCLUSIONS Our results suggest that the larger morphology of autotetraploids is not a constraint to establishment. However, other observable effects of genome doubling disappeared with time, suggesting that solving cellular and fitness constraints are critical aspects for polyploid establishment.
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Affiliation(s)
- Josselin Clo
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01, Prague, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01, Prague, Czech Republic
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ, 252 43, Czech Republic
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23
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Palmqvist B, Brazeau HA, Parachnowitsch AL. Differences in Floral Scent and Petal Reflectance Between Diploid and Tetraploid Chamerion angustifolium. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.734128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genome duplication in plants is thought to be a route to speciation due to cytotype incompatibility. However, to reduce cross-pollination between cytotypes in animal-pollinated species, distinctive floral phenotypes, which would allow pollinator-mediated assortative mating between flowers, are also expected. Chamerion angustifolium is a Holarctic species that forms a hybrid zone between diploid and tetraploid populations in the North American Rocky Mountains. Extensive research has shown that these cytotypes differ in many ways, including some floral traits, and that pollinators can discriminate between cytotypes, leading to assortative mating. However, two signals commonly used by insect pollinators have not been measured for this species, namely petal colour and floral scent. Using greenhouse-grown diploids and tetraploids of C. angustifolium from the ploidy hybrid-zone in the North American Rocky Mountains, we show that both floral scent signals and petal reflectance differ between cytotypes. These differences, along with differences in flower size shown previously, could help explain pollinator-mediated assortative mating observed in previous studies. However, these differences in floral phenotypes may vary in importance to pollinators. While the differences in scent included common floral volatiles readily detected by bumblebees, the differences in petal reflectance may not be perceived by bees based on their visual sensitivity across the spectra. Thus, our results suggest that differences in floral volatile emissions are more likely to contribute to pollinator discrimination between cytotypes and highlight the importance of understanding the sensory systems of pollinators when examining floral signals.
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Li M, Sun W, Wang F, Wu X, Wang J. Asymmetric epigenetic modification and homoeolog expression bias in the establishment and evolution of allopolyploid Brassica napus. THE NEW PHYTOLOGIST 2021; 232:898-913. [PMID: 34265096 DOI: 10.1111/nph.17621] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/09/2021] [Indexed: 05/26/2023]
Abstract
This study explores how allopolyploidization reshapes the biased expression and asymmetric epigenetic modification of homoeologous gene pairs, and examines the regulation types and epigenetic basis of expression bias. We analyzed the gene expression and four epigenetic modifications (DNA methylation, H3K4me3, H3K27me3 and H3K27ac) of 29 976 homoeologous gene pairs in resynthesized, natural allopolyploid Brassica napus and an in silico 'hybrid'. We comprehensively elucidated the biased gene expression, asymmetric epigenetic modifications and the generational transmission characteristics of these homoeologous gene pairs in B. napus. We analyzed cis/trans effects and the epigenetic basis of homoeolog expression bias. There was a significant positive correlation between two active histone modifications and biased gene expression. We revealed that parental legacy was the dominant principle in the remodeling of homoeolog expression bias and asymmetric epigenetic modifications in B. napus, and further clarified that this depends on whether there were differences in the expression/epigenetic modifications of gene pairs in parents/progenitors. The maternal genome was dominant in the homoeolog expression bias of resynthesized B. napus, and this phenomenon was attenuated in natural B. napus. Furthermore, cis rather than trans effects were dominant when epigenetic modifications potentially affected biased expression of gene pairs in B. napus.
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Affiliation(s)
- Mengdi Li
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weiqi Sun
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fan Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan, 430062, China
| | - Jianbo Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
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Huang J, Li X, Chen X, Guo Y, Liang W, Wang H. Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity. Int J Mol Sci 2021; 22:6556. [PMID: 34207256 PMCID: PMC8234336 DOI: 10.3390/ijms22126556] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.
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Affiliation(s)
| | | | | | | | | | - Huahua Wang
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.H.); (X.L.); (X.C.); (Y.G.); (W.L.)
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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: 252] [Impact Index Per Article: 84.0] [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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Laport RG, Minckley RL, Pilson D. Pollinator assemblage and pollen load differences on sympatric diploid and tetraploid cytotypes of the desert-dominant Larrea tridentata. AMERICAN JOURNAL OF BOTANY 2021; 108:297-308. [PMID: 33580499 PMCID: PMC7986067 DOI: 10.1002/ajb2.1605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 09/21/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Whole-genome duplication (polyploidy) is an important force shaping flowering-plant evolution. Ploidy-specific plant-pollinator interactions represent important community-level biotic interactions that can lead to nonrandom mating and the persistence of mixed-ploidy populations. METHODS At a naturally occurring diploid-tetraploid contact zone of the autopolyploid desert shrub Larrea tridentata, we combined flower phenology analyses, collections of bees on plants of known cytotype, and flow cytometry analyses of bee-collected pollen loads to investigate whether (1) diploid and tetraploid plants have unique bee pollinator assemblages, (2) bee taxa exhibit ploidy-specific visitation and pollen collection biases, and (3) specialist and generalist bee taxa have ploidy-specific visitation and pollen collection biases. RESULTS Although bee assemblages overlapped, we found significant differences in bee visitation to co-occurring diploids and tetraploids, with the introduced honeybee (Apis mellifera) and one native species (Andrena species 12) more frequently visiting tetraploids. Consistent with bee assemblage differences, we found that diploid pollen was overrepresented among pollen loads on native bees, while pollen loads on A. mellifera did not deviate from the random expectation. However, mismatches between the ploidy of pollen loads and plants were common, consistent with ongoing intercytotype gene flow. CONCLUSIONS Our data are consistent with cytotype-specific bee visitation and suggest that pollinator behavior contributes to reduced diploid-tetraploid mating. Differences in bee visitation and pollen movement potentially contribute to an easing of minority cytotype exclusion and the facilitation of cytotype co-occurrence.
