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Renner SS, Sokoloff DD. The sexual lability hypothesis for the origin of the land plant generation cycle. Curr Biol 2024; 34:R697-R707. [PMID: 39043145 DOI: 10.1016/j.cub.2024.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
The evolution of the land plant alternation of generations has been an open question for the past 150 years. Two hypotheses have dominated the discussion: the antithetic hypothesis, which posits that the diploid sporophyte generation arose de novo and gradually increased in complexity, and the homologous hypothesis, which holds that land plant ancestors had independently living sporophytes and haploid gametophytes of similar complexity. Changes in ploidy levels were unknown to early researchers. The antithetic hypothesis is contradicted by generation cycles in Lower Devonian Rhynie chert plants, whose sporophytes and gametophytes have similar morphologies and by some Silurian sporophytes whose complexity exceeds that of Rhynie chert sporophytes. The oldest unambiguous bryophyte gametophytes (thalli) are from the upper Middle Devonian, with an unconnected sporophyte nearby. Based on the 2024 discovery that conjugate algae are paraphyletic to land plants, we present a new hypothesis for the evolution of the land plant generation cycle, focusing on labile ploidy levels and types of reproduction found in conjugate algae. Our 'sexual lability' hypothesis assumes a period of unstable generation cycles (as regards ploidy), likely with predominant clonal growth, as is common in conjugate algae, resulting in sporophytes and gametophytes of similar morphology. When sexual reproduction became stabilized, the timing of gamete fusion, meiosis, and resistant wall formation, which are heterochronic in some conjugate algae, became standardized, with wall formation permanently delayed. In our scenario, independently living adult sporophytes are the land plant ancestral condition, and life-long sporophyte retention on the gametophyte is a bryophyte apomorphy.
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Affiliation(s)
- Susanne S Renner
- Department of Biology, Washington University in Saint Louis, St. Louis, MO 63130, USA.
| | - Dmitry D Sokoloff
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997820, Israel
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2
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Güngör E, Savary J, Adema K, Dijkhuizen LW, Keilwagen J, Himmelbach A, Mascher M, Koppers N, Bräutigam A, Van Hove C, Riant O, Nierzwicki-Bauer S, Schluepmann H. The crane fly glycosylated triketide δ-lactone cornicinine elicits akinete differentiation of the cyanobiont in aquatic Azolla fern symbioses. PLANT, CELL & ENVIRONMENT 2024; 47:2675-2692. [PMID: 38600764 DOI: 10.1111/pce.14907] [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: 12/14/2023] [Revised: 03/02/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024]
Abstract
The restriction of plant-symbiont dinitrogen fixation by an insect semiochemical had not been previously described. Here we report on a glycosylated triketide δ-lactone from Nephrotoma cornicina crane flies, cornicinine, that causes chlorosis in the floating-fern symbioses from the genus Azolla. Only the glycosylated trans-A form of chemically synthesized cornicinine was active: 500 nM cornicinine in the growth medium turned all cyanobacterial filaments from Nostoc azollae inside the host leaf-cavities into akinetes typically secreting CTB-bacteriocins. Cornicinine further inhibited akinete germination in Azolla sporelings, precluding re-establishment of the symbiosis during sexual reproduction. It did not impact development of the plant Arabidopsis thaliana or several free-living cyanobacteria from the genera Anabaena or Nostoc but affected the fern host without cyanobiont. Fern-host mRNA sequencing from isolated leaf cavities confirmed high NH4-assimilation and proanthocyanidin biosynthesis in this trichome-rich tissue. After cornicinine treatment, it revealed activation of Cullin-RING ubiquitin-ligase-pathways, known to mediate metabolite signaling and plant elicitation consistent with the chlorosis phenotype, and increased JA-oxidase, sulfate transport and exosome formation. The work begins to uncover molecular mechanisms of cyanobiont differentiation in a seed-free plant symbiosis important for wetland ecology or circular crop-production today, that once caused massive CO2 draw-down during the Eocene geological past.
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Affiliation(s)
- Erbil Güngör
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Jérôme Savary
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Kelvin Adema
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | | | | | - Axel Himmelbach
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Nils Koppers
- Computational Biology, Center for Biotechnology and Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Andrea Bräutigam
- Computational Biology, Center for Biotechnology and Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Charles Van Hove
- Emeritus Professor from the Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Olivier Riant
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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3
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Güngör E, Bartels B, Bolchi G, Heeren RMA, Ellis SR, Schluepmann H. Biosynthesis and differential spatial distribution of the 3-deoxyanthocyanidins apigenidin and luteolinidin at the interface of a plant-cyanobacteria symbiosis exposed to cold. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38932650 DOI: 10.1111/pce.15010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Aquatic ferns of the genus Azolla (Azolla) form highly productive symbioses with filamentous cyanobacteria fixing N2 in their leaf cavities, Nostoc azollae. Stressed symbioses characteristically turn red due to 3-deoxyanthocyanidin (DA) accumulation, rare in angiosperms and of unknown function. To understand DA accumulation upon cold acclimation and recovery, we integrated laser-desorption-ionization mass-spectrometry-imaging (LDI-MSI), a new Azolla filiculoides genome-assembly and annotation, and dual RNA-sequencing into phenotypic analyses of the symbioses. Azolla sp. Anzali recovered even when cold-induced DA-accumulation was inhibited by abscisic acid. Cyanobacterial filaments generally disappeared upon cold acclimation and Nostoc azollae transcript profiles were unlike those of resting stages formed in cold-resistant sporocarps, yet filaments re-appeared in leaf cavities of newly formed green fronds upon cold-recovery. The high transcript accumulation upon cold acclimation of AfDFR1 encoding a flavanone 4-reductase active in vitro suggested that the enzyme of the first step in the DA-pathway may regulate accumulation of DAs in different tissues. However, LDI-MSI highlighted the necessity to describe metabolite accumulation beyond class assignments as individual DA and caffeoylquinic acid metabolites accumulated differentially. For example, luteolinidin accumulated in epithelial cells, including those lining the leaf cavity, supporting a role for the former in the symbiotic interaction during cold acclimation.
