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Dorrell RG, Nef C, Altan-Ochir S, Bowler C, Smith AG. Presence of vitamin B 12 metabolism in the last common ancestor of land plants. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230354. [PMID: 39343018 PMCID: PMC11439496 DOI: 10.1098/rstb.2023.0354] [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: 09/12/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 10/01/2024] Open
Abstract
Vitamin B12, also known as cobalamin, is an essential organic cofactor for methionine synthase (METH), and is only synthesized by a subset of bacteria. Plants and fungi have an alternative methionine synthase (METE) that does not need B12 and are typically considered not to utilize it. Some algae facultatively utilize B12 because they encode both METE and METH, while other algae are dependent on B12 as they encode METH only. We performed phylogenomic analyses of METE, METH and 11 further proteins involved in B12 metabolism across more than 1600 plant and algal genomes and transcriptomes (e.g. from OneKp), demonstrating the presence of B12-associated metabolism deep into the streptophytes. METH and five further accessory proteins (MTRR, CblB, CblC, CblD and CblJ) were detected in the hornworts (Anthocerotophyta), and two (CblB and CblJ) were identified in liverworts (Marchantiophyta) in the bryophytes, suggesting a retention of B12-metabolism in the last common land plant ancestor. Our data further show more limited distributions for other B12-related proteins (MCM and RNR-II) and B12 dependency in several algal orders. Finally, considering the collection sites of algae that have lost B12 metabolism, we propose freshwater-to-land transitions and symbiotic associations to have been constraining factors for B12 availability in early plant evolution. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Richard G. Dorrell
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative—UMR 7238, Sorbonne Université, 4 place Jussieu, 75005 Paris, France
| | - Charlotte Nef
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS,INSERM, Université PSL, Paris75005, France
| | - Setsen Altan-Ochir
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS,INSERM, Université PSL, Paris75005, France
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS,INSERM, Université PSL, Paris75005, France
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, CambridgeCB2 3EA, UK
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2
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de Vries J, de Vries S, Fernie AR. Current and future perspectives for enhancing our understanding of the evolution of plant metabolism. Philos Trans R Soc Lond B Biol Sci 2024; 379:20240253. [PMID: 39343013 PMCID: PMC11439503 DOI: 10.1098/rstb.2024.0253] [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: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 10/01/2024] Open
Abstract
The special issue 'The evolution of plant metabolism' has brought together original research, reviews and opinions that cover various aspects from the full breath of plant metabolism including its interaction with the environment including other species. Here, we briefly summarize these efforts and attempts to extract a consensus opinion of the best manner in which to tackle this subject both now and in the future. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Jan de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr.1, Goettingen37077, Germany
- Department of Applied Bioinformatics, University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Goldschmidtstr. 1, Goettingen37077, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm14476, Germany
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3
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Rieseberg TP, Holzhausen A, Bierenbroodspot MJ, Zhang W, Abreu IN, de Vries J. Conserved carotenoid pigmentation in reproductive organs of Charophyceae. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230372. [PMID: 39343025 PMCID: PMC11449214 DOI: 10.1098/rstb.2023.0372] [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: 03/15/2024] [Revised: 05/10/2024] [Accepted: 06/19/2024] [Indexed: 10/01/2024] Open
Abstract
Sexual reproduction in Charophyceae abounds in complex traits. Their gametangia develop as intricate structures, with oogonia spirally surrounded by envelope cells and richly pigmented antheridia. The red-probably protectant-pigmentation of antheridia is conserved across Charophyceae. Chara tomentosa is, however, unique in exhibiting this pigmentation and also in vegetative tissue. Here, we investigated the two sympatric species, C. tomentosa and Chara baltica, and compared their molecular chassis for pigmentation. Using reversed phase C30 high performance liquid chromatography (RP-C30-HPLC), we uncover that the major pigments are β-carotene, δ-carotene and γ-carotene; using headspace solid-phase microextraction coupled to gas chromatography equipped with a mass spectrometer (HS-SPME-GC-MS), we pinpoint that the unusually large carotenoid pool in C. tomentosa gives rise to diverse volatile apocarotenoids, including abundant 6-methyl-5-hepten-2-one. Based on transcriptome analyses, we uncover signatures of the unique biology of Charophycaee and genes for pigment production, including monocyclized carotenoids. The rich carotenoid pool probably serves as a substrate for diverse carotenoid-derived metabolites, signified not only by (i) the volatile apocarotenoids we detected but (ii) the high expression of a gene coding for a cytochrome P450 enzyme related to land plant proteins involved in the biosynthesis of carotenoid-derived hormones. Overall, our data shed light on a key protection strategy of sexual reproduction in the widespread group of macroalgae. The genetic underpinnings of this are shared across hundreds of millions of years of plant and algal evolution. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Tim P Rieseberg
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
| | - Anja Holzhausen
- Department of Crop Physiology, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Betty Heimann-Str. 5 , Halle (Saale) 06120, Germany
| | - Maaike J Bierenbroodspot
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
| | - Wanchen Zhang
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
| | - Ilka N Abreu
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
- Department of Plant Biochemistry, Albrecht Haller Institute of Plant Science, Justus-von-Liebig-Weg, University of Goettingen , Goettingen 37077, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Goettingen Metabolomics and Lipidomics Laboratory, Justus-von-Liebig Weg 11, University of Goettingen , Goettingen 37077, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Goldschmidtstr. 1, University of Goettingen , Goettingen 37077, Germany
- Department of Applied Bioinformatics, Campus Institute Data Science, University of Goettingen , Goettingen 37077, Germany
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Permann C, Holzinger A. Zygospore formation in Zygnematophyceae predates several land plant traits. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230356. [PMID: 39343014 PMCID: PMC11449217 DOI: 10.1098/rstb.2023.0356] [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: 03/05/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 10/01/2024] Open
Abstract
Recent research on a special type of sexual reproduction and zygospore formation in Zygnematophyceae, the sister group of land plants, is summarized. Within this group, gamete fusion occurs by conjugation. Zygospore development in Mougeotia, Spirogyra and Zygnema is highlighted, which has recently been studied using Raman spectroscopy, allowing chemical imaging and detection of changes in starch and lipid accumulation. Three-dimensional reconstructions after serial block-face scanning electron microscopy (SBF-SEM) or focused ion beam SEM (FIB-SEM) made it possible to visualize and quantify cell wall and organelle changes during zygospore development. The zygospore walls undergo strong modifications starting from uniform thin cell walls to a multilayered structure. The mature cell wall is composed of a cellulosic endospore and exospore and a central mesospore built up by aromatic compounds. In Spirogyra, the exospore and endospore consist of thick layers of helicoidally arranged cellulose fibrils, which are otherwise only known from stone cells of land plants. While starch is degraded during maturation, providing building blocks for cell wall formation, lipid droplets accumulate and fill large parts of the ripe zygospores, similar to spores and seeds of land plants. Overall, data show similarities between streptophyte algae and embryophytes, suggesting that the genetic toolkit for many land plant traits already existed in their shared algal ancestor. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Charlotte Permann
- Department of Botany, University of Innsbruck, Sternwartestraße 15,6020 Innsbruck, Austria
| | - Andreas Holzinger
- Department of Botany, University of Innsbruck, Sternwartestraße 15,6020 Innsbruck, Austria
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Conrado AC, Lemes Jorge G, Rao RSP, Xu C, Xu D, Li-Beisson Y, Thelen JJ. Evolution of the regulatory subunits for the heteromeric acetyl-CoA carboxylase. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230353. [PMID: 39343023 PMCID: PMC11449227 DOI: 10.1098/rstb.2023.0353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/22/2024] [Accepted: 09/02/2024] [Indexed: 10/01/2024] Open
Abstract
The committed step for de novo fatty acid (FA) synthesis is the ATP-dependent carboxylation of acetyl-coenzyme A catalysed by acetyl-CoA carboxylase (ACCase). In most plants, ACCase is a multi-subunit complex orthologous to prokaryotes. However, unlike prokaryotes, the plant and algal orthologues are comprised both catalytic and additional dedicated regulatory subunits. Novel regulatory subunits, biotin lipoyl attachment domain-containing proteins (BADC) and carboxyltransferase interactors (CTI) (both three-gene families in Arabidopsis) represent new effectors specific to plants and certain algal species. The evolutionary history of these genes in autotrophic eukaryotes remains elusive, making it an ongoing area of research. Analyses of potential protein-protein and co-occurrence interactions, informed by gene network patterns using the STRING database, in Arabidopsis thaliana and Chlamydomonas reinhardtii unveil intricate gene associations with ACCase, suggesting a complex interplay between FA synthesis and other cellular processes. Among both species, a higher number of co-expressed genes was identified in Arabidopsis, indicating a wider potential regulatory network of ACCase in plants. This review investigates the extent to which these genes arose in autotrophic eukaryotes and provides insights into their evolutionary trajectory. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Ana Caroline Conrado
- Division of Biochemistry and Interdisciplinary Plant Grou, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211, USA
| | - Gabriel Lemes Jorge
- Division of Biochemistry and Interdisciplinary Plant Grou, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211, USA
| | - R. S. P. Rao
- Center for Bioinformatics, NITTE University Centre, Mangaluru575018, India
| | - Chunhui Xu
- Institute for Data Science and Informatics, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Institute for Data Science and Informatics, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211, USA
| | - Yonghua Li-Beisson
- Aix Marseille Univ, CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille,Aix Marseille Univ, CEA Cadarache, Saint Paul-Lez-Durance13108, France
| | - Jay J. Thelen
- Division of Biochemistry and Interdisciplinary Plant Grou, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211, USA
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Kunz CF, de Vries S, de Vries J. Plant terrestrialization: an environmental pull on the evolution of multi-sourced streptophyte phenolics. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230358. [PMID: 39343031 DOI: 10.1098/rstb.2023.0358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/19/2024] [Accepted: 05/20/2024] [Indexed: 10/01/2024] Open
Abstract