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Affiliation(s)
| | | | - Diana Pilson
- School of Biological SciencesUniversity of Nebraska‐LincolnLincolnNE68588USA
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GhN/AINV13 positively regulates cotton stress tolerance by interacting with the 14-3-3 protein. Genomics 2020; 113:44-56. [PMID: 33276005 DOI: 10.1016/j.ygeno.2020.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 02/06/2023]
Abstract
Neutral/alkaline invertases (N/AINVs) are sucrose hydrolases with important roles in plants. In this study, 15, 15, 15, 29, and 30 N/AINVs were identified in the Gossypium species, G. raimondii, G. herbaceum, G. arboreum, G. hirsutum, and G. barbadense, respectively. Along with two previously discovered branches, α and β, a new clade γ was first discovered in our study. Investigation of gene collinearity showed that whole-genome duplication (WGD) and polyploidization were responsible for the expansion of the N/AINV gene family in allopolyploid Gossypium. Moreover, expression patterns revealed that GhN/AINV3/13/17/23/24/28 from the β clade is highly expressed during the period of fiber initiation. The invertase activity of GhN/AINV13 and GhN/AINV23 were confirmed by restoring defects of invertase-deficient yeast mutant SEY2102. Treatments of abiotic stress showed that most GhN/AINVs were induced in response to polyethylene glycol (PEG) or salt stress. A virus-induced gene-silencing (VIGS) experiment and yeast two-hybrid assay demonstrated that GhN/AINV13 may interact with their positive regulators Gh14-3-3 proteins and participate in the fiber initiation or stress tolerance of cotton. Our results provided fundamental information regarding N/AINVs and highlight their potential functions in cotton stress tolerance.
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Scarrow M, Wang Y, Sun G. Molecular regulatory mechanisms underlying the adaptability of polyploid plants. Biol Rev Camb Philos Soc 2020; 96:394-407. [PMID: 33098261 DOI: 10.1111/brv.12661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
Polyploidization influences the genetic composition and gene expression of an organism. This multi-level genetic change allows the formation of new regulatory pathways leading to increased adaptability. Although both forms of polyploidization provide advantages, autopolyploids were long thought to have little impact on plant divergence compared to allopolyploids due to their formation through genome duplication only, rather than in combination with hybridization. Recent advances have begun to clarify the molecular regulatory mechanisms such as microRNAs, alternative splicing, RNA-binding proteins, histone modifications, chromatin remodelling, DNA methylation, and N6 -methyladenosine (m6A) RNA methylation underlying the evolutionary success of polyploids. Such research is expanding our understanding of the evolutionary adaptability of polyploids and the regulatory pathways that allow adaptive plasticity in a variety of plant species. Herein we review the roles of individual molecular regulatory mechanisms and their potential synergistic pathways underlying plant evolution and adaptation. Notably, increasing interest in m6A methylation has provided a new component in potential mechanistic coordination that is still predominantly unexplored. Future research should attempt to identify and functionally characterize the evolutionary impact of both individual and synergistic pathways in polyploid plant species.