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Affiliation(s)
- Erbil Güngör
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Benjamin Bartels
- Division of Imaging Mass Spectrometry, Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, The Netherlands
| | - Giorgio Bolchi
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Ron M A Heeren
- Division of Imaging Mass Spectrometry, Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, The Netherlands
| | - Shane R Ellis
- Division of Imaging Mass Spectrometry, Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, The Netherlands
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
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4
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Hörandl E. Apomixis and the paradox of sex in plants. ANNALS OF BOTANY 2024; 134:1-18. [PMID: 38497809 PMCID: PMC11161571 DOI: 10.1093/aob/mcae044] [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: 12/11/2023] [Accepted: 03/15/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, remains an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are, in part, not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species. SCOPE This review compares the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity in comparison to asexuality are discussed in the light of developmental, evolutionary, genetic and phylogenetic studies. CONCLUSIONS Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms for oxidative damage in reproductive tissues. The ploidy alternations of meiosis-syngamy cycles and prolonged multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy and can purge the mutational load via facultative sexuality. The role of organelle-nuclear genome compatibility for maintenance of genome integrity is not well understood. In plants in general, the costs of mating are low because of predominant hermaphroditism. Phylogenetic patterns in the archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long-term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), University of Göttingen, Göttingen, Germany
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5
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Gajski D, Wolff JO, Melcher A, Weber S, Prost S, Krehenwinkel H, Kennedy SR. Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing. Mol Phylogenet Evol 2024; 192:107988. [PMID: 38072140 DOI: 10.1016/j.ympev.2023.107988] [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: 08/03/2023] [Revised: 10/22/2023] [Accepted: 12/07/2023] [Indexed: 12/31/2023]
Abstract
Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.
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Affiliation(s)
- Domagoj Gajski
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic
| | - Jonas O Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany; School of Natural Sciences, Macquarie University, NSW 2109, Sydney, Australia
| | - Anja Melcher
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Sven Weber
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, Linnanmaa, Finland
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Susan R Kennedy
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany.
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6
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Donoghue PCJ, Clark JW. Plant evolution: Streptophyte multicellularity, ecology, and the acclimatisation of plants to life on land. Curr Biol 2024; 34:R86-R89. [PMID: 38320478 DOI: 10.1016/j.cub.2023.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Land plants are celebrated as one of the three great instances of complex multicellularity, but new phylogenomic and phenotypic analyses are revealing deep evolutionary roots of multicellularity among algal relatives, prompting questions about the causal basis of this major evolutionary transition.
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Affiliation(s)
- Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, UK.
| | - James W Clark
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AZ, UK
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Furuta T, Yamamoto T. MCPtaggR: R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison. DNA Res 2024; 31:dsad027. [PMID: 38134958 PMCID: PMC10799318 DOI: 10.1093/dnares/dsad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023] Open
Abstract
Reduced representation sequencing (RRS) offers cost-effective, high-throughput genotyping platforms such as genotyping-by-sequencing (GBS). RRS reads are typically mapped onto a reference genome. However, mapping reads harbouring mismatches against the reference can potentially result in mismapping and biased mapping, leading to the detection of error-prone markers that provide incorrect genotype information. We established a genotype-calling pipeline named mappable collinear polymorphic tag genotyping (MCPtagg) to achieve accurate genotyping by eliminating error-prone markers. MCPtagg was designed for the RRS-based genotyping of a population derived from a biparental cross. The MCPtagg pipeline filters out error-prone markers prior to genotype calling based on marker collinearity information obtained by comparing the genome sequences of the parents of a population to be genotyped. A performance evaluation on real GBS data from a rice F2 population confirmed its effectiveness. Furthermore, our performance test using a genome assembly that was obtained by genome sequence polishing on an available genome assembly suggests that our pipeline performs well with converted genomes, rather than necessitating de novo assembly. This demonstrates its flexibility and scalability. The R package, MCPtaggR, was developed to provide functions for the pipeline and is available at https://github.com/tomoyukif/MCPtaggR.
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Affiliation(s)
- Tomoyuki Furuta
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Toshio Yamamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
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8
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Xiang Y, Zhang T, Zhao Y, Dong H, Chen H, Hu Y, Huang CH, Xiang J, Ma H. Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:228-251. [PMID: 38351714 DOI: 10.1111/jipb.13618] [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: 12/15/2023] [Accepted: 01/11/2024] [Indexed: 02/22/2024]
Abstract
Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types, yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families. Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny, with resolved relationships for orders and families with previously uncertain placements. Using this phylogeny as a framework, molecular dating supports a Triassic origin of the crown angiosperms, followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution. The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types, revealing a trend of parallel carpel fusions during early diversifications in eudicots, monocots, and magnoliids. Moreover, taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits; such associations of ovary, dry and fleshy fruits define several ovary-fruit "modules" each found in multiple families. One of the frequent modules has an ovary containing multiple ovules, capsules and berries, and another with an ovary having one or two ovules, achenes (or other single-seeded dry fruits) and drupes. This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types, such as capsule and berry, that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules (such as achenes and drupes). Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications, supporting a possible role of whole-genome duplications, in combination with climate changes and animal behaviors, in angiosperm fruit and ovary diversification.
