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Alenazi AS, Pereira L, Christin PA, Osborne CP, Dunning LT. Identifying genomic regions associated with C 4 photosynthetic activity and leaf anatomy in Alloteropsis semialata. THE NEW PHYTOLOGIST 2024. [PMID: 38953386 DOI: 10.1111/nph.19933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024]
Abstract
C4 photosynthesis is a complex trait requiring multiple developmental and metabolic alterations. Despite this complexity, it has independently evolved over 60 times. However, our understanding of the transition to C4 is complicated by the fact that variation in photosynthetic type is usually segregated between species that diverged a long time ago. Here, we perform a genome-wide association study (GWAS) using the grass Alloteropsis semialata, the only known species to have C3, intermediate, and C4 accessions that recently diverged. We aimed to identify genomic regions associated with the strength of the C4 cycle (measured using δ13C), and the development of C4 leaf anatomy. Genomic regions correlated with δ13C include regulators of C4 decarboxylation enzymes (RIPK), nonphotochemical quenching (SOQ1), and the development of Kranz anatomy (SCARECROW-LIKE). Regions associated with the development of C4 leaf anatomy in the intermediate individuals contain additional leaf anatomy regulators, including those responsible for vein patterning (GSL8) and meristem determinacy (GIF1). The parallel recruitment of paralogous leaf anatomy regulators between A. semialata and other C4 lineages implies the co-option of these genes is context-dependent, which likely has implications for the engineering of the C4 trait into C3 species.
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Affiliation(s)
- Ahmed S Alenazi
- Department of Biological Sciences, College of Science, Northern Border University, Arar, 91431, Saudi Arabia
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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2
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Yu H, Li Y, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S. Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nat Protoc 2024; 19:1623-1678. [PMID: 38514839 DOI: 10.1038/s41596-024-00966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/20/2023] [Indexed: 03/23/2024]
Abstract
The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.
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Affiliation(s)
- Hongwei Yu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Wentao Han
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fuyun Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuanting Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
- Laboratory for Marine Fisheries and Aquaculture, Laoshan Laboratory, Qingdao, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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Keeling PJ. Horizontal gene transfer in eukaryotes: aligning theory with data. Nat Rev Genet 2024; 25:416-430. [PMID: 38263430 DOI: 10.1038/s41576-023-00688-5] [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: 12/06/2023] [Indexed: 01/25/2024]
Abstract
Horizontal gene transfer (HGT), or lateral gene transfer, is the non-sexual movement of genetic information between genomes. It has played a pronounced part in bacterial and archaeal evolution, but its role in eukaryotes is less clear. Behaviours unique to eukaryotic cells - phagocytosis and endosymbiosis - have been proposed to increase the frequency of HGT, but nuclear genomes encode fewer HGTs than bacteria and archaea. Here, I review the existing theory in the context of the growing body of data on HGT in eukaryotes, which suggests that any increased chance of acquiring new genes through phagocytosis and endosymbiosis is offset by a reduced need for these genes in eukaryotes, because selection in most eukaryotes operates on variation not readily generated by HGT.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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Sotelo G, Gamboa S, Dunning LT, Christin PA, Varela S. C 4 photosynthesis provided an immediate demographic advantage to populations of the grass Alloteropsis semialata. THE NEW PHYTOLOGIST 2024; 242:774-785. [PMID: 38389217 DOI: 10.1111/nph.19606] [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: 08/29/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
C4 photosynthesis is a key innovation in land plant evolution, but its immediate effects on population demography are unclear. We explore the early impact of the C4 trait on the trajectories of C4 and non-C4 populations of the grass Alloteropsis semialata. We combine niche models projected into paleoclimate layers for the last 5 million years with demographic models based on genomic data. The initial split between C4 and non-C4 populations was followed by a larger expansion of the ancestral C4 population, and further diversification led to the unparalleled expansion of descendant C4 populations. Overall, C4 populations spread over three continents and achieved the highest population growth, in agreement with a broader climatic niche that rendered a large potential range over time. The C4 populations that remained in the region of origin, however, experienced lower population growth, rather consistent with local geographic constraints. Moreover, the posterior transfer of some C4-related characters to non-C4 counterparts might have facilitated the recent expansion of non-C4 populations in the region of origin. Altogether, our findings support that C4 photosynthesis provided an immediate demographic advantage to A. semialata populations, but its effect might be masked by geographic contingencies.