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Affiliation(s)
- Margaret Scarrow
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, 041000, China
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
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Khan N, You FM, Datla R, Ravichandran S, Jia B, Cloutier S. Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.). BMC Genomics 2020; 21:722. [PMID: 33076828 PMCID: PMC7574471 DOI: 10.1186/s12864-020-07121-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
Background The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The ABC transporter and HMA gene families are important in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide analysis of these two gene families has been successfully conducted in some plant species, but no systematic evolutionary analysis is available for the flax genome. Results Here we describe the ABC transporter and HMA gene families in flax to provide a comprehensive overview of its evolution and some support towards the functional annotation of its members. The 198 ABC transporter and 12 HMA genes identified in the flax genome were classified into eight ABC transporter and four HMA subfamilies based on their phylogenetic analysis and domains’ composition. Nine of these genes, i.e., LuABCC9, LuABCC10, LuABCG58, LuABCG59, LuABCG71, LuABCG72, LuABCG73, LuHMA3, and LuHMA4, were orthologous with the Cd associated genes in Arabidopsis, rice and maize. Ten motifs were identified from all ABC transporter and HMA genes. Also, several motifs were conserved among genes of similar length, but each subfamily each had their own motif structures. Both the ABC transporter and HMA gene families were highly conserved among subfamilies of flax and with those of Arabidopsis. While four types of gene duplication were observed at different frequencies, whole-genome or segmental duplications were the most frequent with 162 genes, followed by 29 dispersed, 14 tandem and 4 proximal duplications, suggesting that segmental duplications contributed the most to the expansion of both gene families in flax. The rates of non-synonymous to synonymous (Ka/Ks) mutations of paired duplicated genes were for the most part lower than one, indicative of a predominant purifying selection. Only five pairs of genes clearly exhibited positive selection with a Ka/Ks ratio greater than one. Gene ontology analyses suggested that most flax ABC transporter and HMA genes had a role in ATP binding, transport, catalytic activity, ATPase activity, and metal ion binding. The RNA-Seq analysis of eight different organs demonstrated diversified expression profiling patterns of the genes and revealed their functional or sub-functional conservation and neo-functionalization. Conclusion Characterization of the ABC transporter and HMA gene families will help in the functional analysis of candidate genes in flax and other crop species.
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Affiliation(s)
- Nadeem Khan
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.,Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada
| | - Frank M You
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Bosen Jia
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.,Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada. .,Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada.
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31
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Inoue K, Takahagi K, Kouzai Y, Koda S, Shimizu M, Uehara-Yamaguchi Y, Nakayama R, Kita T, Onda Y, Nomura T, Matsui H, Nagaki K, Nishii R, Mochida K. Parental legacy and regulatory novelty in Brachypodium diurnal transcriptomes accompanying their polyploidy. NAR Genom Bioinform 2020; 2:lqaa067. [PMID: 33575616 PMCID: PMC7671347 DOI: 10.1093/nargab/lqaa067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/15/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022] Open
Abstract
Polyploidy is a widespread phenomenon in eukaryotes that can lead to phenotypic novelty and has important implications for evolution and diversification. The modification of phenotypes in polyploids relative to their diploid progenitors may be associated with altered gene expression. However, it is largely unknown how interactions between duplicated genes affect their diurnal expression in allopolyploid species. In this study, we explored parental legacy and hybrid novelty in the transcriptomes of an allopolyploid species and its diploid progenitors. We compared the diurnal transcriptomes of representative Brachypodium cytotypes, including the allotetraploid Brachypodium hybridum and its diploid progenitors Brachypodium distachyon and Brachypodium stacei. We also artificially induced an autotetraploid B. distachyon. We identified patterns of homoeolog expression bias (HEB) across Brachypodium cytotypes and time-dependent gain and loss of HEB in B. hybridum. Furthermore, we established that many genes with diurnal expression experienced HEB, while their expression patterns and peak times were correlated between homoeologs in B. hybridum relative to B. distachyon and B. stacei, suggesting diurnal synchronization of homoeolog expression in B. hybridum. Our findings provide insight into the parental legacy and hybrid novelty associated with polyploidy in Brachypodium, and highlight the evolutionary consequences of diurnal transcriptional regulation that accompanied allopolyploidy.
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Affiliation(s)
- Komaki Inoue
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kotaro Takahagi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, 236-0027, Japan
| | - Yusuke Kouzai
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoru Koda
- Graduate School of Mathematics, Kyushu University, Fukuoka, 819-0395, Japan
| | - Minami Shimizu
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | | | - Risa Nakayama
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshie Kita
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yoshihiko Onda
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshihisa Nomura
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hidetoshi Matsui
- Faculty of Data Science, Shiga University, Hikone, 522-8522, Japan
| | - Kiyotaka Nagaki
- Institute of Plant Science and Resources, Okayama University,710-0046, Kurashiki, Japan
| | - Ryuei Nishii
- School of Information and Data Science, Nagasaki University, Nagasaki, 852-8131, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, 236-0027, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University,710-0046, Kurashiki, Japan
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Gaynor ML, Lim-Hing S, Mason CM. Impact of genome duplication on secondary metabolite composition in non-cultivated species: a systematic meta-analysis. ANNALS OF BOTANY 2020; 126:363-376. [PMID: 32504537 PMCID: PMC7424755 DOI: 10.1093/aob/mcaa107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Whole-genome duplication is known to influence ecological interactions and plant physiology; however, despite abundant case studies, much is still unknown about the typical impact of genome duplication on plant secondary metabolites (PSMs). In this study, we assessed the impact of polyploidy events on PSM characteristics in non-cultivated plants. METHODS We conducted a systematic review and meta-analysis to compare composition and concentration of PSMs among closely related plant species or species complexes differing in ploidy level. KEY RESULTS We assessed 53 studies that focus on PSMs among multiple cytotypes, of which only 14 studies compared concentration quantitatively among cytotypes. We found that whole-genome duplication can have a significant effect on PSM concentration; however, these effects are highly inconsistent. CONCLUSION Overall, there was no consistent effect of whole-genome duplication on PSM concentrations or profiles.