Phenolic compounds of land plants are varied: they are chemodiverse, are sourced from different biosynthetic routes and fulfil a broad spectrum of functions that range from signalling phytohormones, to protective shields against stressors, to structural compounds. Their action defines the biology of land plants as we know it. Often, their roles are tied to environmental responses that, however, impacted already the algal progenitors of land plants, streptophyte algae. Indeed, many streptophyte algae successfully dwell in terrestrial habitats and have homologues for enzymatic routes for the production of important phenolic compounds, such as the phenylpropanoid pathway. Here, we synthesize what is known about the production of specialized phenolic compounds across hundreds of millions of years of streptophyte evolution. We propose an evolutionary scenario in which selective pressures borne out of environmental cues shaped the chemodiversity of phenolics in streptophytes. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Cäcilia F Kunz
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen , Goettingen 37077, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen , Goettingen 37077, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen , Goettingen 37077, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen , Goettingen 37077, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, University of Goettingen , Goettingen 37077, Germany
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7
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de Vries S, Feussner I. Biotic interactions, evolutionary forces and the pan-plant specialized metabolism. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230362. [PMID: 39343027 PMCID: PMC11449213 DOI: 10.1098/rstb.2023.0362] [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: 02/16/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 10/01/2024] Open
Abstract
Plant specialized metabolism has a complex evolutionary history. Some aspects are conserved across the green lineage, but many metabolites are unique to certain lineages. The network of specialized metabolism continuously diversified, simplified or reshaped during the evolution of streptophytes. Many routes of pan-plant specialized metabolism are involved in plant defence. Biotic interactions are recalled as major drivers of lineage-specific metabolomic diversification. However, the consequences of this diversity of specialized metabolism in the context of plant terrestrialization and land plant diversification into the major lineages of bryophytes, lycophytes, ferns, gymnosperms and angiosperms remain only little explored. Overall, this hampers conclusions on the evolutionary scenarios that shaped specialized metabolism. Recent efforts have brought forth new streptophyte model systems, an increase in genetically accessible species from distinct major plant lineages, and new functional data from a diversity of land plants on specialized metabolic pathways. In this review, we will integrate the recent data on the evolution of the plant immune system with the molecular data of specialized metabolism and its recognition. Based on this we will provide a contextual framework of the pan-plant specialized metabolism, the evolutionary aspects that shape it and the impact on adaptation to the terrestrial environment.This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, Goettingen 37077, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig Weg 11, Goettingen 37077, Germany
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8
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Fernie AR, de Vries S, de Vries J. Evolution of plant metabolism: the state-of-the-art. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230347. [PMID: 39343029 PMCID: PMC11449224 DOI: 10.1098/rstb.2023.0347] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 10/01/2024] Open
Abstract
Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm14476, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, Goettingen37077, Germany
- Department of Applied Bioinformatics, University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Goldschmidtstr. 1, Goettingen37077, Germany
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Xie DF, Li J, Sun JH, Cheng RY, Wang Y, Song BN, He XJ, Zhou SD. Peering through the hedge: Multiple datasets yield insights into the phylogenetic relationships and incongruences in the tribe Lilieae (Liliaceae). Mol Phylogenet Evol 2024; 200:108182. [PMID: 39222738 DOI: 10.1016/j.ympev.2024.108182] [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: 11/09/2023] [Revised: 08/06/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
The increasing use of genome-scale data has significantly facilitated phylogenetic analyses, contributing to the dissection of the underlying evolutionary mechanisms that shape phylogenetic incongruences, such as incomplete lineage sorting (ILS) and hybridization. Lilieae, a prominent member of the Liliaceae family, comprises four genera and approximately 260 species, representing 43% of all species within Liliaceae. They possess high ornamental, medicinal and edible values. Yet, no study has explored the validity of various genome-scale data in phylogenetic analyses within this tribe, nor have potential evolutionary mechanisms underlying its phylogenetic incongruences been investigated. Here, transcriptome, Angiosperms353, plastid and mitochondrial data, were collected from 50 to 93 samples of Lilieae, covering all four recognized genera. Multiple datasets were created and used for phylogenetic analyses based on concatenated and coalescent-based methods. Evolutionary rates of different datasets were calculated, and divergence times were estimated. Various approaches, including coalescence simulation, Quartet Sampling (QS), calculation of concordance factors (gCF and sCF), as well as MSCquartets and reticulate network inference, were carried out to infer the phylogenetic discordances and analyze their underlying mechanisms using a reduced 33-taxon dataset. Despite extensive phylogenetic discordances among gene trees, robust phylogenies were inferred from nuclear and plastid data compared to mitochondrial data, with lower synonymous substitution detected in mitochondrial genes than in nuclear and plastid genes. Significant ILS was detected across the phylogeny of Lilieae, with clear evidence of reticulate evolution identified. Divergence time estimation indicated that most of lineages in Lilieae diverged during a narrow time frame (ranging from 5.0 Ma to 10.0 Ma), consistent with the notion of rapid radiation evolution. Our results suggest that integrating transcriptomic and plastid data can serve as cost-effective and efficient tools for phylogenetic inference and evolutionary analysis within Lilieae, and Angiosperms353 data is also a favorable choice. Mitochondrial data are more suitable for phylogenetic analyses at higher taxonomic levels due to their stronger conservation and lower synonymous substitution rates. Significant phylogenetic incongruences detected in Lilieae were caused by both incomplete lineage sorting (ILS) and reticulate evolution, with hybridization and "ghost introgression" likely prevalent in the evolution of Lilieae species. Our findings provide new insights into the phylogeny of Lilieae, enhancing our understanding of the evolution of species in this tribe.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China.
| | - Juan Li
- Southwest Minzu University, Institute Of Qinghai-Tibetan Plateau, 610225 Chengdu, Sichuan, PR China
| | - Jia-Hui Sun
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China
| | - Rui-Yu Cheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China
| | - Yuan Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China
| | - Bo-Ni Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, PR China.
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Vences M, Sachs M, Irisarri I, Bartels F, Eriksson PF, Künzel S, Kurabayashi A, Laugen AT, Vegso ZT, Bishop CD, Kerney R, Arndt H. Phylotranscriptomic relationships of the Oophila clade of green algae associated to amphibian egg masses. Mol Phylogenet Evol 2024; 200:108165. [PMID: 39117294 DOI: 10.1016/j.ympev.2024.108165] [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: 01/11/2024] [Revised: 06/26/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024]
Abstract
Green algae usually assigned to the genus Oophila are known to colonize egg capsules of amphibian egg masses across the Nearctic and Palearctic regions. We study the phylogenetic relationships of these algae using a phylotranscriptomic data set of 76 protein-coding single-copy nuclear genes. Our data set includes novel RNAseq data for six amphibian-associated and five free-living green algae, and draft genomes of two of the latter. Within the Oophila clade (nested within Moewusinia), we find samples from two European frogs (Rana dalmatina and R. temporaria) closely related to those of the North American frog R. aurora (Oophila subclade III). An isolate from the North American R. sylvatica (subclade IV) appears to be sister to the Japanese isolate from the salamander Hynobius nigrescens (subclade J1), and subclade I algae from Ambystoma maculatum are sister to all other lineages in the Oophila clade. Two free-living algae (Chlamydomonas nasuta and Cd. pseudogloeogama) are nested within the Oophila clade, and a strain of the type species of Chlorococcum (Cc. infusionum) is related to this assemblage. Our phylotranscriptomic tree suggests that recognition of different species within the Oophila clade ("clade B" of earlier studies) is warranted, and calls for a comprehensive taxonomic revision of Moewusinia.
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Affiliation(s)
- Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
| | - Maria Sachs
- Institute of Zoology, University of Cologne, Zülpicherstr. 47b, 50674 Köln, Germany
| | - Iker Irisarri
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Fabian Bartels
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Pontus F Eriksson
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute, for Evolutionary Biology, 24306 Plön, Germany
| | - Atsushi Kurabayashi
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany; Ise City, Mie Prefecture, Japan
| | - Ane T Laugen
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
| | - Zachary T Vegso
- Department of Biological Sciences, California State Polytechnic University, Humboldt, 1 Harpst St, Arcata, CA 95521, USA
| | - Cory D Bishop
- Department of Biology, St. Francis-Xavier University, 2320 Notre Dame Avenue, Antigonish, Nova Scotia B2G 2W5, Canada
| | - Ryan Kerney
- Department of Biology, Gettysburg College, Gettysburg, PA, USA
| | - Hartmut Arndt
- Institute of Zoology, University of Cologne, Zülpicherstr. 47b, 50674 Köln, Germany
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Yu L, Wilson LFL, Terrett OM, Wurman-Rodrich J, Łyczakowski JJ, Yu X, Krogh KBRM, Dupree P. Evolution of glucuronoxylan side chain variability in vascular plants and the compensatory adaptations of cell wall-degrading hydrolases. THE NEW PHYTOLOGIST 2024; 244:1024-1040. [PMID: 39001592 DOI: 10.1111/nph.19957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/07/2024] [Indexed: 10/04/2024]
Abstract
Polysaccharide structural complexity not only influences cell wall strength and extensibility but also hinders pathogenic and biotechnological attempts to saccharify the wall. In certain species and tissues, glucuronic acid side groups on xylan exhibit arabinopyranose or galactose decorations whose genetic and evolutionary basis is completely unknown, impeding efforts to understand their function and engineer wall digestibility. Genetics and polysaccharide profiling were used to identify the responsible loci in Arabidopsis and Eucalyptus from proposed candidates, while phylogenies uncovered a shared evolutionary origin. GH30-family endo-glucuronoxylanase activities were analysed by electrophoresis, and their differing specificities were rationalised by phylogeny and structural analysis. The newly identified xylan arabinopyranosyltransferases comprise an overlooked subfamily in the GT47-A family of Golgi glycosyltransferases, previously assumed to comprise mainly xyloglucan galactosyltransferases, highlighting an unanticipated adaptation of both donor and acceptor specificities. Further neofunctionalisation has produced a Myrtaceae-specific xylan galactosyltransferase. Simultaneously, GH30 endo-glucuronoxylanases have convergently adapted to overcome these decorations, suggesting a role for these structures in defence. The differential expression of glucuronoxylan-modifying genes across Eucalyptus tissues, however, hints at further functions. Our results demonstrate the rapid adaptability of biosynthetic and degradative carbohydrate-active enzyme activities, providing insight into plant-pathogen interactions and facilitating plant cell wall biotechnological utilisation.