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Affiliation(s)
- Graciela Sotelo
- Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
| | - Sara Gamboa
- Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
- Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, S10 2TN, Sheffield, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, S10 2TN, Sheffield, UK
| | - Sara Varela
- Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
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Raimondeau P, Bianconi ME, Pereira L, Parisod C, Christin PA, Dunning LT. Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage. THE NEW PHYTOLOGIST 2023; 240:2072-2084. [PMID: 37793435 DOI: 10.1111/nph.19272] [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: 06/05/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023]
Abstract
Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes (32-100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6-28 per Ma) and subsequent losses (11-24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02-0.8% per Ma). This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.
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Affiliation(s)
- Pauline Raimondeau
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Laboratoire Evolution et Diversité Biologique, UMR5174, CNRS/IRD/Université Toulouse 3, Toulouse, 31062, France
| | - Matheus E Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Christian Parisod
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, 1700, Switzerland
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, 1700, Switzerland
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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Pereira L, Bianconi ME, Osborne CP, Christin PA, Dunning LT. Alloteropsis semialata as a study system for C4 evolution in grasses. ANNALS OF BOTANY 2023; 132:365-382. [PMID: 37422712 PMCID: PMC10667010 DOI: 10.1093/aob/mcad078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/07/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND Numerous groups of plants have adapted to CO2 limitations by independently evolving C4 photosynthesis. This trait relies on concerted changes in anatomy and biochemistry to concentrate CO2 within the leaf and thereby boost productivity in tropical conditions. The ecological and economic importance of C4 photosynthesis has motivated intense research, often relying on comparisons between distantly related C4 and non-C4 plants. The photosynthetic type is fixed in most species, with the notable exception of the grass Alloteropsis semialata. This species includes populations exhibiting the ancestral C3 state in southern Africa, intermediate populations in the Zambezian region and C4 populations spread around the palaeotropics. SCOPE We compile here the knowledge on the distribution and evolutionary history of the Alloteropsis genus as a whole and discuss how this has furthered our understanding of C4 evolution. We then present a chromosome-level reference genome for a C3 individual and compare the genomic architecture with that of a C4 accession of A. semialata. CONCLUSIONS Alloteropsis semialata is one of the best systems in which to investigate the evolution of C4 photosynthesis because the genetic and phenotypic variation provides a fertile ground for comparative and population-level studies. Preliminary comparative genomic investigations show that the C3 and C4 genomes are highly syntenic and have undergone a modest amount of gene duplication and translocation since the different photosynthetic groups diverged. The background knowledge and publicly available genomic resources make A. semialata a great model for further comparative analyses of photosynthetic diversification.
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Affiliation(s)
- Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN,UK
| | - Matheus E Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN,UK
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN,UK
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN,UK
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7
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Schlüter U, Bouvier JW, Guerreiro R, Malisic M, Kontny C, Westhoff P, Stich B, Weber APM. Brassicaceae display variation in efficiency of photorespiratory carbon-recapturing mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6631-6649. [PMID: 37392176 PMCID: PMC10662225 DOI: 10.1093/jxb/erad250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/30/2023] [Indexed: 07/03/2023]
Abstract
Carbon-concentrating mechanisms enhance the carboxylase efficiency of Rubisco by providing supra-atmospheric concentrations of CO2 in its surroundings. Beside the C4 photosynthesis pathway, carbon concentration can also be achieved by the photorespiratory glycine shuttle which requires fewer and less complex modifications. Plants displaying CO2 compensation points between 10 ppm and 40 ppm are often considered to utilize such a photorespiratory shuttle and are termed 'C3-C4 intermediates'. In the present study, we perform a physiological, biochemical, and anatomical survey of a large number of Brassicaceae species to better understand the C3-C4 intermediate phenotype, including its basic components and its plasticity. Our phylogenetic analysis suggested that C3-C4 metabolism evolved up to five times independently in the Brassicaceae. The efficiency of the pathway showed considerable variation. Centripetal accumulation of organelles in the bundle sheath was consistently observed in all C3-C4-classified taxa, indicating a crucial role for anatomical features in CO2-concentrating pathways. Leaf metabolite patterns were strongly influenced by the individual species, but accumulation of photorespiratory shuttle metabolites glycine and serine was generally observed. Analysis of phosphoenolpyruvate carboxylase activities suggested that C4-like shuttles have not evolved in the investigated Brassicaceae. Convergent evolution of the photorespiratory shuttle indicates that it represents a distinct photosynthesis type that is beneficial in some environments.