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Affiliation(s)
- Michelle L Gaynor
- Department of Biology, University of Central Florida, Orlando, FL, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Simone Lim-Hing
- Department of Biology, University of Central Florida, Orlando, FL, USA
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Chase M Mason
- Department of Biology, University of Central Florida, Orlando, FL, USA
- For correspondence. E-mail
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Cheng J, Yang X, Xue L, Yao B, Lu H, Tian Z, Li J, Zhou X, Zhang Y, Zia Ul Haq M, Wu S, Song X, Hu S, Qiang S. Polyploidization contributes to evolution of competitive ability: a long term common garden study on the invasive
Solidago canadensis
in China. OIKOS 2020. [DOI: 10.1111/oik.07095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jiliang Cheng
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Xianghong Yang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Lifang Xue
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Beibei Yao
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Huan Lu
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Zhongsai Tian
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Jun Li
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Xin Zhou
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Yu Zhang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Muhammad Zia Ul Haq
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Shuqi Wu
- College of Resources and Environmental Sciences, Nanjing Agricultural Univ. Nanjing PR China
| | - Xiaoling Song
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Shuijin Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural Univ. Nanjing PR China
| | - Sheng Qiang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
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Wang W, Chen D, Liu D, Cheng Y, Zhang X, Song L, Hu M, Dong J, Shen F. Comprehensive analysis of the Gossypium hirsutum L. respiratory burst oxidase homolog (Ghrboh) gene family. BMC Genomics 2020; 21:91. [PMID: 31996127 PMCID: PMC6988335 DOI: 10.1186/s12864-020-6503-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/16/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Plant NADPH oxidase (NOX), also known as respiratory burst oxidase homolog (rboh), encoded by the rboh gene, is a key enzyme in the reactive oxygen species (ROS) metabolic network. It catalyzes the formation of the superoxide anion (O2•-), a type of ROS. In recent years, various studies had shown that members of the plant rboh gene family were involved in plant growth and developmental processes as well as in biotic and abiotic stress responses, but little is known about its functional role in upland cotton. RESULTS In the present study, 26 putative Ghrboh genes were identified and characterized. They were phylogenetically classified into six subfamilies and distributed at different densities across 18 of the 26 chromosomes or scaffolds. Their exon-intron structures, conserved domains, synteny and collinearity, gene family evolution, regulation mediated by cis-acting elements and microRNAs (miRNAs) were predicted and analyzed. Additionally, expression profiles of Ghrboh gene family were analyzed in different tissues/organs and at different developmental stages and under different abiotic stresses, using RNA-Seq data and real-time PCR. These profiling studies indicated that the Ghrboh genes exhibited temporal and spatial specificity with respect to expression, and might play important roles in cotton development and in stress tolerance through modulating NOX-dependent ROS induction and other signaling pathways. CONCLUSIONS This comprehensive analysis of the characteristics of the Ghrboh gene family determined features such as sequence, synteny and collinearity, phylogenetic and evolutionary relationship, expression patterns, and cis-element- and miRNA-mediated regulation of gene expression. Our results will provide valuable information to help with further gene cloning, evolutionary analysis, and biological function analysis of cotton rbohs.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai’an, Shandong 271018 People’s Republic of China
| | - Dongdong Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai’an, Shandong 271018 People’s Republic of China
| | - Dan Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai’an, Shandong 271018 People’s Republic of China
| | - Yingying Cheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai’an, Shandong 271018 People’s Republic of China
| | - Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai’an, Shandong 271018 People’s Republic of China
| | - Lirong Song
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai’an, Shandong 271018 People’s Republic of China
| | - Mengjiao Hu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai’an, Shandong 271018 People’s Republic of China
| | - Jie Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai’an, Shandong 271018 People’s Republic of China
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai’an, Shandong 271018 People’s Republic of China
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Han TS, Zheng QJ, Onstein RE, Rojas-Andrés BM, Hauenschild F, Muellner-Riehl AN, Xing YW. Polyploidy promotes species diversification of Allium through ecological shifts. THE NEW PHYTOLOGIST 2020; 225:571-583. [PMID: 31394010 DOI: 10.1111/nph.16098] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/01/2019] [Indexed: 05/14/2023]
Abstract
Despite the role of polyploidy in multiple evolutionary processes, its impact on plant diversification remains controversial. An increased polyploid frequency may facilitate speciation through shifts in ecology, morphology or both. Here we used Allium to evaluate: (1) the relationship between intraspecific polyploid frequency and species diversification rate; and (2) whether this process is associated with habitat and/or trait shifts. Using eight plastid and nuclear ribosomal markers, we built a phylogeny of 448 Allium species, representing 46% of the total. We quantified intraspecific ploidy diversity, heterogeneity in diversification rates and their relationship along the phylogeny using trait-dependent diversification models. Finally, we evaluated the association between polyploidisation and habitat or trait shifts. We detected high ploidy diversity in Allium and a polyploidy-related diversification rate shift with a probability of 95% in East Asia. Allium lineages with high polyploid frequencies had higher species diversification rates than those of diploids or lineages with lower polyploid frequencies. Shifts in speciation rates were strongly correlated with habitat shifts linked to particular soil conditions; 81.7% of edaphic variation could be explained by polyploidisation. Our study emphasises the role of intraspecific polyploid frequency combined with ecological drivers on Allium diversification, which may explain plant radiations more generally.