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Affiliation(s)
- Yezi Xiang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, 27708, NC, USA
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, 16802, PA, USA
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hongjin Dong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, China
| | - Hongyi Chen
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, China
| | - Yi Hu
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, 16802, PA, USA
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jun Xiang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, China
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, 16802, PA, USA
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Ebadi M, Bafort Q, Mizrachi E, Audenaert P, Simoens P, Van Montagu M, Bonte D, Van de Peer Y. The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil. Proc Natl Acad Sci U S A 2023; 120:e2307289120. [PMID: 37788315 PMCID: PMC10576144 DOI: 10.1073/pnas.2307289120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/07/2023] [Indexed: 10/05/2023] Open
Abstract
The importance of whole-genome duplication (WGD) for evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary dead end, there is growing evidence that polyploidization can help overcome environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete or outlive nonpolyploids at times of environmental upheaval remain elusive, especially for autopolyploids, in which heterosis effects are limited. On the longer term, WGD might increase both mutational and environmental robustness due to redundancy and increased genetic variation, but on the short-or even immediate-term, selective advantages of WGDs are harder to explain. Here, by duplicating artificially generated Gene Regulatory Networks (GRNs), we show that duplicated GRNs-and thus duplicated genomes-show higher signal output variation than nonduplicated GRNs. This increased variation leads to niche expansion and can provide polyploid populations with substantial advantages to survive environmental turmoil. In contrast, under stable environments, GRNs might be maladaptive to changes, a phenomenon that is exacerbated in duplicated GRNs. We believe that these results provide insights into how genome duplication and (auto)polyploidy might help organisms to adapt quickly to novel conditions and to survive ecological uproar or even cataclysmic events.
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Affiliation(s)
- Mehrshad Ebadi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria0028, South Africa
| | - Pieter Audenaert
- Department of Information Technology–IDLab, Ghent University-IMEC, Gent9052, Belgium
| | - Pieter Simoens
- Department of Information Technology–IDLab, Ghent University-IMEC, Gent9052, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Dries Bonte
- Department of Biology, Terrestrial Ecology Unit, Ghent University, Ghent9000, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing210095, China
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10
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Govorunova EG, Sineshchekov OA. Channelrhodopsins: From Phototaxis to Optogenetics. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1555-1570. [PMID: 38105024 DOI: 10.1134/s0006297923100115] [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: 06/24/2023] [Revised: 07/09/2023] [Accepted: 07/09/2023] [Indexed: 12/19/2023]
Abstract
Channelrhodopsins stand out among other retinal proteins because of their capacity to generate passive ionic currents following photoactivation. Owing to that, channelrhodopsins are widely used in neuroscience and cardiology as instruments for optogenetic manipulation of the activity of excitable cells. Photocurrents generated by channelrhodopsins were first discovered in the cells of green algae in the 1970s. In this review we describe this discovery and discuss the current state of research in the field.
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11
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Koenemann DM, Kistler L, Burke JM. A plastome phylogeny of Rumex (Polygonaceae) illuminates the divergent evolutionary histories of docks and sorrels. Mol Phylogenet Evol 2023; 182:107755. [PMID: 36906194 DOI: 10.1016/j.ympev.2023.107755] [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: 11/01/2022] [Revised: 02/07/2023] [Accepted: 03/05/2023] [Indexed: 03/12/2023]
Abstract
The genus Rumex L. (Polygonaceae) provides a unique system for investigating the evolutionary development of sex determination and molecular rate evolution. Historically, Rumex has been divided, both taxonomically and colloquially into two groups: 'docks' and 'sorrels'. A well-resolved phylogeny can help evaluate a genetic basis for this division. Here we present a plastome phylogeny for 34 species of Rumex, inferred using maximum likelihood criteria. The historical 'docks' (Rumex subgenus Rumex) were resolved as monophyletic. The historical 'sorrels' (Rumex subgenera Acetosa and Acetosella) were resolved together, though not monophyletic due to the inclusion of R. bucephalophorus (Rumex subgenus Platypodium). Emex is supported as its own subgenus within Rumex, instead of resolved as sister taxa. We found remarkably low nucleotide diversity among the docks, consistent with recent diversification in that group, especially as compared to the sorrels. Fossil calibration of the phylogeny suggested that the common ancestor for Rumex (including Emex) has origins in the lower Miocene (22.13 MYA). The sorrels appear to have subsequently diversified at a relatively constant rate. The origin of the docks, however, was placed in the upper Miocene, but with most speciation occurring in the Plio-Pleistocene.
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Affiliation(s)
- Daniel M Koenemann
- Claflin University, Department of Biology, 400 Magnolia Street, Orangeburg, SC 29115, USA.
| | - Logan Kistler
- National Museum of Natural History, Anthropology Department, 10th Street & Constitution Avenue NW, Washington, DC 20560, USA.
| | - Janelle M Burke
- Howard University, Department of Biology, EE Just Hall, 415 College Street NW, Washington, DC 20059, USA.
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12
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Tang W, Shi JJ, Liu W, Lu X, Li B. MALDI Imaging Assisted Discovery of a Di-O-glycosyltransferase from Platycodon grandiflorum Root. Angew Chem Int Ed Engl 2023; 62:e202301309. [PMID: 36861146 DOI: 10.1002/anie.202301309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/03/2023]
Abstract
A matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) assisted genome mining strategy was developed for the discovery of glycosyltransferase (GT) from the root of Platycodon grandiflorum. A di-O-glycosyltransferase PgGT1 was discovered and characterized that is capable of catalyzing platycoside E (PE) synthesis through the attachment of two β-1,6-linked glucosyl residues sequentially to the glucosyl residue at the C3 position of platycodin D (PD). Although UDP-glucose is the preferred sugar donor for PgGT1, it could also utilize UDP-xylose and UDP-N-acetylglucosamine as weak donors. Residues S273, E274, and H350 played important roles in stabilizing the glucose donor and positioning the glucose in the optimal orientation for the glycosylation reaction. This study clarified two key steps involved in the biosynthetic pathway of PE and could greatly contribute to improving its industrial biotransformation.