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Affiliation(s)
- Urte Schlüter
- Institute of Plant Biochemistry, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Jacques W Bouvier
- Institute of Plant Biochemistry, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Ricardo Guerreiro
- Institute for Quantitative Genetics and Genomics of Plants, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Milena Malisic
- Institute of Plant Biochemistry, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Carina Kontny
- Institute of Plant Biochemistry, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Philipp Westhoff
- Metabolomics and Metabolism Laboratory, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence for Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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Carscadden KA, Batstone RT, Hauser FE. Origins and evolution of biological novelty. Biol Rev Camb Philos Soc 2023; 98:1472-1491. [PMID: 37056155 DOI: 10.1111/brv.12963] [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: 01/28/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.
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Affiliation(s)
- Kelly A Carscadden
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St, Boulder, CO, 80309, USA
| | - Rebecca T Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
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Chen K, Liu H, Blevins T, Hao J, Otten L. Extensive natural Agrobacterium-induced transformation in the genus Camellia. PLANTA 2023; 258:81. [PMID: 37715842 DOI: 10.1007/s00425-023-04234-9] [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: 07/11/2023] [Accepted: 08/30/2023] [Indexed: 09/18/2023]
Abstract
MAIN CONCLUSION The genus Camellia underwent extensive natural transformation by Agrobacterium. Over a period of 15 million years, at least 12 different inserts accumulated in 72 investigated Camellia species. Like a wide variety of other wild and cultivated plants, Camellia species carry cellular T-DNA sequences (cT-DNAs) in their nuclear genomes, resulting from natural Agrobacterium-mediated transformation. Short and long DNA sequencing reads of 435 accessions belonging to 72 Camellia species (representing 12 out of 14 sections) were investigated for the occurrence of cT-DNA insertions. In all, 12 different cT-DNAs were recovered, either completely or partially, called CaTA to CaTL. Divergence analysis of internal cT-DNA repeats revealed that the insertion events span a period from 0.075 to 15 Mio years ago, and yielded an average transformation frequency of one event per 1.25 Mio years. The two oldest inserts, CaTA and CaTD, have been modified by spontaneous deletions and inversions, and by insertion of various plant sequences. In those cases where enough accessions were available (C. japonica, C. oleifera, C. chekiangoleosa, C. sasanqua and C. pitardii), the younger cT-DNA inserts showed a patchy distribution among different accessions of each species, indicating that they are not genetically fixed. It could be shown that Camellia breeding has led to intersectional transfer of cT-DNAs. Altogether, the cT-DNAs cover 374 kb, and carry 47 open reading frames (ORFs). Two Camellia cT-DNA genes, CaTH-orf358 and CaTK-orf8, represent new types of T-DNA genes. With its large number of cT-DNA sequences, the genus Camellia constitutes an interesting model for the study of natural Agrobacterium transformants.