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Affiliation(s)
- Li Yu
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Louis F L Wilson
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Joel Wurman-Rodrich
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Jan J Łyczakowski
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
| | - Xiaolan Yu
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | | | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
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12
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Sussmilch FC, Maierhofer T, Herrmann J, Voss LJ, Lind C, Messerer M, Müller HM, Bünner MS, Ache P, Mayer KFX, Becker D, Roelfsema MRG, Geiger D, Schultz J, Hedrich R. Gaining or cutting SLAC: the evolution of plant guard cell signalling pathways. THE NEW PHYTOLOGIST 2024. [PMID: 39370767 DOI: 10.1111/nph.20172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 09/08/2024] [Indexed: 10/08/2024]
Abstract
The evolution of adjustable stomatal pores, enabling CO2 acquisition, was one of the most significant events in the development of life on land. Here, we investigate how the guard cell signalling pathways that regulate stomatal movements evolved. We compare fern and angiosperm guard cell transcriptomes and physiological responses, and examine the functionality of ion channels from diverse plant species. We find that, despite conserved expression in guard cells, fern anion channels from the SLAC/SLAH family are not activated by the same abscisic acid (ABA) pathways that provoke stomatal closure in angiosperms. Accordingly, we find an insensitivity of fern stomata to ABA. Moreover, our analysis points to a complex evolutionary history, featuring multiple gains and/or losses of SLAC activation mechanisms, as these channels were recruited to a role in stomatal closure. Our results show that the guard cells of flowering and nonflowering plants share similar core features, with lineage-specific and ecological niche-related adaptations, likely underlying differences in behaviour.
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Affiliation(s)
- Frances C Sussmilch
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, 7001, TAS, Australia
| | - Tobias Maierhofer
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
| | - Johannes Herrmann
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
| | - Lena J Voss
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
| | - Christof Lind
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
| | - Maxim Messerer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Heike M Müller
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
| | - Maria S Bünner
- Department of Bioinformatics, Biozentrum, University of Würzburg, Am Hubland, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, Würzburg, D-97074, Germany
- Center for Computational and Theoretical Biology, University of Würzburg, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, Würzburg, D-97074, Germany
| | - Peter Ache
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, Freising, 85354, Germany
| | - Dirk Becker
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
| | - M Rob G Roelfsema
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
| | - Dietmar Geiger
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
| | - Jörg Schultz
- Department of Bioinformatics, Biozentrum, University of Würzburg, Am Hubland, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, Würzburg, D-97074, Germany
- Center for Computational and Theoretical Biology, University of Würzburg, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, Würzburg, D-97074, Germany
| | - Rainer Hedrich
- Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Platz 2, Würzburg, D-97082, Germany
- College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
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13
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Mehta N, Meng Y, Zare R, Kamenetsky-Goldstein R, Sattely E. A developmental gradient reveals biosynthetic pathways to eukaryotic toxins in monocot geophytes. Cell 2024; 187:5620-5637.e10. [PMID: 39276773 DOI: 10.1016/j.cell.2024.08.027] [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: 04/08/2023] [Revised: 01/23/2024] [Accepted: 08/13/2024] [Indexed: 09/17/2024]
Abstract
Numerous eukaryotic toxins that accumulate in geophytic plants are valuable in the clinic, yet their biosynthetic pathways have remained elusive. A notable example is the >150 Amaryllidaceae alkaloids (AmAs), including galantamine, an FDA-approved treatment for Alzheimer's disease. We show that while AmAs accumulate to high levels in many daffodil tissues, biosynthesis is localized to nascent, growing tissue at the leaf base. A similar trend is found in the production of steroidal alkaloids (e.g., cyclopamine) in corn lily. This model of active biosynthesis enabled the elucidation of a complete set of biosynthetic genes that can be used to produce AmAs. Taken together, our work sheds light on the developmental and enzymatic logic of diverse alkaloid biosynthesis in daffodils. More broadly, it suggests a paradigm for biosynthesis regulation in monocot geophytes, where plants are protected from herbivory through active charging of newly formed cells with eukaryotic toxins that persist as above-ground tissue develops.
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Affiliation(s)
- Niraj Mehta
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Yifan Meng
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Richard Zare
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Elizabeth Sattely
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; HHMI, Stanford University, Stanford, CA 94305, USA.
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14
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Ambrose BA, Stevenson DW. The evolution and development of sporangia-The fundamental reproductive organ of land plant sporophytes. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102563. [PMID: 38838582 DOI: 10.1016/j.pbi.2024.102563] [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: 01/15/2024] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
A key innovation of land plants is the origin and evolution of the sporangium, the fundamental reproductive structure of the diploid sporophyte. In vascular plants, whether the structure is a cone, fertile leaf, or flower-all are clusters of sporangia. The evolution of morphologically distinct sporangia (heterospory) and retention of the gametophyte evolved three times independently as a prerequisite for the evolution of seeds. This review summarizes the development of vascular plant sporangia, molecular genetics of angiosperm sporangia, and provides a framework to investigate evolution and development in vascular plant sporangia.
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Affiliation(s)
- Barbara A Ambrose
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, NY, 10458, USA.
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15
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McDaniel SF. Local adaptation, recombination, and the fate of neopolyploids. THE NEW PHYTOLOGIST 2024; 244:32-38. [PMID: 39045612 DOI: 10.1111/nph.20011] [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: 06/06/2024] [Accepted: 07/09/2024] [Indexed: 07/25/2024]
Abstract
Polyploidy is widely recognized as an important speciation mechanism because it isolates tetraploids from their diploid progenitors. Polyploidy also provides new genetic material that may facilitate adaptive evolution. However, new mutations are more likely to arise after a neopolyploid has already successfully invaded a population. Thus, the role of adaptive forces in establishing a polyploid remains unclear. One solution to this apparent paradox may lie in the capacity of polyploids to suppress recombination among preexisting locally adapted alleles. The local adaptation mechanism requires that spatially heterogeneous selection acts on multiple loci and that gene flow introduces maladapted alleles to the population where the polyploid forms. The mechanism requires neither strong genetic drift nor any intrinsic benefit of genome doubling and can accommodate any mode of gene action. A unique prediction of the mechanism is that adaptive alleles should predate polyploidization, a pattern consistent with observations from a few well-studied polyploids. The mechanism is also consistent with the coexistence of both diploid and tetraploid cytotypes, fitness heterogeneity among independently derived polyploids, and the prevalence of outcrossing among older polyploids. The local adaptation mechanism also makes novel predictions about circumstances favoring polyploid invasions that can be tested using molecular genetic or comparative approaches.
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Affiliation(s)
- Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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16
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Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2024; 23:579-594. [PMID: 37952099 DOI: 10.1093/bfgp/elad050] [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: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.
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Affiliation(s)
- Natalia Kielich
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oliwia Mazur
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oskar Musidlak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Gracz-Bernaciak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
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17
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Xiong J, Huang B, Peng D, Shen Q, Wu D, Zhang G. JAZ2 Negatively Regulates Drought Tolerance in Barley by Modulating PLT2 Expression. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39323024 DOI: 10.1111/pce.15149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/27/2024]
Abstract
Drought is an important abiotic factor constricting crop production globally. Although the roles of JAZ proteins in regulating jasmonic acid signalling and plant responses to environmental stress are well documented, their specific functions and underlying mechanisms remain little known. In this study, JAZ proteins in barley were thoroughly analyzed, revealing a total of 11 members classified into three phylogenetic subgroups. HvJAZ2, based on its distinct expression patterns, is considered a key candidate gene for regulating drought tolerance in barley. Using the HvJAZ2 knockout mutants, we revealed that the gene negatively regulates drought tolerance by inhibiting barley root growth. Notably, the jaz2 mutants upregulated the expression of root development genes, including SHR1, PLT1, PLT2 and PLT6. plt2 and plt1/plt2 mutants exhibited suppressed root development and reduced drought tolerance. Analysis of interactions between HvJAZ2 and other proteins showed that HvJAZ2 does not directly interact with HvPLT1/2/6, but interacts with some other proteins. BIFC and LCA assays further confirmed the nuclear interaction between HvJAZ2 and HvMYC2. Y1H and Dual-Luciferase experiments demonstrated that HvMYC2 can bind to and activate the HvPLT2 promoter. In summary, HvJAZ2 negatively regulates root development and drought tolerance in barley by suppressing HvPLT2 expression through interacting with HvMYC2.
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Affiliation(s)
- Jiangyan Xiong
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Binbin Huang
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Di Peng
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Qiufang Shen
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - DeZhi Wu
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Guoping Zhang
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou, China
- Zhongyuan Institute, Zhejiang University, Zhengzhou, P.R. China
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18
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Yelina NE, Frangedakis E, Wang Z, Schreier TB, Rever J, Tomaselli M, Forestier ECF, Billakurthi K, Ren S, Bai Y, Stewart-Wood J, Haseloff J, Zhong S, Hibberd JM. Streamlined regulation of chloroplast development in the liverwort Marchantia polymorpha. Cell Rep 2024; 43:114696. [PMID: 39235940 DOI: 10.1016/j.celrep.2024.114696] [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: 02/02/2024] [Revised: 07/23/2024] [Accepted: 08/13/2024] [Indexed: 09/07/2024] Open
Abstract
Chloroplasts develop from undifferentiated plastids in response to light. In angiosperms, after the perception of light, the Elongated Hypocotyl 5 (HY5) transcription factor initiates photomorphogenesis, and two families of transcription factors known as GOLDEN2-LIKE (GLK) and GATA are considered master regulators of chloroplast development. In addition, the MIR171-targeted SCARECROW-LIKE GRAS transcription factors also impact chlorophyll biosynthesis. The extent to which these proteins carry out conserved roles in non-seed plants is not known. Using the model liverwort Marchantia polymorpha, we show that GLK controls chloroplast biogenesis, and HY5 shows a small conditional effect on chlorophyll content. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed that MpGLK has a broader set of targets than has been reported in angiosperms. We also identified a functional GLK homolog in green algae. In summary, our data support the hypothesis that GLK carries out a conserved role relating to chloroplast biogenesis in land plants and green algae.
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Affiliation(s)
- Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Zhemin Wang
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tina B Schreier
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Jenna Rever
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Kumari Billakurthi
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Sibo Ren
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yahui Bai
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Julia Stewart-Wood
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Silin Zhong
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK.