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Affiliation(s)
- Ting-Shen Han
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Quan-Jing Zheng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
| | - Blanca M Rojas-Andrés
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Frank Hauenschild
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Alexandra N Muellner-Riehl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Yao-Wu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
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Levin DA. Plant speciation in the age of climate change. ANNALS OF BOTANY 2019; 124:769-775. [PMID: 31250895 PMCID: PMC6868396 DOI: 10.1093/aob/mcz108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/25/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Species diversity is likely to undergo a sharp decline in the next century. Perhaps as many as 33 % of all plant species may expire as a result of climate change. All parts of the globe will be impacted, and all groups of organisms will be affected. Hundreds of species throughout the world have already experienced local extinction. PERSPECTIVES While thousands of species may become extinct in the next century and beyond, species formation will still occur. I consider which modes of plant species formation are likely to prevail in the next 500 years. I argue that speciation primarily will involve mechanisms that produce reproductively isolated lineages within less (often much less) than 100 generations. I will not especially consider the human element in promoting species formation, because it will continue and because the conclusions presented here are unaffected by it. The impact of climate change may be much more severe and widespread. CONCLUSIONS The most common modes of speciation likely to be operative in the next 500 years ostensibly will be auto- and allopolyploidy. Polyploid species or the antecedents thereof can arise within two generations. Moreover, polyploids often have broader ecological tolerances, and are likely to be more invasive than are their diploid relatives. Polyploid species may themselves spawn additional higher level polyploids either through crosses with diploid species or between pre-existing polyploids. The percentage of polyploid species is likely to exceed 50 % within the next 500 years vs. 35 % today. The stabilized hybrid derivatives (homoploid hybrid speciation) could emerge within a hundred generations after species contact, as could speciation involving chromosomal rearrangements (and perhaps number), but the number of such events is likely to be low. Speciation involving lineage splitting will be infrequent because the formation of substantive pre- and post-zygotic barriers typically takes many thousands of years.
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Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas, Austin, USA
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Porturas LD, Anneberg TJ, Curé AE, Wang S, Althoff DM, Segraves KA. A meta-analysis of whole genome duplication and the effects on flowering traits in plants. AMERICAN JOURNAL OF BOTANY 2019; 106:469-476. [PMID: 30901499 DOI: 10.1002/ajb2.1258] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Polyploidy, or whole genome duplication (WGD), is common in plants despite theory suggesting that polyploid establishment is challenging and polyploids should be evolutionarily transitory. There is renewed interest in understanding the mechanisms that could facilitate polyploid establishment and explain their pervasiveness in nature. In particular, premating isolation from their diploid progenitors is suggested to be a crucial factor. To evaluate how changes in assortative mating occur, we need to understand the phenotypic effects of WGD on reproductive traits. METHODS We used literature surveys and a meta-analysis to assess how WGD affects floral morphology, flowering phenology, and reproductive output in plants. We focused specifically on comparisons of newly generated polyploids (neopolyploids) and their parents to mitigate potential confounding effects of adaptation and drift that may be present in ancient polyploids. KEY RESULTS The results indicated that across a broad representation of angiosperms, floral morphology traits increased in size, reproductive output decreased, and flowering phenology was unaffected by WGD. Additionally, we found that increased trait variation after WGD was uncommon for the phenotypic traits examined. CONCLUSIONS Our results suggest that the phenotypic effects on traits important to premating isolation of neopolyploids are small, in general. Changes in flowering phenology, reproductive output, and phenotypic variation resulting from WGD may be less critical in facilitating premating isolation and neopolyploid establishment. However, floral traits for which size is an important component of function (e.g., pollen transfer) could be strongly influenced by WGD.