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Affiliation(s)
- Ke Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Hai Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes du C.N.R.S., Rue du Général Zimmer 12, 67084, Strasbourg, France
| | - Jie Hao
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Léon Otten
- Institut de Biologie Moléculaire des Plantes du C.N.R.S., Rue du Général Zimmer 12, 67084, Strasbourg, France
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10
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Lesica P, Lavin M. Will molecular phylogenetics help decrease nomenclatural instability? AMERICAN JOURNAL OF BOTANY 2023; 110:e16219. [PMID: 37561649 DOI: 10.1002/ajb2.16219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/12/2023]
Affiliation(s)
- Peter Lesica
- Division of Biological Sciences, University of Montana, Missoula, 59812, Montana, USA
| | - Matt Lavin
- Plant Sciences and Plant Pathology Department, Montana State University, Bozeman, 59717, Montana, USA
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11
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Li J, Shen J, Wang R, Chen Y, Zhang T, Wang H, Guo C, Qi J. The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution. PLANT COMMUNICATIONS 2023; 4:100422. [PMID: 35957520 PMCID: PMC9860166 DOI: 10.1016/j.xplc.2022.100422] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 05/27/2023]
Abstract
Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation. Polyploidization events have been extensively studied in some Fabaceae plants, but the occurrence of new genes is still concealed, owing to a lack of genomic information on certain species of the basal clade of Fabaceae. Cercis chinensis (Cercidoideae) is one such species; it diverged earliest from Fabaceae and is essential for phylogenomic studies and new gene predictions in Fabaceae. To facilitate genomic studies on Fabaceae, we performed genome sequencing of C. chinensis and obtained a 352.84 Mb genome, which was further assembled into seven pseudochromosomes with 30 612 predicted protein-coding genes. Compared with other legume genomes, that of C. chinensis exhibits no lineage-specific polyploidization event. Further phylogenomic analyses of 22 legumes and 11 other angiosperms revealed that many gene families are lineage specific before and after the diversification of Fabaceae. Among them, dozens of genes are candidates for new genes that have evolved from intergenic regions and are thus regarded as de novo-originated genes. They differ significantly from established genes in coding sequence length, exon number, guanine-cytosine content, and expression patterns among tissues. Functional analysis revealed that many new genes are related to asparagine metabolism. This study represents an important advance in understanding the evolutionary pattern of new genes in legumes and provides a valuable resource for plant phylogenomic studies.
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Affiliation(s)
- Jinglong Li
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jingting Shen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Rui Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yamao Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Haifeng Wang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
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12
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Wang Y, Shahid MQ. Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Gastrodia elata Blume. FRONTIERS IN PLANT SCIENCE 2023; 13:1035157. [PMID: 36684780 PMCID: PMC9848658 DOI: 10.3389/fpls.2022.1035157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Gastrodia elata Blume (GE) (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). GE is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. G. elata Blume forma elata (GEE) and G. elata Bl.f.glauca (GEG) are two common forms that naturally grow in different habitats with difference in altitude and latitude. G. elata Bl.f.viridis (GEV) often occurs sporadically in cultivated populations of GEE and GEG. However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of GEE and GEG have not been revealed. Here, we assembled a chromosome-level draft genome of GEE with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 GEE accessions, nine GEG accessions, and 10 GEV accessions, and identified two independent genetic lineages: GEG_pedigree (GEG individuals and GEV individuals collected from GEG populations) and GEE_pedigree (GEE individuals and GEV individuals collected from GEE populations), which strongly support the taxonomic status of GEE and GEG as subspecies, not as different forms. In highly differentiated genomic regions of GEE_pedigree and GEG_pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between GEE_pedigree and GEG_pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of GE and the new findings would deepen the understanding about ecological adaptation and evolution of GE.
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Affiliation(s)
- Yunsheng Wang
- School of Health and Life Science, Kaili University, Kaili, Guizhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
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13
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Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence. Nat Ecol Evol 2023; 7:155-170. [PMID: 36604553 PMCID: PMC9834058 DOI: 10.1038/s41559-022-01932-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/12/2022] [Indexed: 01/07/2023]
Abstract
On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype-phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of non-synonymous to synonymous substitution rate ratios and developed the novel metric ωC, which measures the error-corrected convergence rate of protein evolution. While ωC distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally non-trivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype-phenotype associations, even in lineages that diverged for hundreds of millions of years.