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19
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Qin H, Cheng J, Han GZ, Gong Z. Phylogenomic insights into the diversity and evolution of RPW8-NLRs and their partners in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39312623 DOI: 10.1111/tpj.17034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 09/05/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024]
Abstract
Plants use nucleotide-binding leucine-rich repeat receptors (NLRs) to sense pathogen effectors, initiating effector-triggered immunity (ETI). NLRs containing RESISTANCE TO POWDERY MILDEW 8 domain (RNLs) function as "helper" NLRs in flowering plants and support the immune responses mediated by "sensor" NLRs in cooperation with lipase-EP domain fused proteins (EP proteins). Despite their crucial roles in ETI, much remains unclear about the evolutionary trajectories of RNLs and their functional partners EP proteins. Here, we perform phylogenomic analyses of RNLs in 90 plants, covering the major diversity of plants, and identify the presence of RNLs in land plants and green algae, expanding the distribution of RNLs. We uncover a neglected major RNL group in gymnosperms, besides the canonical major group with NRG1s and ADR1s, and observe a drastic increase in RNL repertoire size in conifers. Phylogenetic analyses indicate that RNLs originated multiple times through domain shuffling, and the evolution of RNLs underwent a birth-and-death process. Moreover, we trace the origin of EP proteins back to the last common ancestor of vascular plants. We find that both RNLs and EP proteins evolve mainly under negative selection, revealing strong constraints on their function. Concerted losses and positive correlation in copy number are observed between RNL and EP sublineages, suggesting their cooperation in function. Together, our findings provide insights into the origin and evolution of plant helper NLRs, with implications for predicting novel innate immune signaling modules.
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Affiliation(s)
- Huiyu Qin
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Junyuan Cheng
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Zhen Gong
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
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20
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Holmes EC, Krammer F, Goodrum FD. Virology-The next fifty years. Cell 2024; 187:5128-5145. [PMID: 39303682 DOI: 10.1016/j.cell.2024.07.025] [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: 02/29/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 09/22/2024]
Abstract
Virology has made enormous advances in the last 50 years but has never faced such scrutiny as it does today. Herein, we outline some of the major advances made in virology during this period, particularly in light of the COVID-19 pandemic, and suggest some areas that may be of research importance in the next 50 years. We focus on several linked themes: cataloging the genomic and phenotypic diversity of the virosphere; understanding disease emergence; future directions in viral disease therapies, vaccines, and interventions; host-virus interactions; the role of viruses in chronic diseases; and viruses as tools for cell biology. We highlight the challenges that virology will face moving forward-not just the scientific and technical but also the social and political. Although there are inherent limitations in trying to outline the virology of the future, we hope this article will help inspire the next generation of virologists.
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Affiliation(s)
- Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
| | - Felicia D Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, AZ, USA
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21
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Bowles AMC. A Year at the Forefront of Streptophyte Algal Evolution. Biol Open 2024; 13:bio061673. [PMID: 39297435 PMCID: PMC11423916 DOI: 10.1242/bio.061673] [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] [Indexed: 09/27/2024] Open
Abstract
Land plants originated from an algal ancestor ∼500 million years ago in one of the most important evolutionary events for life on Earth. Extant streptophyte algae, their closest living relatives, have subsequently received much attention to better understand this major evolutionary transition. Streptophyte algae occupy many different environments, have diverse genomes and display contrasting morphologies (e.g. unicellular, filamentous, three-dimensional). This has historically made inferring these evolutionary events challenging. This A Year at the Forefront Review focusses on research published between July 2023 and June 2024 and intends to provide a short overview of recent discoveries, innovations, resources, and hypotheses regarding streptophyte algal evolution. This work has provided mechanistic insights into ancient evolutionary events that prefigured the origin of land plants and raises new questions for future research into streptophyte algae.
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22
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Grzech D, Smit SJ, Alam RM, Boccia M, Nakamura Y, Hong B, Barbole R, Heinicke S, Kunert M, Seibt W, Grabe V, Caputi L, Lichman BR, O'Connor SE, Aharoni A, Sonawane PD. Incorporation of nitrogen in antinutritional Solanum alkaloid biosynthesis. Nat Chem Biol 2024:10.1038/s41589-024-01735-w. [PMID: 39271954 DOI: 10.1038/s41589-024-01735-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 08/19/2024] [Indexed: 09/15/2024]
Abstract
Steroidal glycoalkaloids (SGAs) are specialized metabolites produced by hundreds of Solanum species including food crops, such as tomato, potato and eggplant. Unlike true alkaloids, nitrogen is introduced at a late stage of SGA biosynthesis through an unknown transamination reaction. Here, we reveal the mechanism by which GLYCOALKALOID METABOLISM12 (GAME12) directs the biosynthesis of nitrogen-containing steroidal alkaloid aglycone in Solanum. We report that GAME12, a neofunctionalized γ-aminobutyric acid (GABA) transaminase, undergoes changes in both active site specificity and subcellular localization to switch from its renown and generic activity in core metabolism to function in a specialized metabolic pathway. Moreover, overexpression of GAME12 alone in engineered S. nigrum leaves is sufficient for de novo production of nitrogen-containing SGAs. Our results highlight how hijacking a core metabolism GABA shunt enzyme is crucial in numerous Solanum species for incorporating a nitrogen to a steroidal-specialized metabolite backbone and form defensive alkaloids.
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Affiliation(s)
- Dagny Grzech
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Ryan M Alam
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Marianna Boccia
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yoko Nakamura
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Benke Hong
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ranjit Barbole
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Heinicke
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Maritta Kunert
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Wibke Seibt
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Veit Grabe
- Microscopic Imaging Service Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Prashant D Sonawane
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
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23
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Bjornson S, Verbruggen H, Upham NS, Steenwyk JL. Reticulate evolution: Detection and utility in the phylogenomics era. Mol Phylogenet Evol 2024; 201:108197. [PMID: 39270765 DOI: 10.1016/j.ympev.2024.108197] [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: 05/12/2024] [Revised: 08/13/2024] [Accepted: 09/08/2024] [Indexed: 09/15/2024]
Abstract
Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.
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Affiliation(s)
- Saelin Bjornson
- School of BioSciences, University of Melbourne, Victoria, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Victoria, Australia; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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24
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Fortin JP, Friedman WE. A stomate by any other name? The open question of hornwort gametophytic pores, their homology, and implications for the evolution of stomates. THE NEW PHYTOLOGIST 2024. [PMID: 39256934 DOI: 10.1111/nph.20094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 08/14/2024] [Indexed: 09/12/2024]
Abstract
Advances in bryophyte genomics and the phylogenetic recovery of hornworts, mosses, and liverworts as a clade have spurred considerable recent interest in character evolution among early embryophytes. Discussion of stomatal evolution, however, has been incomplete; the result of the neglect of certain potential stomate homologues, namely the two-celled epidermal gametophytic pores of hornworts (typically referred to as 'mucilage clefts'). Confusion over the potential homology of these structures is the consequence of a relatively recent consensus that hornwort gametophytic pores ('HGPs' - our term) are not homologous to stomates. We explore the occurrence and diverse functions of stomates throughout the evolutionary history and diversity of extinct and extant embryophytes. We then address arguments for and against homology between known sporophyte- and gametophyte-borne stomates and HGPs and conclude that there is little to no evidence that contradicts the hypothesis of homology. We propose that 'intergenerational heterotopy' might well account for the novel expression of stomates in gametophytes of hornworts, if stomates first evolved in the sporophyte generation of embryophytes. We then explore phylogenetically based hypotheses for the evolution of stomates in both the gametophyte and sporophyte generations of early lineages of embryophytes.
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Affiliation(s)
- James Paul Fortin
- The Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA, 02131, USA
| | - William E Friedman
- The Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA, 02131, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
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25
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Ghosh S, Mellado Sanchez M, Sue-Ob K, Roy D, Jones A, Blazquez MA, Sadanandom A. Charting the evolutionary path of the SUMO modification system in plants reveals molecular hardwiring of development to stress adaptation. THE PLANT CELL 2024; 36:3131-3144. [PMID: 38923935 PMCID: PMC11371177 DOI: 10.1093/plcell/koae192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024]
Abstract
SUMO modification is part of the spectrum of Ubiquitin-like (UBL) systems that give rise to proteoform complexity through post-translational modifications (PTMs). Proteoforms are essential modifiers of cell signaling for plant adaptation to changing environments. Exploration of the evolutionary emergence of Ubiquitin-like (UBL) systems unveils their origin from prokaryotes, where it is linked to the mechanisms that enable sulfur uptake into biomolecules. We explore the emergence of the SUMO machinery across the plant lineage from single-cell to land plants. We reveal the evolutionary point at which plants acquired the ability to form SUMO chains through the emergence of SUMO E4 ligases, hinting at its role in facilitating multicellularity. Additionally, we explore the possible mechanism for the neofunctionalization of SUMO proteases through the fusion of conserved catalytic domains with divergent sequences. We highlight the pivotal role of SUMO proteases in plant development and adaptation, offering new insights into target specificity mechanisms of SUMO modification during plant evolution. Correlating the emergence of adaptive traits in the plant lineage with established experimental evidence for SUMO in developmental processes, we propose that SUMO modification has evolved to link developmental processes to adaptive functions in land plants.