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Affiliation(s)
- Weiwei Tang
- State Key Laboratory of Natural Medicines and School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jun-Jie Shi
- State Key Laboratory of Natural Medicines and School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Wei Liu
- State Key Laboratory of Natural Medicines and School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xu Lu
- State Key Laboratory of Natural Medicines and School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Bin Li
- State Key Laboratory of Natural Medicines and School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
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13
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Heslop-Harrison JS(P, Schwarzacher T, Liu Q. Polyploidy: its consequences and enabling role in plant diversification and evolution. ANNALS OF BOTANY 2023; 131:1-10. [PMID: 36282971 PMCID: PMC9904344 DOI: 10.1093/aob/mcac132] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/24/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Most, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility. SCOPE World-wide interest in how green plants have evolved under different conditions - whether in small, isolated populations, or globally - suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany, consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids. CONCLUSION Chromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy - generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses.
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Affiliation(s)
- J S (Pat) Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Leicester, Institute for Environmental Futures, Department of Genetics and Genome Biology, Leicester, LE1 7RH, UK
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Leicester, Institute for Environmental Futures, Department of Genetics and Genome Biology, Leicester, LE1 7RH, UK
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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Abstract
Polyploidizations, or whole-genome duplications (WGDs), in plants have increased biological complexity, facilitated evolutionary innovation, and likely enabled adaptation under harsh conditions. Besides genomic data, transcriptome data have been widely employed to detect WGDs, due to their efficient accessibility to the gene space of a species. Age distributions based on synonymous substitutions (so-called KS age distributions) for paralogs assembled from transcriptome data have identified numerous WGDs in plants, paving the way for further studies on the importance of WGDs for the evolution of seed and flowering plants. However, it is still unclear how transcriptome-based age distributions compare to those based on genomic data. In this chapter, we implemented three different de novo transcriptome assembly pipelines with two popular assemblers, i.e., Trinity and SOAPdenovo-Trans. We selected six plant species with published genomes and transcriptomes to evaluate how assembled transcripts from different pipelines perform when using KS distributions to detect previously documented WGDs in the six species. Further, using genes predicted in each genome as references, we evaluated the effects of missing genes, gene family clustering, and de novo assembled transcripts on the transcriptome-based KS distributions. Our results show that, although the transcriptome-based KS distributions differ from the genome-based ones with respect to their shapes and scales, they are still reasonably reliable for unveiling WGDs, except in species where most duplicates originated from a recent WGD. We also discuss how to overcome some possible pitfalls when using transcriptome data to identify WGDs.
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Affiliation(s)
- Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
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15
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Yang S, Li G, Li H. Molecular characterizations of genes in chloroplast genomes of the genus Arachis L. (Fabaceae) based on the codon usage divergence. PLoS One 2023; 18:e0281843. [PMID: 36917565 PMCID: PMC10013919 DOI: 10.1371/journal.pone.0281843] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/01/2023] [Indexed: 03/16/2023] Open
Abstract
Studies on the molecular characteristics of chloroplast genome are generally important for clarifying the evolutionary processes of plant species. The base composition, the effective number of codons, the relative synonymous codon usage, the codon bias index, and their correlation coefficients of a total of 41 genes in 21 chloroplast genomes of the genus Arachis were investigated to further perform the correspondence and clustering analyses, revealing significantly higher variations in genomes of wild species than those of the cultivated taxa. The codon usage patterns of all 41 genes in the genus Arachis were AT-rich, suggesting that the natural selection was the main factor affecting the evolutionary history of these genomes. Five genes (i.e., ndhC, petD, atpF, rpl14, and rps11) and five genes (i.e., atpE, psbD, psaB, ycf2, and rps12) showed higher and lower base usage divergences, respectively. This study provided novel insights into our understanding of the molecular evolution of chloroplast genomes in the genus Arachis.
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Affiliation(s)
- Shuwei Yang
- School of Intelligent Science and Information Engineering, Xi’an Peihua University, Xi’An, Shaanxi, China
| | - Gun Li
- Department of Biomedical Engineering, Laboratory for Biodiversity Science, School of Electronic Information Engineering, Xi’An Technological University, Xi’An, Shaanxi, China
- * E-mail: (GL); (HL)
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, Jilin, China
- * E-mail: (GL); (HL)
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16
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Wang QH, Zhang J, Liu Y, Jia Y, Jiao YN, Xu B, Chen ZD. Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4306-4322. [PMID: 35437589 DOI: 10.1093/jxb/erac127] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.
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Affiliation(s)
- Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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17
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Schenck CA, Busta L. Using interdisciplinary, phylogeny-guided approaches to understand the evolution of plant metabolism. PLANT MOLECULAR BIOLOGY 2022; 109:355-367. [PMID: 34816350 DOI: 10.1007/s11103-021-01220-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
To cope with relentless environmental pressures, plants produce an arsenal of structurally diverse chemicals, often called specialized metabolites. These lineage-specific compounds are derived from the simple building blocks made by ubiquitous core metabolic pathways. Although the structures of many specialized metabolites are known, the underlying metabolic pathways and the evolutionary events that have shaped the plant chemical diversity landscape are only beginning to be understood. However, with the advent of multi-omics data sets and the relative ease of studying pathways in previously intractable non-model species, plant specialized metabolic pathways are now being systematically identified. These large datasets also provide a foundation for comparative, phylogeny-guided studies of plant metabolism. Comparisons of metabolic traits and features like chemical abundances, enzyme activities, or gene sequences from phylogenetically diverse plants provide insights into how metabolic pathways evolved. This review highlights the power of studying evolution through the lens of comparative biochemistry, particularly how placing metabolism into a phylogenetic context can help a researcher identify the metabolic innovations enabling the evolution of structurally diverse plant metabolites.
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Affiliation(s)
- Craig A Schenck
- Department of Biochemistry, University of Missouri, Columbia, MO, USA.