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14
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Li L, Peng S, Wang Z, Zhang T, Li H, Xiao Y, Li J, Liu Y, Yin H. Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT. FRONTIERS IN PLANT SCIENCE 2022; 13:1025122. [PMID: 36407614 PMCID: PMC9667741 DOI: 10.3389/fpls.2022.1025122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na+/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | | | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Teng Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- Hunan Urban and Rural Environmental Construction Co., Ltd, Changsha, China
| | - Hongguang Li
- Hunan Tobacco Science Institute, Changsha, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Jingjun Li
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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15
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Dunning LT, Olofsson JK, Papadopulos AST, Hibdige SGS, Hidalgo O, Leitch IJ, Baleeiro PC, Ntshangase S, Barker N, Jobson RW. Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia. Mol Ecol 2022; 31:5846-5860. [PMID: 36089907 PMCID: PMC9828686 DOI: 10.1111/mec.16691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023]
Abstract
Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonized by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason that T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.
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Affiliation(s)
- Luke T. Dunning
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Jill K. Olofsson
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenFrederiksberg CDenmark
| | | | - Samuel G. S. Hibdige
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Oriane Hidalgo
- Royal Botanic GardensSurreyUK,Institut Botànic de Barcelona (IBB), CSIC‐Ajuntament de BarcelonaBarcelonaSpain
| | | | - Paulo C. Baleeiro
- Department of Biological ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | | | - Nigel Barker
- Department of Plant and Soil SciencesUniversity of PretoriaHatfieldSouth Africa
| | - Richard W. Jobson
- National Herbarium of New South Wales, Australian Institute of Botanical ScienceSydneyNew South WalesAustralia
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16
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Wu D, Hu Y, Akashi S, Nojiri H, Guo L, Ye C, Zhu Q, Okada K, Fan L. Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1354-1367. [PMID: 35781905 PMCID: PMC9544640 DOI: 10.1111/tpj.15893] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 05/31/2023]
Abstract
Momilactone A, an important plant labdane-related diterpenoid, functions as a phytoalexin against pathogens and an allelochemical against neighboring plants. The genes involved in the biosynthesis of momilactone A are found in clusters, i.e., momilactone A biosynthetic gene clusters (MABGCs), in the rice and barnyardgrass genomes. In addition, we know little about the origin and evolution of MABGCs. Here, we integrated results from comprehensive phylogeny and comparative genomic analyses of the core genes of MABGC-like clusters and MABGCs in 40 monocot plant genomes, providing convincing evidence for the birth and evolution of MABGCs in grass species. The MABGCs found in the PACMAD clade of the core grass lineage (including Panicoideae and Chloridoideae) originated from a MABGC-like cluster in Triticeae (BOP clade) via lateral gene transfer (LGT) and followed by recruitment of MAS1/2 and CYP76L1 genes. The MABGCs in Oryzoideae originated from PACMAD through another LGT event and lost CYP76L1 afterwards. The Oryza MABGC and another Oryza diterpenoid cluster c2BGC are two distinct clusters, with the latter originating from gene duplication and relocation within Oryzoideae. Further comparison of the expression patterns of the MABGC genes between rice and barnyardgrass in response to pathogen infection and allelopathy provides novel insights into the functional innovation of MABGCs in plants. Our results demonstrate LGT-mediated origination of MABGCs in grass and shed lights into the evolutionary innovation and optimization of plant biosynthetic pathways.
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Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang UniversityYonyou Industrial ParkSanya572025China
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Yiyu Hu
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Shota Akashi
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Hideaki Nojiri
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou310006China
| | - Chu‐Yu Ye
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Qian‐Hao Zhu
- CSIRO Agriculture and Food, Black Mountain LaboratoriesCanberraACT2601Australia
| | - Kazunori Okada
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Longjiang Fan
- Hainan Institute of Zhejiang UniversityYonyou Industrial ParkSanya572025China
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
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17
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Philips JG, Martin-Avila E, Robold AV. Horizontal gene transfer from genetically modified plants - Regulatory considerations. Front Bioeng Biotechnol 2022; 10:971402. [PMID: 36118580 PMCID: PMC9471246 DOI: 10.3389/fbioe.2022.971402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.