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Affiliation(s)
- Srayan Ghosh
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | | | - Kawinnat Sue-Ob
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Dipan Roy
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Andrew Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Miguel A Blazquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, 46022, Spain
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
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26
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Dorrell RG, Zhang Y, Liang Y, Gueguen N, Nonoyama T, Croteau D, Penot-Raquin M, Adiba S, Bailleul B, Gros V, Pierella Karlusich JJ, Zweig N, Fernie AR, Jouhet J, Maréchal E, Bowler C. Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid. THE PLANT CELL 2024; 36:3584-3610. [PMID: 38842420 PMCID: PMC11371179 DOI: 10.1093/plcell/koae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
Organic carbon fixed in chloroplasts through the Calvin-Benson-Bassham Cycle can be diverted toward different metabolic fates, including cytoplasmic and mitochondrial respiration, gluconeogenesis, and synthesis of diverse plastid metabolites via the pyruvate hub. In plants, pyruvate is principally produced via cytoplasmic glycolysis, although a plastid-targeted lower glycolytic pathway is known to exist in non-photosynthetic tissue. Here, we characterized a lower plastid glycolysis-gluconeogenesis pathway enabling the direct interconversion of glyceraldehyde-3-phosphate and phospho-enol-pyruvate in diatoms, ecologically important marine algae distantly related to plants. We show that two reversible enzymes required to complete diatom plastid glycolysis-gluconeogenesis, Enolase and bis-phosphoglycerate mutase (PGAM), originated through duplications of mitochondria-targeted respiratory isoforms. Through CRISPR-Cas9 mutagenesis, integrative 'omic analyses, and measured kinetics of expressed enzymes in the diatom Phaeodactylum tricornutum, we present evidence that this pathway diverts plastid glyceraldehyde-3-phosphate into the pyruvate hub, and may also function in the gluconeogenic direction. Considering experimental data, we show that this pathway has different roles dependent in particular on day length and environmental temperature, and show that the cpEnolase and cpPGAM genes are expressed at elevated levels in high-latitude oceans where diatoms are abundant. Our data provide evolutionary, meta-genomic, and functional insights into a poorly understood yet evolutionarily recurrent plastid metabolic pathway.
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Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris-Seine (IBPS), CNRS, INSERM, Sorbonne Université, Paris 75005, France
| | - Youjun Zhang
- Department of Plant Metabolomics, Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Central Plant Metabolism Group, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Liang
- Center of Deep Sea Research, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Nolwenn Gueguen
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Tomomi Nonoyama
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Dany Croteau
- Institut de Biologie Physico-Chimique (IBPC), Université PSL, Paris 75005, France
| | - Mathias Penot-Raquin
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris-Seine (IBPS), CNRS, INSERM, Sorbonne Université, Paris 75005, France
| | - Sandrine Adiba
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique (IBPC), Université PSL, Paris 75005, France
| | - Valérie Gros
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Juan José Pierella Karlusich
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Nathanaël Zweig
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Alisdair R Fernie
- Department of Plant Metabolomics, Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Central Plant Metabolism Group, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
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27
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Ren X, Zhang X, Qi X, Zhang T, Wang H, Twell D, Gong Y, Fu Y, Wang B, Kong H, Xu B. The BNB-GLID module regulates germline fate determination in Marchantia polymorpha. THE PLANT CELL 2024; 36:3824-3837. [PMID: 39041486 PMCID: PMC11371191 DOI: 10.1093/plcell/koae206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/05/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Germline fate determination is a critical event in sexual reproduction. Unlike animals, plants specify the germline by reprogramming somatic cells at the late stages of their development. However, the genetic basis of germline fate determination and how it evolved during the land plant evolution are still poorly understood. Here, we report that the plant homeodomain finger protein GERMLINE IDENTITY DETERMINANT (GLID) is a key regulator of the germline specification in liverwort, Marchantia polymorpha. Loss of the MpGLID function causes failure of germline initiation, leading to the absence of sperm and egg cells. Remarkably, the overexpression of MpGLID in M. polymorpha induces the ectopic formation of cells with male germline cell features exclusively in male thalli. We further show that MpBONOBO (BNB), with an evolutionarily conserved function, can induce the formation of male germ cell-like cells through the activation of MpGLID by directly binding to its promoter. The Arabidopsis (Arabidopsis thaliana) MpGLID ortholog, MALE STERILITY1 (AtMS1), fails to replace the germline specification function of MpGLID in M. polymorpha, demonstrating that a derived function of MpGLID orthologs has been restricted to tapetum development in flowering plants. Collectively, our findings suggest the presence of the BNB-GLID module in complex ancestral land plants that has been retained in bryophytes, but rewired in flowering plants for male germline fate determination.
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Affiliation(s)
- Xiaolong Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxia Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xiaotong Qi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huijie Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Yu Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baichen Wang
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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28
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Knosp S, Kriegshauser L, Tatsumi K, Malherbe L, Erhardt M, Wiedemann G, Bakan B, Kohchi T, Reski R, Renault H. An ancient role for CYP73 monooxygenases in phenylpropanoid biosynthesis and embryophyte development. EMBO J 2024; 43:4092-4109. [PMID: 39090438 PMCID: PMC11405693 DOI: 10.1038/s44318-024-00181-7] [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: 10/29/2023] [Revised: 07/03/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024] Open
Abstract
The phenylpropanoid pathway is one of the plant metabolic pathways most prominently linked to the transition to terrestrial life, but its evolution and early functions remain elusive. Here, we show that activity of the t-cinnamic acid 4-hydroxylase (C4H), the first plant-specific step in the pathway, emerged concomitantly with the CYP73 gene family in a common ancestor of embryophytes. Through structural studies, we identify conserved CYP73 residues, including a crucial arginine, that have supported C4H activity since the early stages of its evolution. We further demonstrate that impairing C4H function via CYP73 gene inactivation or inhibitor treatment in three bryophyte species-the moss Physcomitrium patens, the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis-consistently resulted in a shortage of phenylpropanoids and abnormal plant development. The latter could be rescued in the moss by exogenous supply of p-coumaric acid, the product of C4H. Our findings establish the emergence of the CYP73 gene family as a foundational event in the development of the plant phenylpropanoid pathway, and underscore the deep-rooted function of the C4H enzyme in embryophyte biology.
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Affiliation(s)
- Samuel Knosp
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
| | - Lucie Kriegshauser
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
- Amatera Biosciences, Pépinière Genopole Entreprise, 91000, Evry, France
| | - Kanade Tatsumi
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Ludivine Malherbe
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
| | - Mathieu Erhardt
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Inselspital, University of Bern, 3010, Bern, Switzerland
| | - Bénédicte Bakan
- INRAE, Biopolymers, Interactions, Assemblies Research Unit, La Géraudière, Nantes, France
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Hugues Renault
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France.
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29
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Van Gelder K, Lindner SN, Hanson AD, Zhou J. Strangers in a foreign land: 'Yeastizing' plant enzymes. Microb Biotechnol 2024; 17:e14525. [PMID: 39222378 PMCID: PMC11368087 DOI: 10.1111/1751-7915.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/02/2024] [Indexed: 09/04/2024] Open
Abstract
Expressing plant metabolic pathways in microbial platforms is an efficient, cost-effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour-intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost-effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data-driven machine learning framework designed to extract 'yeastizing' rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design-build-test cycle.
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Affiliation(s)
- Kristen Van Gelder
- Horticultural Sciences DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Steffen N. Lindner
- Department of Systems and Synthetic MetabolismMax Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Department of BiochemistryCharité Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt‐UniversitätBerlinGermany
| | - Andrew D. Hanson
- Horticultural Sciences DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Juannan Zhou
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
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30
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Jeon HW, Iwakawa H, Naramoto S, Herrfurth C, Gutsche N, Schlüter T, Kyozuka J, Miyauchi S, Feussner I, Zachgo S, Nakagami H. Contrasting and conserved roles of NPR pathways in diverged land plant lineages. THE NEW PHYTOLOGIST 2024; 243:2295-2310. [PMID: 39056290 DOI: 10.1111/nph.19981] [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: 10/20/2023] [Accepted: 06/26/2024] [Indexed: 07/28/2024]
Abstract
The NPR proteins function as salicylic acid (SA) receptors in Arabidopsis thaliana. AtNPR1 plays a central role in SA-induced transcriptional reprogramming whereby positively regulates SA-mediated defense. NPRs are found in the genomes of nearly all land plants. However, we know little about the molecular functions and physiological roles of NPRs in most plant species. We conducted phylogenetic and alignment analyses of NPRs from 68 species covering the significant lineages of land plants. To investigate NPR functions in bryophyte lineages, we generated and characterized NPR loss-of-function mutants in the liverwort Marchantia polymorpha. Brassicaceae NPR1-like proteins have characteristically gained or lost functional residues identified in AtNPRs, pointing to the possibility of a unique evolutionary trajectory for the Brassicaceae NPR1-like proteins. We find that the only NPR in M. polymorpha, MpNPR, is not the master regulator of SA-induced transcriptional reprogramming and negatively regulates bacterial resistance in this species. The Mpnpr transcriptome suggested roles of MpNPR in heat and far-red light responses. We identify both Mpnpr and Atnpr1-1 display enhanced thermomorphogenesis. Interspecies complementation analysis indicated that the molecular properties of AtNPR1 and MpNPR are partially conserved. We further show that MpNPR has SA-binding activity. NPRs and NPR-associated pathways have evolved distinctively in diverged land plant lineages to cope with different terrestrial environments.
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Affiliation(s)
- Hyung-Woo Jeon
- Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Hidekazu Iwakawa
- Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Satoshi Naramoto
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Cornelia Herrfurth
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
- Department for Plant Biochemistry, Albrecht von Haller Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Nora Gutsche
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Titus Schlüter
- Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Shingo Miyauchi
- Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Ivo Feussner
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
- Department for Plant Biochemistry, Albrecht von Haller Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Sabine Zachgo
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Hirofumi Nakagami
- Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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31
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Chen G, Qin Y, Wang J, Li S, Zeng F, Deng F, Chater C, Xu S, Chen ZH. Stomatal evolution and plant adaptation to future climate. PLANT, CELL & ENVIRONMENT 2024; 47:3299-3315. [PMID: 38757448 DOI: 10.1111/pce.14953] [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: 11/15/2023] [Revised: 03/18/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
Global climate change is affecting plant photosynthesis and transpiration processes, as well as increasing weather extremes impacting socio-political and environmental events and decisions for decades to come. One major research challenge in plant biology and ecology is the interaction of photosynthesis with the environment. Stomata control plant gas exchange and their evolution was a crucial innovation that facilitated the earliest land plants to colonize terrestrial environments. Stomata couple homoiohydry, together with cuticles, intercellular gas space, with the endohydric water-conducting system, enabling plants to adapt and diversify across the planet. Plants control stomatal movement in response to environmental change through regulating guard cell turgor mediated by membrane transporters and signaling transduction. However, the origin, evolution, and active control of stomata remain controversial topics. We first review stomatal evolution and diversity, providing fossil and phylogenetic evidence of their origins. We summarize functional evolution of guard cell membrane transporters in the context of climate changes and environmental stresses. Our analyses show that the core signaling elements of stomatal movement are more ancient than stomata, while genes involved in stomatal development co-evolved de novo with the earliest stomata. These results suggest that novel stomatal development-specific genes were acquired during plant evolution, whereas genes regulating stomatal movement, especially cell signaling pathways, were inherited ancestrally and co-opted by dynamic functional differentiation. These two processes reflect the different adaptation strategies during land plant evolution.