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, USA
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18
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Hörandl E. Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020204. [PMID: 35050093 PMCID: PMC8781807 DOI: 10.3390/plants11020204] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 05/08/2023]
Abstract
Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as "units". Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Göttingen, Germany
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19
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Ma X, Zhang Z, Li G, Gou X, Bian Y, Zhao Y, Wang B, Lang M, Wang T, Xie K, Liu X, Liu B, Gong L. Spatial and Temporal Transcriptomic Heredity and Asymmetry in an Artificially Constructed Allotetraploid Wheat (AADD). FRONTIERS IN PLANT SCIENCE 2022; 13:887133. [PMID: 35651770 PMCID: PMC9150853 DOI: 10.3389/fpls.2022.887133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/08/2022] [Indexed: 05/15/2023]
Abstract
Polyploidy, or whole-genome duplication (WGD), often induces dramatic changes in gene expression due to "transcriptome shock. " However, questions remain about how allopolyploidy (the merging of multiple nuclear genomes in the same nucleus) affects gene expression within and across multiple tissues and developmental stages during the initial foundation of allopolyploid plants. Here, we systematically investigated the immediate effect of allopolyploidy on gene expression variation in an artificial allopolyploidy system consisting of a constructed allotetraploid wheat (AADD genome, accession AT2) and its diploid progenitors Triticum urartu and Aegilops tauschii. We performed comprehensive RNA sequencing of 81 samples from different genotypes, tissues, and developmental stages. First, we found that intrinsic interspecific differences between the diploid parents played a major role in establishing the expression architecture of the allopolyploid. Nonetheless, allopolyploidy per se also induced dramatic and asymmetric patterns of differential gene expression between the subgenomes, and genes from the D subgenome exhibited a more drastic response. Second, analysis of homoeolog expression bias (HEB) revealed that the D subgenome exhibited significant expression bias and that de novo-generated HEB was attributed mainly to asymmetrical differential gene expression. Homoeolog-specific expression (HSE) analyses showed that the cis-only regulatory pattern was predominant in AT2, reflecting significant divergence between the parents. Co-expression network analysis revealed that homoeolog expression connectivity (HEC) was significantly correlated with sequence divergence in cis elements between subgenomes. Interestingly, allopolyploidy-induced reconstruction of network modules was also associated with different HSE patterns. Finally, a transcriptome atlas of spike development demonstrated that the phenotypic similarity of AT2 to T. urartu may be attributed to the combination of relatively stable expression of A-subgenome genes and drastic downregulation of their D-subgenome homoeologs. These findings provide a broad, multidimensional characterization of allopolyploidy-induced transcriptomic responses and suggest that allopolyploidy can have immediate and complex regulatory effects on the expression of nuclear genes.
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Affiliation(s)
- Xintong Ma
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaowan Gou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yao Bian
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Yue Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Man Lang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Kun Xie
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaoming Liu
- Jia Sixie College of Agriculture, Weifang University of Science and Technology, Shouguang, China
- *Correspondence: Xiaoming Liu
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- Bao Liu
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- Lei Gong
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20
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Sharma V, Clark AJ, Kawashima T. Insights into the molecular evolution of fertilization mechanism in land plants. PLANT REPRODUCTION 2021; 34:353-364. [PMID: 34061252 DOI: 10.1007/s00497-021-00414-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/14/2021] [Indexed: 05/27/2023]
Abstract
Comparative genetics and genomics among green plants, including algae, provide deep insights into the evolution of land plant sexual reproduction. Land plants have evolved successive changes during their conquest of the land and innovations in sexual reproduction have played a major role in their terrestrialization. Recent years have seen many revealing dissections of the molecular mechanisms of sexual reproduction and much new genomics data from the land plant lineage, including early diverging land plants, as well as algae. This new knowledge is being integrated to further understand how sexual reproduction in land plants evolved, identifying highly conserved factors and pathways, but also molecular changes that underpinned the emergence of new modes of sexual reproduction. Here, we review recent advances in the knowledge of land plant sexual reproduction from an evolutionary perspective and also revisit the evolution of angiosperm double fertilization.
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Affiliation(s)
- Vijyesh Sharma
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Anthony J Clark
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Tomokazu Kawashima
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA.
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21
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Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production. Commun Biol 2021; 4:1203. [PMID: 34671091 PMCID: PMC8528922 DOI: 10.1038/s42003-021-02697-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/18/2021] [Indexed: 11/08/2022] Open
Abstract
Taxol, a natural product derived from Taxus, is one of the most effective natural anticancer drugs and the biosynthetic pathway of Taxol is the basis of heterologous bio-production. Here, we report a high-quality genome assembly and annotation of Taxus yunnanensis based on 10.7 Gb sequences assembled into 12 chromosomes with contig N50 and scaffold N50 of 2.89 Mb and 966.80 Mb, respectively. Phylogenomic analyses show that T. yunnanensis is most closely related to Sequoiadendron giganteum among the sampled taxa, with an estimated divergence time of 133.4-213.0 MYA. As with most gymnosperms, and unlike most angiosperms, there is no evidence of a recent whole-genome duplication in T. yunnanensis. Repetitive sequences, especially long terminal repeat retrotransposons, are prevalent in the T. yunnanensis genome, contributing to its large genome size. We further integrated genomic and transcriptomic data to unveil clusters of genes involved in Taxol synthesis, located on the chromosome 12, while gene families encoding hydroxylase in the Taxol pathway exhibited significant expansion. Our study contributes to the further elucidation of gymnosperm relationships and the Taxol biosynthetic pathway.
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22
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Abstract
There can be no doubt that early land plant evolution transformed the planet but, until recently, how and when this was achieved was unclear. Coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 are an artefact of the paucity of earlier terrestrial rocks. Disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles has been precluded by uncertainty concerning the relationships of bryophytes to one another and to the tracheophytes, as well as the timescale over which these events unfolded. New genome and transcriptome sequencing projects, combined with the application of sophisticated phylogenomic modelling methods, have yielded increasing support for the Setaphyta clade of liverworts and mosses, within monophyletic bryophytes. We consider the evolution of anatomy, genes, genomes and of development within this phylogenetic context, concluding that many vascular plant (tracheophytes) novelties were already present in a comparatively complex last common ancestor of living land plants (embryophytes). Molecular clock analyses indicate that embryophytes emerged in a mid-Cambrian to early Ordovician interval, compatible with hypotheses on their role as geoengineers, precipitating early Palaeozoic glaciations.