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18
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Bartha L, Mandáková T, Kovařík A, Bulzu PA, Rodde N, Mahelka V, Lysak MA, Fustier MA, Šafář J, Cápal P, Keresztes L, Banciu HL. Intact ribosomal DNA arrays of Potentilla origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer. THE NEW PHYTOLOGIST 2022; 235:1246-1259. [PMID: 35460285 DOI: 10.1111/nph.18171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support this hypothesis by carrying out genomic, molecular, and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host, albeit much less efficiently than the native counterpart. This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer.
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Affiliation(s)
- László Bartha
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeş-Bolyai University, 400271, Cluj-Napoca, Romania
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265, Brno, Czech Republic
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, 370 05, České Budějovice, Czech Republic
| | - Nathalie Rodde
- French Plant Genomic Resource Center, INRAE-CNRGV, 31320, Castanet Tolosan, France
| | - Václav Mahelka
- Institute of Botany, Czech Academy of Sciences, 25243, Průhonice, Czech Republic
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | | | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, 779 00, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, 779 00, Olomouc, Czech Republic
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology, Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
- Centre of Systems Biology, Biodiversity and Bioresources (3B), Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
| | - Horia L Banciu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeş-Bolyai University, 400271, Cluj-Napoca, Romania
- Centre of Systems Biology, Biodiversity and Bioresources (3B), Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
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19
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Li W, Liu J, Zhang H, Liu Z, Wang Y, Xing L, He Q, Du H. Plant pan-genomics: recent advances, new challenges, and roads ahead. J Genet Genomics 2022; 49:833-846. [PMID: 35750315 DOI: 10.1016/j.jgg.2022.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 10/18/2022]
Abstract
Pan-genomics can encompass most of the genetic diversity of a species or population and has proved to be a powerful tool for studying genomic evolution and the origin and domestication of species, and for providing information for plant improvement. Plant genomics has greatly progressed because of improvements in sequencing technologies and the rapid reduction of sequencing costs. Nevertheless, pan-genomics still presents many challenges, including computationally intensive assembly methods, high costs with large numbers of samples, ineffective integration of big data, and difficulty in applying it to downstream multi-omics analysis and breeding research. In this review, we summarize the definition and recent achievements of plant pan-genomics, computational technologies used for pan-genome construction, and the applications of pan-genomes in plant genomics and molecular breeding. We also discuss challenges and perspectives for future pan-genomics studies and provide a detailed pipeline for sample selection, genome assembly and annotation, structural variation identification, and construction and application of graph-based pan-genomes. The aim is to provide important guidance for plant pan-genome research and a better understanding of the genetic basis of genome evolution, crop domestication, and phenotypic diversity for future studies.
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Affiliation(s)
- Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Jianan Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Hongyu Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Ze Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Yu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Longsheng Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Qiang He
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071000, China.
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20
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Mercado MA, Studer AJ. Meeting in the Middle: Lessons and Opportunities from Studying C 3-C 4 Intermediates. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:43-65. [PMID: 35231181 DOI: 10.1146/annurev-arplant-102720-114201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The discovery of C3-C4 intermediate species nearly 50 years ago opened up a new avenue for studying the evolution of photosynthetic pathways. Intermediate species exhibit anatomical, biochemical, and physiological traits that range from C3 to C4. A key feature of C3-C4 intermediates that utilize C2 photosynthesis is the improvement in photosynthetic efficiency compared with C3 species. Although the recruitment of some core enzymes is shared across lineages, there is significant variability in gene expression patterns, consistent with models that suggest numerous evolutionary paths from C3 to C4 photosynthesis. Despite the many evolutionary trajectories, the recruitment of glycine decarboxylase for C2 photosynthesis is likely required. As technologies enable high-throughput genotyping and phenotyping, the discovery of new C3-C4 intermediates species will enrich comparisons between evolutionary lineages. The investigation of C3-C4 intermediate species will enhance our understanding of photosynthetic mechanisms and evolutionary processes and will potentially aid in crop improvement.