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Affiliation(s)
- Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuan Qin
- College of Agriculture, Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, China
| | - Jian Wang
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sujuan Li
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fanrong Zeng
- College of Agriculture, Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, China
| | - Fenglin Deng
- College of Agriculture, Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, China
| | - Caspar Chater
- Royal Botanic Gardens, Kew, Richmond, UK
- Plants, Photosynthesis, and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Shengchun Xu
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Xianghu Laboratory, Hangzhou, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia
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Mu B, Nair AM, Zhao R. Plastid HSP90C C-terminal extension region plays a regulatory role in chaperone activity and client binding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2288-2302. [PMID: 38969341 DOI: 10.1111/tpj.16917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/22/2024] [Indexed: 07/07/2024]
Abstract
HSP90Cs are essential molecular chaperones localized in the plastid stroma that maintain protein homeostasis and assist the import and thylakoid transport of chloroplast proteins. While HSP90C contains all conserved domains as an HSP90 family protein, it also possesses a unique feature in its variable C-terminal extension (CTE) region. This study elucidated the specific function of this HSP90C CTE region. Our phylogenetic analyses revealed that this intrinsically disordered region contains a highly conserved DPW motif in the green lineages. With biochemical assays, we showed that the CTE is required for the chaperone to effectively interact with client proteins PsbO1 and LHCB2 to regulate ATP-independent chaperone activity and to effectuate its ATP hydrolysis. The CTE truncation mutants could support plant growth and development reminiscing the wild type under normal conditions except for a minor phenotype in cotyledon when expressed at a level comparable to wild type. However, higher HSP90C expression was observed to correlate with a stronger response to specific photosystem II inhibitor DCMU, and CTE truncations dampened the response. Additionally, when treated with lincomycin to inhibit chloroplast protein translation, CTE truncation mutants showed a delayed response to PsbO1 expression repression, suggesting its role in chloroplast retrograde signaling. Our study therefore provides insights into the mechanism of HSP90C in client protein binding and the regulation of green chloroplast maturation and function, especially under stress conditions.
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Affiliation(s)
- Bona Mu
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Adheip Monikantan Nair
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Rongmin Zhao
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
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Huang P, Li Z, Wang H, Huang J, Tan G, Fu Y, Liu X, Zheng S, Xu P, Sun M, Zeng J. A genome assembly of decaploid Houttuynia cordata provides insights into the evolution of Houttuynia and the biosynthesis of alkaloids. HORTICULTURE RESEARCH 2024; 11:uhae203. [PMID: 39308792 PMCID: PMC11415239 DOI: 10.1093/hr/uhae203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/14/2024] [Indexed: 09/25/2024]
Abstract
Houttuynia cordata Thunb., commonly known as yuxingcao in China, is known for its characteristic fishy smell and is widely recognized as an important herb and vegetable in many parts of Asia. However, the lack of genomic information on H. cordata limits the understanding of its population structure, genetic diversity, and biosynthesis of medicinal compounds. Here we used single-molecule sequencing, Illumina paired-end sequencing, and chromosome conformation capture technology to construct the first chromosome-scale decaploid H. cordata reference genome. The genome assembly was 2.63 Gb in size, with 1348 contigs and a contig N50 of 21.94 Mb further clustered and ordered into 88 pseudochromosomes based on Hi-C analysis. The results of genome evolution analysis showed that H. cordata underwent a whole-genome duplication (WGD) event ~17 million years ago, and an additional WGD event occurred 3.3 million years ago, which may be the main factor leading to the high abundance of multiple copies of orthologous genes. Here, transcriptome sequencing across five different tissues revealed significant expansion and distinct expression patterns of key gene families, such as l-amino acid/l-tryptophan decarboxylase and strictosidine synthase, which are essential for the biosynthesis of isoquinoline and indole alkaloids, along with the identification of genes such as TTM3, which is critical for root development. This study constructed the first decaploid medicinal plant genome and revealed the genome evolution and polyploidization events of H. cordata .
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Affiliation(s)
- Peng Huang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha 410128, Hunan, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, Hunan, China
- Traditional Chinese Medicine Breeding Center of Yuelushan Laboratory, Changsha 410128, Hunan, China
| | - Zhu Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Huan Wang
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan 430075, Hubei, China
| | - Jinqiang Huang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Guifeng Tan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Yue Fu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Xiubin Liu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha 410128, Hunan, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, Hunan, China
- Traditional Chinese Medicine Breeding Center of Yuelushan Laboratory, Changsha 410128, Hunan, China
| | - Shang Zheng
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan 430075, Hubei, China
| | - Peng Xu
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan 430075, Hubei, China
| | - Mengshan Sun
- Hunan Institute of Agricultural Environment and Ecology, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan, China
| | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha 410128, Hunan, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, Hunan, China
- Traditional Chinese Medicine Breeding Center of Yuelushan Laboratory, Changsha 410128, Hunan, China
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Bentz PC, Leebens‐Mack J. Developing Asparagaceae1726: An Asparagaceae-specific probe set targeting 1726 loci for Hyb-Seq and phylogenomics in the family. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11597. [PMID: 39360194 PMCID: PMC11443443 DOI: 10.1002/aps3.11597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/18/2024] [Accepted: 02/19/2024] [Indexed: 10/04/2024]
Abstract
Premise Target sequence capture (Hyb-Seq) is a cost-effective sequencing strategy that employs RNA probes to enrich for specific genomic sequences. By targeting conserved low-copy orthologs, Hyb-Seq enables efficient phylogenomic investigations. Here, we present Asparagaceae1726-a Hyb-Seq probe set targeting 1726 low-copy nuclear genes for phylogenomics in the angiosperm family Asparagaceae-which will aid the often-challenging delineation and resolution of evolutionary relationships within Asparagaceae. Methods Here we describe and validate the Asparagaceae1726 probe set (https://github.com/bentzpc/Asparagaceae1726) in six of the seven subfamilies of Asparagaceae. We perform phylogenomic analyses with these 1726 loci and evaluate how inclusion of paralogs and bycatch plastome sequences can enhance phylogenomic inference with target-enriched data sets. Results We recovered at least 82% of target orthologs from all sampled taxa, and phylogenomic analyses resulted in strong support for all subfamilial relationships. Additionally, topology and branch support were congruent between analyses with and without inclusion of target paralogs, suggesting that paralogs had limited effect on phylogenomic inference. Discussion Asparagaceae1726 is effective across the family and enables the generation of robust data sets for phylogenomics of any Asparagaceae taxon. Asparagaceae1726 establishes a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family.
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Affiliation(s)
- Philip C. Bentz
- Department of Plant BiologyUniversity of Georgia120 Carlton St.Athens30605GeorgiaUSA
| | - Jim Leebens‐Mack
- Department of Plant BiologyUniversity of Georgia120 Carlton St.Athens30605GeorgiaUSA
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Lyczakowski JJ, Wightman R. Convergent and adaptive evolution drove change of secondary cell wall ultrastructure in extant lineages of seed plants. THE NEW PHYTOLOGIST 2024; 243:2061-2065. [PMID: 39079702 DOI: 10.1111/nph.19983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/01/2024] [Indexed: 08/23/2024]
Affiliation(s)
- Jan J Lyczakowski
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
| | - Raymond Wightman
- Microscopy Core Facility, Sainsbury Laboratory Cambridge University, 47 Bateman St., Cambridge, CB2 1LR, UK
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Wang T, van Dijk ADJ, Zhao R, Bonnema G, Wang X. Contribution of homoeologous exchange to domestication of polyploid Brassica. Genome Biol 2024; 25:231. [PMID: 39192349 DOI: 10.1186/s13059-024-03370-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 08/10/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Polyploidy is widely recognized as a significant evolutionary force in the plant kingdom, contributing to the diversification of plants. One of the notable features of allopolyploidy is the occurrence of homoeologous exchange (HE) events between the subgenomes, causing changes in genomic composition, gene expression, and phenotypic variations. However, the role of HE in plant adaptation and domestication remains unclear. RESULTS Here we analyze the whole-genome resequencing data from Brassica napus accessions representing the different morphotypes and ecotypes, to investigate the role of HE in domestication. Our findings demonstrate frequent occurrence of HEs in Brassica napus, with substantial HE patterns shared across populations, indicating their potential role in promoting crop domestication. HE events are asymmetric, with the A genome more frequently replacing C genome segments. These events show a preference for specific genomic regions and vary among populations. We also identify candidate genes in HE regions specific to certain populations, which likely contribute to flowering-time diversification across diverse morphotypes and ecotypes. In addition, we assemble a new genome of a swede accession, confirming the HE signals on the genome and their potential involvement in root tuber development. By analyzing HE in another allopolyploid species, Brassica juncea, we characterize a potential broader role of HE in allopolyploid crop domestication. CONCLUSIONS Our results provide novel insights into the domestication of polyploid Brassica species and highlight homoeologous exchange as a crucial mechanism for generating variations that are selected for crop improvement in polyploid species.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Ranze Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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Dougherty K, Prashar T, Hudak KA. Improved pokeweed genome assembly and early gene expression changes in response to jasmonic acid. BMC PLANT BIOLOGY 2024; 24:801. [PMID: 39179987 PMCID: PMC11344361 DOI: 10.1186/s12870-024-05446-1] [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: 10/22/2023] [Accepted: 07/22/2024] [Indexed: 08/26/2024]
Abstract
BACKGROUND Jasmonic acid (JA) is a phytohormone involved in regulating responses to biotic and abiotic stress. Although the JA pathway is well characterized in model plants such as Arabidopsis thaliana, less is known about many non-model plants. Phytolacca americana (pokeweed) is native to eastern North Americana and is resilient to environmental stress. The goal of this study was to produce a publicly available pokeweed genome assembly and annotations and use this resource to determine how early response to JA changes gene expression, with particular focus on genes involved in defense. RESULTS We assembled the pokeweed genome de novo from approximately 30 Gb of PacBio Hifi long reads and achieved an NG50 of ~ 13.2 Mb and a minimum 93.9% complete BUSCO score for gene annotations. With this reference, we investigated the early changes in pokeweed gene expression following JA treatment. Approximately 5,100 genes were differentially expressed during the 0-6 h time course with almost equal number of genes with increased and decreased transcript levels. Cluster and gene ontology analyses indicated the downregulation of genes associated with photosynthesis and upregulation of genes involved in hormone signaling and defense. We identified orthologues of key transcription factors and constructed the first JA gene response network integrated with our transcriptomic data from orthologues of Arabidopsis genes. We discovered that pokeweed did not use leaf senescence as a means of reallocating resources during stress; rather, most secondary metabolite synthesis genes were constitutively expressed, suggesting that pokeweed directs its resources for survival over the long term. In addition, pokeweed synthesizes several RNA N-glycosylases hypothesized to function in defense, each with unique expression profiles in response to JA. CONCLUSIONS Our investigation of the early response of pokeweed to JA illustrates patterns of gene expression involved in defence and stress tolerance. Pokeweed provides insight into the defense mechanisms of plants beyond those observed in research models and crops, and further study may yield novel approaches to improving the resilience of plants to environmental changes. Our assembled pokeweed genome is the first within the taxonomic family Phytolaccaceae to be publicly available for continued research.