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Affiliation(s)
- Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jordi Paps
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Harald Schneider
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
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23
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Fang T, Motte H, Parizot B, Beeckman T. Early "Rootprints" of Plant Terrestrialization: Selaginella Root Development Sheds Light on Root Evolution in Vascular Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:735514. [PMID: 34671375 PMCID: PMC8521068 DOI: 10.3389/fpls.2021.735514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Roots provide multiple key functions for plants, including anchorage and capturing of water and nutrients. Evolutionarily, roots represent a crucial innovation that enabled plants to migrate from aquatic to terrestrial environment and to grow in height. Based on fossil evidence, roots evolved at least twice independently, once in the lycophyte clade and once in the euphyllophyte (ferns and seed plants) clade. In lycophytes, roots originated in a stepwise manner. Despite their pivotal position in root evolution, it remains unclear how root development is controlled in lycophytes. Getting more insight into lycophyte root development might shed light on how genetic players controlling the root meristem and root developmental processes have evolved. Unfortunately, genetic studies in lycophytes are lagging behind, lacking advanced biotechnological tools, partially caused by the limited economic value of this clade. The technology of RNA sequencing (RNA-seq) at least enabled transcriptome studies, which could enhance the understanding or discovery of genes involved in the root development of this sister group of euphyllophytes. Here, we provide an overview of the current knowledge on root evolution followed by a survey of root developmental events and how these are genetically and hormonally controlled, starting from insights obtained in the model seed plant Arabidopsis and where possible making a comparison with lycophyte root development. Second, we suggest possible key genetic regulators in root development of lycophytes mainly based on their expression profiles in Selaginella moellendorffii and phylogenetics. Finally, we point out challenges and possible future directions for research on root evolution.
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Affiliation(s)
- Tao Fang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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24
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Asymmetric expansions of FT and TFL1 lineages characterize differential evolution of the EuPEBP family in the major angiosperm lineages. BMC Biol 2021; 19:181. [PMID: 34465318 PMCID: PMC8408984 DOI: 10.1186/s12915-021-01128-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/18/2021] [Indexed: 12/17/2022] Open
Abstract
Background In flowering plants, precise timing of the floral transition is crucial to maximize chances of reproductive success, and as such, this process has been intensively studied. FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) have been identified as closely related eukaryotic phosphatidylethanolamine-binding proteins (‘EuPEBPs’) that integrate multiple environmental stimuli, and act antagonistically to determine the optimal timing of the floral transition. Extensive research has demonstrated that FT acts similar to hormonal signals, being transported in the phloem from its primary site of expression in leaves to its primary site of action in the shoot meristem; TFL1 also appears to act as a mobile signal. Recent work implicates FT, TFL1, and the other members of the EuPEBP family, in the control of other important processes, suggesting that the EuPEBP family may be key general regulators of developmental transitions in flowering plants. In eudicots, there are a small number of EuPEBP proteins, but in monocots, and particularly grasses, there has been a large, but uncharacterized expansion of EuPEBP copy number, with unknown consequences for the EuPEBP function. Results To systematically characterize the evolution of EuPEBP proteins in flowering plants, and in land plants more generally, we performed a high-resolution phylogenetic analysis of 701 PEBP sequences from 208 species. We refine previous models of EuPEBP evolution in early land plants, demonstrating the algal origin of the family, and pin-pointing the origin of the FT/TFL1 clade at the base of monilophytes. We demonstrate how a core set of genes (MFT1, MFT2, FT, and TCB) at the base of flowering plants has undergone differential evolution in the major angiosperm lineages. This includes the radical expansion of the FT family in monocots into 5 core lineages, further re-duplicated in the grass family to 12 conserved clades. Conclusions We show that many grass FT proteins are strongly divergent from other FTs and are likely neo-functional regulators of development. Our analysis shows that monocots and eudicots have strongly divergent patterns of EuPEBP evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01128-8.
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25
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Höng K, Austerlitz T, Bohlmann T, Bohlmann H. The thionin family of antimicrobial peptides. PLoS One 2021; 16:e0254549. [PMID: 34260649 PMCID: PMC8279376 DOI: 10.1371/journal.pone.0254549] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/28/2021] [Indexed: 11/19/2022] Open
Abstract
Thionins are antimicrobial peptides found only in plants. They are first produced as preproproteins and then processed to yield the usually 5 kDa, basic thionin peptide with three or four disulfide bridges. So far, thionins had only been found in some plant families of angiosperms. The One Thousand Plant Transcriptomes Initiative (1KP project) has sequenced the transcriptomes of more than 1000 plant species. We have used these data to search for new thionin sequences which gave 225 hits. After removing doublets these resulted in 133 new thionins. No sequences were found in algae and mosses. The phylogenetically earliest hits were from Selaginella species and from conifers. Many hits were from angiosperm plant families which were previously not known to contain thionins. A large gene family for thionins was found in Papaver. We isolated a genomic clone from Papaver somniferum which confirmed the general genomic structure with two small introns within the acidic domain. We also expressed the thionin encoded by the genomic clone and found that it had antimicrobial activity in vitro, especially against fungi. Previously, we had grouped thionins into four classes. The new data reported here led us to revise this classification. We now recognize only class 1 thionins with eight cysteine residues and class 2 thionins with six cysteine residues. The different variants that we found (and also previously known variants) can all be traced back to one of these two classes. Some of the variants had an uneven number of cysteine residues and it is not clear at the moment what that means for their threedimensional structure.