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Affiliation(s)
- Laura D Porturas
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Thomas J Anneberg
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Anne E Curé
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Shengpei Wang
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - David M Althoff
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Kari A Segraves
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
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O’Connor TK, Laport RG, Whiteman NK. Polyploidy in creosote bush ( Larrea tridentata) shapes the biogeography of specialist herbivores. JOURNAL OF BIOGEOGRAPHY 2019; 46:597-610. [PMID: 31534296 PMCID: PMC6749999 DOI: 10.1111/jbi.13490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/05/2018] [Indexed: 06/10/2023]
Abstract
AIM Whole-genome duplication (polyploidy) can influence the biogeography and ecology of plants that differ in ploidy level (cytotype). Here, we address how two consequences of plant polyploidy (parapatry of cytotypes and altered species interactions) shape the biogeography of herbivorous insects. LOCATION Warm deserts of North America. TAXA Gall midges (Asphondylia auripila group, Diptera: Cecidomyiidae) that attack three parapatric cytotypes of creosote bush (Larrea tridentata, Zygophyllaceae). METHODS We surveyed Asphondylia species diversity at 177 sites across a 2300-km extent. After noting a correspondence between the distributions of eight Asphondylia species and L. tridentata cytotypes, we fine-mapped Asphondylia species range limits with transects spanning cytotype contact zones. We then tested whether plant-insect interactions and/or abiotic factors explain this coincidence by (1) comparing attack rates and gall midge communities on alternative cytotypes in a narrow zone of sympatry and (2) using species distribution models (SDMs) to determine if climatically suitable habitat for each midge species extended beyond cytotype contact zones. RESULTS The range limits of 6/17 Asphondylia species (including two novel putative species confirmed with COI sequencing) perfectly coincided with the contact zone of diploid and tetraploid L. tridentata. One midge species was restricted to diploid host plants while five were restricted to tetraploid and hexaploid host plants. Where diploid and tetraploid L. tridentata are sympatric, cytotype-restricted midge species more frequently attacked their typical host and Asphondylia community structure differed markedly between cytotypes. SDMs predicted that distributions of cytotype-restricted midge species were not constrained by climatic conditions near cytotype contact zones. MAIN CONCLUSIONS Contact zones between plant cytotypes are dispersal barriers for many Asphondylia species due to plant-insect interactions. The distribution of L. tridentata cytotypes therefore shapes herbivore species ranges and herbivore community structure across North American deserts. Our results demonstrate that polyploidy in plants can affect the biogeography of ecological communities.
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Affiliation(s)
- Timothy K. O’Connor
- Department of Integrative Biology, University of California, Berkeley CA 94720
| | | | - Noah K. Whiteman
- Department of Integrative Biology, University of California, Berkeley CA 94720
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Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nat Ecol Evol 2019; 3:457-468. [DOI: 10.1038/s41559-019-0807-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/10/2019] [Indexed: 12/30/2022]
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Takahagi K, Inoue K, Shimizu M, Uehara-Yamaguchi Y, Onda Y, Mochida K. Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass Brachypodium hybridum. Gigascience 2018; 7:4924998. [PMID: 29697823 PMCID: PMC5915950 DOI: 10.1093/gigascience/giy020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 03/01/2018] [Indexed: 11/21/2022] Open
Abstract
Background Allopolyploid plants often show wider environmental tolerances than their ancestors; this is expected to be due to the merger of multiple distinct genomes with a fixed heterozygosity. The complex homoeologous gene expression could have been evolutionarily advantageous for the adaptation of allopolyploid plants. Despite multiple previous studies reporting homoeolog-specific gene expression in allopolyploid species, there are no clear examples of homoeolog-specific function in acclimation to a long-term stress condition. Results We found that the allopolyploid grass Brachypodium hybridum and its ancestor Brachypodium stacei show long-term heat stress tolerance, unlike its other ancestor, Brachypodium distachyon. To understand the physiological traits of B. hybridum, we compared the transcriptome of the 3 Brachypodium species grown under normal and heat stress conditions. We found that the expression patterns of approximately 26% and approximately 38% of the homoeolog groups in B. hybridum changed toward nonadditive expression and nonancestral expression, respectively, under normal condition. Moreover, we found that B. distachyon showed similar expression patterns between normal and heat stress conditions, whereas B. hybridum and B. stacei significantly altered their transcriptome in response to heat after 3 days of stress exposure, and homoeologs that were inherited from B. stacei may have contributed to the transcriptional stress response to heat in B. hybridum. After 15 days of heat exposure, B. hybridum and B. stacei maintained transcriptional states similar to those under normal conditions. These results suggest that an earlier response to heat that was specific to homoeologs originating from B. stacei contributed to cellular homeostasis under long-term heat stress in B. hybridum. Conclusions Our results provide insights into different regulatory events of the homoeo-transcriptome that are associated with stress acclimation in allopolyploid plants.
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Affiliation(s)
- Kotaro Takahagi
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan.,Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Minami Shimizu
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yukiko Uehara-Yamaguchi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihiko Onda
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiichi Mochida
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan.,Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
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Sudová R, Kohout P, Kolaříková Z, Rydlová J, Voříšková J, Suda J, Španiel S, Müller-Schärer H, Mráz P. Sympatric diploid and tetraploid cytotypes of Centaurea stoebe s.l. do not differ in arbuscular mycorrhizal communities and mycorrhizal growth response. AMERICAN JOURNAL OF BOTANY 2018; 105:1995-2007. [PMID: 30552673 DOI: 10.1002/ajb2.1206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/28/2018] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Genome duplication is associated with multiple changes at different levels, including interactions with pollinators and herbivores. Yet little is known whether polyploidy may also shape belowground interactions. METHODS To elucidate potential ploidy-specific interactions with arbuscular mycorrhizal fungi (AMF), we compared mycorrhizal colonization and assembly of AMF communities in roots of diploid and tetraploid Centaurea stoebe s.l. (Asteraceae) co-occurring in a Central European population. In a follow-up greenhouse experiment, we tested inter-cytotype differences in mycorrhizal growth response by combining ploidy, substrate, and inoculation with native AMF in a full-factorial design. KEY RESULTS All sampled plants were highly colonized by AMF, with the Glomeraceae predominating. AMF-community composition revealed by 454-pyrosequencing reflected the spatial distribution of the hosts, but not their ploidy level or soil characteristics. In the greenhouse experiment, the tetraploids produced more shoot biomass than the diploids did when grown in a more fertile substrate, while no inter-cytotype differences were found in a less fertile substrate. AMF inoculation significantly reduced plant growth and improved P uptake, but its effects did not differ between the cytotypes. CONCLUSIONS The results do not support our hypotheses that the cytotype structure in a mixed-ploidy population of C. stoebe is mirrored in AMF-community composition and that ploidy-specific fungal communities contribute to cytotype co-existence. Causes and implications of the observed negative growth response to AMF are discussed.