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Affiliation(s)
- Kyra Dougherty
- Department of Biology, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
| | - Tanya Prashar
- Department of Biology, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
| | - Katalin A Hudak
- Department of Biology, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada.
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Bierenbroodspot MJ, Pröschold T, Fürst-Jansen JMR, de Vries S, Irisarri I, Darienko T, de Vries J. Phylogeny and evolution of streptophyte algae. ANNALS OF BOTANY 2024; 134:385-400. [PMID: 38832756 PMCID: PMC11341676 DOI: 10.1093/aob/mcae091] [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: 03/02/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
The Streptophyta emerged about a billion years ago. Nowadays, this branch of the green lineage is most famous for one of its clades, the land plants (Embryophyta). Although Embryophyta make up the major share of species numbers in Streptophyta, there is a diversity of probably >5000 species of streptophyte algae that form a paraphyletic grade next to land plants. Here, we focus on the deep divergences that gave rise to the diversity of streptophytes, hence particularly on the streptophyte algae. Phylogenomic efforts have not only clarified the position of streptophyte algae relative to land plants, but recent efforts have also begun to unravel the relationships and major radiations within streptophyte algal diversity. We illustrate how new phylogenomic perspectives have changed our view on the evolutionary emergence of key traits, such as intricate signalling networks that are intertwined with multicellular growth and the chemodiverse hotbed from which they emerged. These traits are key for the biology of land plants but were bequeathed from their algal progenitors.
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Affiliation(s)
- Maaike J Bierenbroodspot
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Thomas Pröschold
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Research Department for Limnology, University of Innsbruck, Mondseestr. 9, 5310 Mondsee, Austria
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Iker Irisarri
- Section of Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Tatyana Darienko
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Department of Experimental Phycology and Culture Collection of Algae, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Nikolausberger Weg 18, 37073 Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidstraße 1, 37077 Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
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Zhai J, Gokaslan A, Schiff Y, Berthel A, Liu ZY, Lai WY, Miller ZR, Scheben A, Stitzer MC, Romay MC, Buckler ES, Kuleshov V. Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.596709. [PMID: 38895432 PMCID: PMC11185591 DOI: 10.1101/2024.06.04.596709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Interpreting function and fitness effects in diverse plant genomes requires transferable models. Language models (LMs) pre-trained on large-scale biological sequences can learn evolutionary conservation and offer cross-species prediction better than supervised models through fine-tuning limited labeled data. We introduce PlantCaduceus, a plant DNA LM based on the Caduceus and Mamba architectures, pre-trained on a curated dataset of 16 Angiosperm genomes. Fine-tuning PlantCaduceus on limited labeled Arabidopsis data for four tasks, including predicting translation initiation/termination sites and splice donor and acceptor sites, demonstrated high transferability to 160 million year diverged maize, outperforming the best existing DNA LM by 1.45 to 7.23-fold. PlantCaduceus is competitive to state-of-the-art protein LMs in terms of deleterious mutation identification, and is threefold better than PhyloP. Additionally, PlantCaduceus successfully identifies well-known causal variants in both Arabidopsis and maize. Overall, PlantCaduceus is a versatile DNA LM that can accelerate plant genomics and crop breeding applications.
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Affiliation(s)
- Jingjing Zhai
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
| | - Aaron Gokaslan
- Department of Computer Science, Cornell University, Ithaca, NY, USA 14853
| | - Yair Schiff
- Department of Computer Science, Cornell University, Ithaca, NY, USA 14853
| | - Ana Berthel
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
| | - Zong-Yan Liu
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY USA 14853
| | - Wei-Yun Lai
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
| | - Zachary R. Miller
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY USA 11724
| | | | - M. Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY USA 14853
- USDA-ARS; Ithaca, NY, USA 14853
| | - Volodymyr Kuleshov
- Department of Computer Science, Cornell University, Ithaca, NY, USA 14853
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40
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Largest genomic tree of life of flowering plants to date includes almost 8,000 genera. Nature 2024:10.1038/d41586-024-02631-y. [PMID: 39169130 DOI: 10.1038/d41586-024-02631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
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41
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Gallone B, Kuyper TW, Nuytinck J. The genus Cortinarius should not (yet) be split. IMA Fungus 2024; 15:24. [PMID: 39138570 PMCID: PMC11321212 DOI: 10.1186/s43008-024-00159-4] [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: 03/15/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
The genus Cortinarius (Agaricales, Basidiomycota) is one of the most species-rich fungal genera, with thousands of species reported. Cortinarius species are important ectomycorrhizal fungi and form associations with many vascular plants globally. Until recently Cortinarius was the single genus of the family Cortinariaceae, despite several attempts to provide a workable, lower-rank hierarchical structure based on subgenera and sections. The first phylogenomic study for this group elevated the old genus Cortinarius to family level and the family was split into ten genera, of which seven were described as new. Here, by careful re-examination of the recently published phylogenomic dataset, we detected extensive gene-tree/species-tree conflicts using both concatenation and multispecies coalescent approaches. Our analyses demonstrate that the Cortinarius phylogeny remains unresolved and the resulting phylogenomic hypotheses suffer from very short and unsupported branches in the backbone. We can confirm monophyly of only four out of ten suggested new genera, leaving uncertain the relationships between each other and the general branching order. Thorough exploration of the tree space demonstrated that the topology on which Cortinarius revised classification relies on does not represent the best phylogenetic hypothesis and should not be used as constrained topology to include additional species. For this reason, we argue that based on available evidence the genus Cortinarius should not (yet) be split. Moreover, considering that phylogenetic uncertainty translates to taxonomic uncertainty, we advise for careful evaluation of phylogenomic datasets before proposing radical taxonomic and nomenclatural changes.
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Affiliation(s)
- Brigida Gallone
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
| | - Thomas W Kuyper
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Soil Biology Group, Wageningen University, 6700 AA, Wageningen, The Netherlands
| | - Jorinde Nuytinck
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
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Feng J, Dan X, Cui Y, Gong Y, Peng M, Sang Y, Ingvarsson PK, Wang J. Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change. PLANT COMMUNICATIONS 2024:101044. [PMID: 39095989 DOI: 10.1016/j.xplc.2024.101044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/03/2024] [Accepted: 07/31/2024] [Indexed: 08/04/2024]
Abstract
Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats to biodiversity and nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems and play a crucial and leading role in combating and mitigating the adverse effects of extreme climate events, despite their own vulnerability to these threats. Therefore, understanding and monitoring how natural forests respond to rapid climate change is a key priority for biodiversity conservation. Recent progress in evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools to address several key issues. These include precise delineation of species and evolutionary units, inference of past evolutionary histories and demographic fluctuations, identification of environmentally adaptive variants, and measurement of genetic load levels. As the urgency to deal with more extreme environmental stresses grows, understanding the genomics of evolutionary history, local adaptation, future responses to climate change, and conservation and restoration of natural forest trees will be critical for research at the nexus of global change, population genomics, and conservation biology. In this review, we explore the application of evolutionary genomics to assess the effects of global climate change using multi-omics approaches and discuss the outlook for breeding of climate-adapted trees.
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Affiliation(s)
- Jiajun Feng
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xuming Dan
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yangkai Cui
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi Gong
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Minyue Peng
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yupeng Sang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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Irisarri I, Lorente-Martínez H, Strassert JFH, Agorreta A, Zardoya R, San Mauro D, de Vries J. Early Diversification of Membrane Intrinsic Proteins (MIPs) in Eukaryotes. Genome Biol Evol 2024; 16:evae164. [PMID: 39058319 PMCID: PMC11316224 DOI: 10.1093/gbe/evae164] [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: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Membrane intrinsic proteins (MIPs), including aquaporins (AQPs) and aquaglyceroporins (GLPs), form an ancient family of transporters for water and small solutes across biological membranes. The evolutionary history and functions of MIPs have been extensively studied in vertebrates and land plants, but their widespread presence across the eukaryotic tree of life suggests both a more complex evolutionary history and a broader set of functions than previously thought. That said, the early evolution of MIPs remains obscure. The presence of one GLP and four AQP clades across both bacteria and archaea suggests that the first eukaryotes could have possessed up to five MIPs. Here, we report on a previously unknown richness in MIP diversity across all major eukaryotic lineages, including unicellular eukaryotes, which make up the bulk of eukaryotic diversity. Three MIP clades have likely deep evolutionary origins, dating back to the last eukaryotic common ancestor (LECA), and support the presence of a complex MIP repertoire in early eukaryotes. Overall, our findings highlight the growing complexity of the reconstructed LECA genome: the dynamic evolutionary history of MIPs was set in motion when eukaryotes were in their infancy followed by radiative bursts across all main eukaryotic lineages.