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Affiliation(s)
- Katharina Höng
- Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Tina Austerlitz
- Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Timo Bohlmann
- Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Holger Bohlmann
- Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences, Vienna, Austria
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Vatov E, Ludewig U, Zentgraf U. Disparate Dynamics of Gene Body and cis-Regulatory Element Evolution Illustrated for the Senescence-Associated Cysteine Protease Gene SAG12 of Plants. PLANTS 2021; 10:plants10071380. [PMID: 34371583 PMCID: PMC8309469 DOI: 10.3390/plants10071380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/16/2022]
Abstract
Gene regulation networks precisely orchestrate the expression of genes that are closely associated with defined physiological and developmental processes such as leaf senescence in plants. The Arabidopsis thaliana senescence-associated gene 12 (AtSAG12) encodes a cysteine protease that is (i) involved in the degradation of chloroplast proteins and (ii) almost exclusively expressed during senescence. Transcription factors, such as WRKY53 and WRKY45, bind to W-boxes in the promoter region of AtSAG12 and play key roles in its activation. Other transcription factors, such as bZIPs, might have accessory functions in their gene regulation, as several A-boxes have been identified and appear to be highly overrepresented in the promoter region compared to the whole genome distribution but are not localized within the regulatory regions driving senescence-associated expression. To address whether these two regulatory elements exhibiting these different properties are conserved in other closely related species, we constructed phylogenetic trees of the coding sequences of orthologs of AtSAG12 and screened their respective 2000 bp promoter regions for the presence of conserved cis-regulatory elements, such as bZIP and WRKY binding sites. Interestingly, the functional relevant upstream located W-boxes were absent in plant species as closely related as Arabidopsis lyrata, whereas an A-box cluster appeared to be conserved in the Arabidopsis species but disappeared in Brassica napus. Several orthologs were present in other species, possibly because of local or whole genome duplication events, but with distinct cis-regulatory sites in different locations. However, at least one gene copy in each family analyzed carried one W-box and one A-box in its promoter. These gene differences in SAG12 orthologs are discussed in the framework of cis- and trans-regulatory factors, of promoter and gene evolution, of genetic variation, and of the enhancement of the adaptability of plants to changing environmental conditions.
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Affiliation(s)
- Emil Vatov
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany;
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70599 Stuttgart, Germany;
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70599 Stuttgart, Germany;
| | - Ulrike Zentgraf
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany;
- Correspondence:
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Pérez-Escobar OA, Dodsworth S, Bogarín D, Bellot S, Balbuena JA, Schley RJ, Kikuchi IA, Morris SK, Epitawalage N, Cowan R, Maurin O, Zuntini A, Arias T, Serna-Sánchez A, Gravendeel B, Torres Jimenez MF, Nargar K, Chomicki G, Chase MW, Leitch IJ, Forest F, Baker WJ. Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. AMERICAN JOURNAL OF BOTANY 2021; 108:1166-1180. [PMID: 34250591 DOI: 10.1002/ajb2.1702] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.
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Affiliation(s)
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2UP, UK
| | - Diego Bogarín
- Lankester Botanic Garden, University of Costa Rica, Cartago, Costa Rica
| | | | | | | | | | | | | | - Robyn Cowan
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | | | | | | | | | | | | | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Australia
- National Research Collections, Commonwealth Industrial and Scientific Research Organization, Australia
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | | | - Félix Forest
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
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Baker WJ, Dodsworth S, Forest F, Graham SW, Johnson MG, McDonnell A, Pokorny L, Tate JA, Wicke S, Wickett NJ. Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants. AMERICAN JOURNAL OF BOTANY 2021; 108:1059-1065. [PMID: 34293179 DOI: 10.1002/ajb2.1703] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Affiliation(s)
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Angela McDonnell
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Jennifer A Tate
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Susann Wicke
- Plant Evolutionary Biology, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Plant Systematics and Biodiversity, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
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Huang G, Huang JQ, Chen XY, Zhu YX. Recent Advances and Future Perspectives in Cotton Research. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:437-462. [PMID: 33428477 DOI: 10.1146/annurev-arplant-080720-113241] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cotton is not only the world's most important natural fiber crop, but it is also an ideal system in which to study genome evolution, polyploidization, and cell elongation. With the assembly of five different cotton genomes, a cotton-specific whole-genome duplication with an allopolyploidization process that combined the A- and D-genomes became evident. All existing A-genomes seemed to originate from the A0-genome as a common ancestor, and several transposable element bursts contributed to A-genome size expansion and speciation. The ethylene production pathway is shown to regulate fiber elongation. A tip-biased diffuse growth mode and several regulatory mechanisms, including plant hormones, transcription factors, and epigenetic modifications, are involved in fiber development. Finally, we describe the involvement of the gossypol biosynthetic pathway in the manipulation of herbivorous insects, the role of GoPGF in gland formation, and host-induced gene silencing for pest and disease control. These new genes, modules, and pathways will accelerate the genetic improvement of cotton.
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Affiliation(s)
- Gai Huang
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China;
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jin-Quan Huang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu-Xian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China;
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Fischer K, Lachner LAM, Olsen S, Mulisch M, Krause K. The Enigma of Interspecific Plasmodesmata: Insight From Parasitic Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:641924. [PMID: 33868340 PMCID: PMC8049502 DOI: 10.3389/fpls.2021.641924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/09/2021] [Indexed: 05/29/2023]
Abstract
Parasitic plants live in intimate physical connection with other plants serving as their hosts. These host plants provide the inorganic and organic compounds that the parasites need for their propagation. The uptake of the macromolecular compounds happens through symplasmic connections in the form of plasmodesmata. In contrast to regular plasmodesmata, which connect genetically identical cells of an individual plant, the plasmodesmata that connect the cells of host and parasite join separate individuals belonging to different species and are therefore termed "interspecific". The existence of such interspecific plasmodesmata was deduced either indirectly using molecular approaches or observed directly by ultrastructural analyses. Most of this evidence concerns shoot parasitic Cuscuta species and root parasitic Orobanchaceae, which can both infect a large range of phylogenetically distant hosts. The existence of an interspecific chimeric symplast is both striking and unique and, with exceptions being observed in closely related grafted plants, exist only in these parasitic relationships. Considering the recent technical advances and upcoming tools for analyzing parasitic plants, interspecific plasmodesmata in parasite/host connections are a promising system for studying secondary plasmodesmata. For open questions like how their formation is induced, how their positioning is controlled and if they are initiated by one or both bordering cells simultaneously, the parasite/host interface with two adjacent distinguishable genetic systems provides valuable advantages. We summarize here what is known about interspecific plasmodesmata between parasitic plants and their hosts and discuss the potential of the intriguing parasite/host system for deepening our insight into plasmodesmatal structure, function, and development.