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Affiliation(s)
- Radka Sudová
- Institute of Botany, The Czech Academy of Sciences, CZ-252 43, Průhonice, Czech Republic
| | - Petr Kohout
- Institute of Botany, The Czech Academy of Sciences, CZ-252 43, Průhonice, Czech Republic
- Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, CZ-128 44, Prague, Czech Republic
| | - Zuzana Kolaříková
- Institute of Botany, The Czech Academy of Sciences, CZ-252 43, Průhonice, Czech Republic
| | - Jana Rydlová
- Institute of Botany, The Czech Academy of Sciences, CZ-252 43, Průhonice, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic
- Ecology Department, Climate and Ecosystem Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jan Suda
- Institute of Botany, The Czech Academy of Sciences, CZ-252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic
| | - Stanislav Španiel
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23, Bratislava, Slovakia
| | - Heinz Müller-Schärer
- Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Patrik Mráz
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic
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An D, Li C, Zhou Y, Wu Y, Wang W. Genomes and Transcriptomes of Duckweeds. Front Chem 2018; 6:230. [PMID: 29974050 PMCID: PMC6019479 DOI: 10.3389/fchem.2018.00230] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/31/2018] [Indexed: 11/23/2022] Open
Abstract
Duckweeds (Lemnaceae family) are the smallest flowering plants that adapt to the aquatic environment. They are regarded as the promising sustainable feedstock with the characteristics of high starch storage, fast propagation, and global distribution. The duckweed genome size varies 13-fold ranging from 150 Mb in Spirodela polyrhiza to 1,881 Mb in Wolffia arrhiza. With the development of sequencing technology and bioinformatics, five duckweed genomes from Spirodela and Lemna genera are sequenced and assembled. The genome annotations discover that they share similar protein orthologs, whereas the repeat contents could mainly explain the genome size difference. The gene families responsible for cell growth and expansion, lignin biosynthesis, and flowering are greatly contracted. However, the gene family of glutamate synthase has experienced expansion, indicating their significance in ammonia assimilation and nitrogen transport. The transcriptome is comprehensively sequenced for the genera of Spirodela, Landoltia, and Lemna, including various treatments such as abscisic acid, radiation, heavy metal, and starvation. The analysis of the underlying molecular mechanism and the regulatory network would accelerate their applications in the fields of bioenergy and phytoremediation. The comparative genomics has shown that duckweed genomes contain relatively low gene numbers and more contracted gene families, which may be in parallel with their highly reduced morphology with a simple leaf and primary roots. Still, we are waiting for the advancement of the long read sequencing technology to resolve the complex genomes and transcriptomes for unsequenced Wolffiella and Wolffia due to the large genome sizes and the similarity in their polyploidy.
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Affiliation(s)
- Dong An
- Department of Plant Sciences, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Changsheng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yong Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wenqin Wang
- Department of Plant Sciences, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Plue J, Kimberley A, Slotte T. Interspecific variation in ploidy as a key plant trait outlining local extinction risks and community patterns in fragmented landscapes. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13127] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jan Plue
- School of Natural Sciences, Technology and Environmental StudiesSödertörn University Stockholm Sweden
- Biogeography and GeomaticsDepartment of Physical GeographyStockholm University Stockholm Sweden
| | - Adam Kimberley
- Biogeography and GeomaticsDepartment of Physical GeographyStockholm University Stockholm Sweden
| | - Tanja Slotte
- Department of Ecology, Environment and Plant SciencesScience for Life LaboratoryStockholm University Stockholm Sweden
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Gaynor ML, Ng J, Laport RG. Phylogenetic Structure of Plant Communities: Are Polyploids Distantly Related to Co-occurring Diploids? Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Vamosi JC, Magallón S, Mayrose I, Otto SP, Sauquet H. Macroevolutionary Patterns of Flowering Plant Speciation and Extinction. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:685-706. [PMID: 29489399 DOI: 10.1146/annurev-arplant-042817-040348] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Species diversity is remarkably unevenly distributed among flowering plant lineages. Despite a growing toolbox of research methods, the reasons underlying this patchy pattern have continued to perplex plant biologists for the past two decades. In this review, we examine the present understanding of transitions in flowering plant evolution that have been proposed to influence speciation and extinction. In particular, ploidy changes, transitions between tropical and nontropical biomes, and shifts in floral form have received attention and have offered some surprises in terms of which factors influence speciation and extinction rates. Mating systems and dispersal characteristics once predominated as determining factors, yet recent evidence suggests that these changes are not as influential as previously thought or are important only when paired with range shifts. Although range extent is an important correlate of speciation, it also influences extinction and brings an applied focus to diversification research. Recent studies that find that past diversification can predict present-day extinction risk open an exciting avenue for future research to help guide conservation prioritization.