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Affiliation(s)
- Iker Irisarri
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, 37077 Göttingen, Germany
- Campus Institute Data Science (CIDAS), 37077 Göttingen, Germany
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, 20146 Hamburg, Germany
| | - Héctor Lorente-Martínez
- Department of Biodiversity Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Jürgen F H Strassert
- Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Ainhoa Agorreta
- Department of Biodiversity Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Rafael Zardoya
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), 28006 Madrid, Spain
| | - Diego San Mauro
- Department of Biodiversity Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Jan de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, 37077 Göttingen, Germany
- Campus Institute Data Science (CIDAS), 37077 Göttingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, University of Goettingen, 37077 Göttingen, Germany
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Kang JS, Yu JG, Xiang QP, Zhang XC. The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae. Mol Biol Evol 2024; 41:msae153. [PMID: 39101470 PMCID: PMC11299036 DOI: 10.1093/molbev/msae153] [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: 09/26/2023] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024] Open
Abstract
Selaginellaceae, originated in the Carboniferous and survived the Permian-Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.
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Affiliation(s)
- Jong-Soo Kang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ji-Gao Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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Beringer M, Choudhury RR, Mandáková T, Grünig S, Poretti M, Leitch IJ, Lysak MA, Parisod C. Biased Retention of Environment-Responsive Genes Following Genome Fractionation. Mol Biol Evol 2024; 41:msae155. [PMID: 39073781 PMCID: PMC11306978 DOI: 10.1093/molbev/msae155] [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: 01/10/2024] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements (TEs), have been postulated to shape genome-wide dominance and biased fractionation, leading to a conserved least-fractionated (LF) subgenome and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. In this study, a chromosome-scale assembly of the alpine buckler mustard (Biscutella laevigata; Brassicaceae) that underwent a WGD event about 11 million years ago is coupled with transcriptional responses to heat, cold, drought, and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of TEs in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the "turn a hobby into a job" model, about one-third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased, but with others showing high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles.
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Affiliation(s)
- Marc Beringer
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Rimjhim Roy Choudhury
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Sandra Grünig
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Manuel Poretti
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | | | - Martin A Lysak
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Christian Parisod
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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Culver KD, Sadecki PW, Jackson JK, Brown ZA, Hnilica ME, Wu J, Shaw LN, Wommack AJ, Hicks LM. Identification and Characterization of CC-AMP1-like and CC-AMP2-like Peptides in Capsicum spp. J Proteome Res 2024; 23:2948-2960. [PMID: 38367000 PMCID: PMC11296913 DOI: 10.1021/acs.jproteome.3c00597] [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] [Indexed: 02/19/2024]
Abstract
Antimicrobial peptides (AMPs) are compounds with a variety of bioactive properties. Especially promising are their antibacterial activities, often toward drug-resistant pathogens. Across different AMP sources, AMPs expressed within plants are relatively underexplored with a limited number of plant AMP families identified. Recently, we identified the novel AMPs CC-AMP1 and CC-AMP2 in ghost pepper plants (Capsicum chinense x frutescens), exerting promising antibacterial activity and not classifying into any known plant AMP family. Herein, AMPs related to CC-AMP1 and CC-AMP2 were identified within both Capsicum annuum and Capsicum baccatum. In silico predictions throughout plants were utilized to illustrate that CC-AMP1-like and CC-AMP2-like peptides belong to two broader AMP families, with three-dimensional structural predictions indicating that CC-AMP1-like peptides comprise a novel subfamily of α-hairpinins. The antibacterial activities of several closely related CC-AMP1-like peptides were compared with a truncated version of CC-AMP1 possessing significantly more activity than the full peptide. This truncated peptide was further characterized to possess broad-spectrum antibacterial activity against clinically relevant ESKAPE pathogens. These findings illustrate the value in continued study of plant AMPs toward characterization of novel AMP families, with CC-AMP1-like peptides possessing promising bioactivity.
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Affiliation(s)
- Kevin D. Culver
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, United States
| | - Patric W. Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, United States
| | - Jessica K. Jackson
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, 33620, United States
| | - Zoe A. Brown
- Department of Chemistry, High Point University, High Point, NC, 27268, United States
| | - Megan E. Hnilica
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, United States
| | - Jingyun Wu
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, United States
| | - Lindsey N. Shaw
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, 33620, United States
| | - Andrew J. Wommack
- Department of Chemistry, High Point University, High Point, NC, 27268, United States
| | - Leslie M. Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, United States
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Karbstein K, Kösters L, Hodač L, Hofmann M, Hörandl E, Tomasello S, Wagner ND, Emerson BC, Albach DC, Scheu S, Bradler S, de Vries J, Irisarri I, Li H, Soltis P, Mäder P, Wäldchen J. Species delimitation 4.0: integrative taxonomy meets artificial intelligence. Trends Ecol Evol 2024; 39:771-784. [PMID: 38849221 DOI: 10.1016/j.tree.2023.11.002] [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: 05/08/2023] [Revised: 10/20/2023] [Accepted: 11/08/2023] [Indexed: 06/09/2024]
Abstract
Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.
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Affiliation(s)
- Kevin Karbstein
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany.
| | - Lara Kösters
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany
| | - Ladislav Hodač
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany
| | - Martin Hofmann
- Technical University of Ilmenau, Institute for Computer and Systems Engineering, 98693 Ilmenau, Germany
| | - Elvira Hörandl
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Salvatore Tomasello
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Natascha D Wagner
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Brent C Emerson
- Institute of Natural Products and Agrobiology (IPNA-CSIC), Island Ecology and Evolution Research Group, 38206 La Laguna, Tenerife, Canary Islands, Spain
| | - Dirk C Albach
- Carl von Ossietzky-Universität Oldenburg, Institute of Biology and Environmental Science, 26129 Oldenburg, Germany
| | - Stefan Scheu
- University of Göttingen, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany; University of Göttingen, Centre of Biodiversity and Sustainable Land Use (CBL), 37073 Göttingen, Germany
| | - Sven Bradler
- University of Göttingen, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany
| | - Jan de Vries
- University of Göttingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, 37077 Göttingen, Germany; University of Göttingen, Campus Institute Data Science (CIDAS), 37077 Göttingen, Germany; University of Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, 37077 Göttingen, Germany
| | - Iker Irisarri
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Centre for Molecular Biodiversity Research, Phylogenomics Section, Museum of Nature, 20146 Hamburg, Germany
| | - He Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Chenshan Botanical Garden, 201602 Shanghai, China
| | - Pamela Soltis
- University of Florida, Florida Museum of Natural History, 32611 Gainesville, USA
| | - Patrick Mäder
- Technical University of Ilmenau, Institute for Computer and Systems Engineering, 98693 Ilmenau, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Friedrich Schiller University Jena, Faculty of Biological Sciences, Institute of Ecology and Evolution, Philosophenweg 16, 07743 Jena, Germany
| | - Jana Wäldchen
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
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Tseng YH, Kuo LY, Borokini I, Fawcett S. The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae. AMERICAN JOURNAL OF BOTANY 2024; 111:e16388. [PMID: 39135339 DOI: 10.1002/ajb2.16388] [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: 01/11/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 08/24/2024]
Abstract
PREMISE Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape. METHODS By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework. RESULTS We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other. CONCLUSIONS The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.
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Affiliation(s)
- Yu-Hsin Tseng
- Department of Life Sciences, National Chung Hsing University, no. 145 Xingda Rd., South District, 40227, Taichung, Taiwan
| | - Li-Yaung Kuo
- College of Life Science, National Tsing Hua University, No. 101, Section 2, Kuang Fu Road, Hsinchu, 30044, Taiwan
| | - Israel Borokini
- Department of Ecology, Montana State University, 310 Lewis Hall, Bozeman, 59717, MT, USA
- University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building, Berkeley, 94720-2465, CA, USA
| | - Susan Fawcett
- University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building, Berkeley, 94720-2465, CA, USA
- National Tropical Botanical Garden, 3530 Papālina Road, Kalāheo, 96741, HI, USA
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49
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Xavier A, Yadav R, Gowda V. Evolutionary patterns of variations in chromosome counts and genome sizes show positive correlations with taxonomic diversity in tropical gingers. AMERICAN JOURNAL OF BOTANY 2024; 111:e16334. [PMID: 38825815 DOI: 10.1002/ajb2.16334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 06/04/2024]
Abstract
PREMISE Cytogenetic traits such as an organism's chromosome number and genome size are taxonomically critical as they are instrumental in defining angiosperm diversity. Variations in these traits can be traced to evolutionary processes such as polyploidization, although geographic variations across cytogenetic traits remain underexplored. In the pantropical monocot family Zingiberaceae (~1500 species), cytogenetic traits have been well documented; however, the role of these traits in shaping taxonomic diversity and biogeographic patterns of gingers is not known. METHODS A time-calibrated Bayesian phylogenetic tree was constructed for 290 taxa covering three of the four subfamilies in Zingiberaceae. We tested models of chromosome number and genome size evolution within the family and whether lineage age, taxonomic diversity, and distributional range explain the variations in the cytogenetic traits. Tests were carried out at two taxonomic ranks: within Zingiberaceae and within genus Hedychium using correlations, generalized linear models and phylogenetic least square models. RESULTS The most frequent changes in chromosome number within Zingiberaceae were noted to be demi-polyploidization and polyploidization (~57% of the time), followed by ascending dysploidy (~27%). The subfamily Zingiberoideae showed descending dysploidy at its base, while Alpinioideae showed polyploidization at its internal nodes. Although chromosome counts and genome sizes did not corroborate with each other, suggesting that they are not equivalent; higher chromosome number variations and higher genome size variations were associated with higher taxonomic diversity and wider biogeographic distribution. CONCLUSIONS Within Zingiberaceae, multiple incidences of polyploidization were discovered, and cytogenetic events appear to have reduced the genome sizes and increased taxonomic diversity, distributional ranges and invasiveness.
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Affiliation(s)
- Aleena Xavier
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, Madhya Pradesh, India
| | - Ritu Yadav
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, Madhya Pradesh, India
| | - Vinita Gowda
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, Madhya Pradesh, India
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50
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Schreiber M, Jayakodi M, Stein N, Mascher M. Plant pangenomes for crop improvement, biodiversity and evolution. Nat Rev Genet 2024; 25:563-577. [PMID: 38378816 DOI: 10.1038/s41576-024-00691-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 02/22/2024]
Abstract
Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.
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Affiliation(s)
- Mona Schreiber
- Department of Biology, University of Marburg, Marburg, Germany
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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