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Affiliation(s)
- Karsten Fischer
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Lena Anna-Maria Lachner
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Stian Olsen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maria Mulisch
- Central Microscopy at the Biology Center, Christian-Albrechts-University, Kiel, Germany
| | - Kirsten Krause
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
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31
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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: 265] [Impact Index Per Article: 88.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
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Affiliation(s)
- Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB - UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - 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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Scossa F, Fernie AR. Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants? Comput Struct Biotechnol J 2021; 19:1579-1594. [PMID: 33868595 PMCID: PMC8039532 DOI: 10.1016/j.csbj.2021.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Whilst substantial research effort has been placed on understanding the interactions of plant proteins with their molecular partners, relatively few studies in plants - by contrast to work in other organisms - address how these interactions evolve. It is thought that ancestral proteins were more promiscuous than modern proteins and that specificity often evolved following gene duplication and subsequent functional refining. However, ancestral protein resurrection studies have found that some modern proteins have evolved de novo from ancestors lacking those functions. Intriguingly, the new interactions evolved as a consequence of just a few mutations and, as such, acquisition of new functions appears to be neither difficult nor rare, however, only a few of them are incorporated into biological processes before they are lost to subsequent mutations. Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. We will present case studies from a range of different eukaryotes before discussing the few instances where ancestral reconstructions have been used in plants. As ASR is used to dig into the remote evolutionary past, we will also present some alternative genetic approaches to investigate molecular evolution on shorter timescales. We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. Indeed, its ancient evolutionary roots and highly diverse landscape provide an ideal context in which to address the focal issue around the emergence of evolutionary novelties and how this affects the chemical diversification of plant metabolism.
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Key Words
- APR, ancestral protein resurrection
- ASR, ancestral sequence reconstruction
- Ancestral sequence reconstruction
- CDS, coding sequence
- Evolution
- GR, glucocorticoid receptor
- GWAS, genome wide association study
- Genomics
- InDel, insertion/deletion
- MCMC, Markov Chain Monte Carlo
- ML, maximum likelihood
- MP, maximum parsimony
- MR, mineralcorticoid receptor
- MSA, multiple sequence alignment
- Metabolism
- NJ, neighbor-joining
- Phylogenetics
- Plants
- SFS, site frequency spectrum
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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Loeuille B, Thode V, Siniscalchi C, Andrade S, Rossi M, Pirani JR. Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera. PeerJ 2021; 9:e10886. [PMID: 33665028 PMCID: PMC7912680 DOI: 10.7717/peerj.10886] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/12/2021] [Indexed: 01/23/2023] Open
Abstract
Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.
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Affiliation(s)
- Benoit Loeuille
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Verônica Thode
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carolina Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States of America
| | - Sonia Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - José Rubens Pirani
- Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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Li M, Wang R, Wu X, Wang J. Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus. BMC Genomics 2020; 21:330. [PMID: 32349676 PMCID: PMC7191788 DOI: 10.1186/s12864-020-6747-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 04/21/2020] [Indexed: 01/01/2023] Open
Abstract
Background Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach. Results The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27,609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48, 29.7 and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus. Conclusions In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7500 years of evolution and domestication and may enhance our understanding of allopolyploidy.
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Affiliation(s)
- Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, 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
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Berckx F, Wibberg D, Kalinowski J, Pawlowski K. The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type. Genes (Basel) 2020; 11:genes11040432. [PMID: 32316316 PMCID: PMC7231273 DOI: 10.3390/genes11040432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/30/2020] [Accepted: 04/08/2020] [Indexed: 11/16/2022] Open
Abstract
Nitrogen-fixing Actinobacteria of the genus Frankia can be subdivided into four phylogenetically distinct clades; members of clusters one to three engage in nitrogen-fixing root nodule symbioses with actinorhizal plants. Mur enzymes are responsible for the biosynthesis of the peptidoglycan layer of bacteria. The four Mur ligases,MurC, MurD, MurE, and MurF, catalyse the addition of a short polypeptide to UDP-N-acetylmuramic acid. Frankia strains of cluster-2 and cluster-3 contain two copies of murC, while the strains of cluster-1 and cluster-4 contain only one. Phylogenetically, the protein encoded by the murC gene shared only by cluster-2 and cluster-3, termed MurC1, groups with MurC proteins of other Actinobacteria. The protein encoded by the murC gene found in all Frankia strains, MurC2, shows a higher similarity to the MurC proteins of plants than of Actinobacteria. MurC2 could have been either acquired via horizontal gene transfer or via gene duplication and convergent evolution, while murC1 was subsequently lost in the cluster-1 and cluster-4 strains. In the nodules induced by the cluster-2 strains, the expression levels of murC2 were significantly higher than those of murC1. Thus, there is clear sequence divergence between both types of Frankia MurC, and Frankia murC1 is in the process of being replaced by murC2, indicating selection in favour of murC2. Nevertheless, protein modelling showed no major structural differences between the MurCs from any phylogenetic group examined.
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Affiliation(s)
- Fede Berckx
- Department of Ecology, Environment, and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden;
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
| | - Katharina Pawlowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
- Correspondence: ; Tel.: +46-8-16-3772; Fax: +46-8-16-5525
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