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Affiliation(s)
- Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada;
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sarah P Otto
- Department of Zoology and the Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Hervé Sauquet
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS UMR 8079, 91405 Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia
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Forrester NJ, Ashman TL. The direct effects of plant polyploidy on the legume-rhizobia mutualism. ANNALS OF BOTANY 2018; 121:209-220. [PMID: 29182713 PMCID: PMC5808787 DOI: 10.1093/aob/mcx121] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/08/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Polyploidy is known to significantly alter plant genomes, phenotypes and interactions with the abiotic environment, yet the impacts of polyploidy on plant-biotic interactions are less well known. A particularly important plant-biotic interaction is the legume-rhizobia mutualism, in which rhizobia fix atmospheric nitrogen in exchange for carbon provided by legume hosts. This mutualism regulates nutrient cycles in natural ecosystems and provides nitrogen to agricultural environments. Despite the ecological, evolutionary and agricultural importance of plant polyploidy and the legume-rhizobia mutualism, it is not yet fully understood whether plant polyploidy directly alters mutualism traits or the consequences on plant growth. SCOPE The aim was to propose a conceptual framework to understand how polyploidy might directly enhance the quantity and quality of rhizobial symbionts hosted by legume plants, resulting in increased host access to fixed nitrogen (N). Mechanistic hypotheses have been devised to examine how polyploidy can directly alter traits that impact the quantity (e.g. nodule number, nodule size, terminal bacteroid differentiation) and quality of symbionts (e.g. nodule environment, partner choice, host sanctions). To evaluate these hypotheses, an exhaustive review of studies testing the effects of plant polyploidy on the mutualism was conducted. In doing so, overall trends were synthesized, highlighting the limited understanding of the mechanisms that underlie variation in results achieved thus far, revealing striking gaps in knowledge and uncovering areas ripe for future research. CONCLUSIONS Plant polyploidy can immediately alter nodule size, N fixation rate and the identity of rhizobial symbionts hosted by polyploid legumes, but many of the mechanistic hypotheses proposed here, such as bacteroid number and enhancements of the nodule environment, remain unexplored. Although current evidence supports a role of plant polyploidy in enhancing key aspects of the legume-rhizobia mutualism, the underlying mechanisms and effects on host benefit from the mutualism remain unresolved.
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Affiliation(s)
- Nicole J Forrester
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
- For correspondence. E-mail
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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Powell AF, Doyle JJ. Non-Additive Transcriptomic Responses to Inoculation with Rhizobia in a Young Allopolyploid Compared with Its Diploid Progenitors. Genes (Basel) 2017; 8:E357. [PMID: 29189710 PMCID: PMC5748675 DOI: 10.3390/genes8120357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/29/2022] Open
Abstract
Root nodule symbioses (nodulation) and whole genome duplication (WGD, polyploidy) are both important phenomena in the legume family (Leguminosae). Recently, it has been proposed that polyploidy may have played a critical role in the origin or refinement of nodulation. However, while nodulation and polyploidy have been studied independently, there have been no direct studies of mechanisms affecting the interactions between these phenomena in symbiotic, nodule-forming species. Here, we examined the transcriptome-level responses to inoculation in the young allopolyploid Glycine dolichocarpa (T2) and its diploid progenitor species to identify underlying processes leading to the enhanced nodulation responses previously identified in T2. We assessed the differential expression of genes and, using weighted gene co-expression network analysis (WGCNA), identified modules associated with nodulation and compared their expression between species. These transcriptomic analyses revealed patterns of non-additive expression in T2, with evidence of transcriptional responses to inoculation that were distinct from one or both progenitors. These differential responses elucidate mechanisms underlying the nodulation-related differences observed between T2 and the diploid progenitors. Our results indicate that T2 has reduced stress-related transcription, coupled with enhanced transcription of modules and genes implicated in hormonal signaling, both of which are important for nodulation.
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Affiliation(s)
- Adrian F Powell
- Section of Plant Biology, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
- Boyce Thompson Institute, Ithaca, NY 14853, USA.
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
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Guignard MS, Leitch AR, Acquisti C, Eizaguirre C, Elser JJ, Hessen DO, Jeyasingh PD, Neiman M, Richardson AE, Soltis PS, Soltis DE, Stevens CJ, Trimmer M, Weider LJ, Woodward G, Leitch IJ. Impacts of Nitrogen and Phosphorus: From Genomes to Natural Ecosystems and Agriculture. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00070] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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