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Affiliation(s)
| | - Anthony J Studer
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA; ,
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21
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Ahmad A, Su X, Harris AJ, Ren Z. Closing the Gap: Horizontal Transfer of Mariner Transposons between Rhus Gall Aphids and Other Insects. BIOLOGY 2022; 11:731. [PMID: 35625459 PMCID: PMC9139091 DOI: 10.3390/biology11050731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022]
Abstract
Horizontal transfer of transposons (HTT) is an essential source of genomic evolution in eukaryotes. The HTT dynamics are well characterized in eukaryotes, including insects; however, there is a considerable gap in knowledge about HTT regarding many eukaryotes' species. In this study, we analyzed the events of the HTT between Rhus gall aphids (Hemiptera) and other insects. We analyzed the Mariner-like transposable elements (MLEs) belonging to Rhus gall aphids for the possible HT events. The MLEs have a patchy distribution and high similarity over the entire element length with insect MLEs from different orders. We selected representative sequences from the Rhus gall MLEs and identified five events of HT between MLEs of Rhus gall aphids and other insects from five different orders. We also found multiple HTT events among the MLEs of insects from the five orders, demonstrating that these Mariner elements have been involved in recurrent HT between Rhus gall aphids and other insects. Our current study closed the knowledge gap surrounding HTT and reported the events between Rhus gall aphids and other insects for the first time. We believe that this study about HTT events will help us understand the evolution and spread of transposable elements in the genomes of Rhus gall aphids.
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Affiliation(s)
- Aftab Ahmad
- School of Life Science, Shanxi University, Taiyuan 030006, China;
| | - Xu Su
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810016, China;
- School of Life Sciences, Qinghai Normal University, Xining 810008, China
| | - AJ Harris
- South China Botanical Garden, Chinese Academy of Sciences, Tianhe District, Guangzhou 510650, China;
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan 030006, China;
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22
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Wu D, Jiang B, Ye CY, Timko MP, Fan L. Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants. PLANT COMMUNICATIONS 2022; 3:100320. [PMID: 35576160 PMCID: PMC9251436 DOI: 10.1016/j.xplc.2022.100320] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 05/11/2023]
Abstract
Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster (BGC) in maize. Data mining of 41 high-quality grass genomes identified complete Bx clusters (containing genes Bx1-Bx5 and Bx8) in three genera (Zea, Echinochloa, and Dichanthelium) of Panicoideae and partial clusters in Triticeae. The Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx genes. An ancient Bx cluster that included additional Bx genes (e.g., Bx6) is presumed to have been present in ancestral Panicoideae. The ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer (HT) from the ancestral Panicoideae and later separated into multiple segments on different chromosomes. Bx6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae, as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays, moved to other chromosomes in Echinochloa, and even lost in Dichanthelium. Further investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass family. This study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs.
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Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Bowen Jiang
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Longjiang Fan
- Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
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23
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Bianconi ME, Sotelo G, Curran EV, Milenkovic V, Samaritani E, Dunning LT, Bertolino LT, Osborne CP, Christin PA. Upregulation of C 4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass. PLANT, CELL & ENVIRONMENT 2022. [PMID: 35201618 DOI: 10.1101/2021.08.10.455822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
C4 photosynthesis is thought to have evolved via intermediate stages, with changes towards the C4 phenotype gradually enhancing photosynthetic performance. This hypothesis is widely supported by modelling studies, but experimental tests are missing. Mixing of C4 components to generate artificial intermediates can be achieved via crossing, and the grass Alloteropsis semialata represents an outstanding study system since it includes C4 and non-C4 populations. Here, we analyse F1 hybrids between C3 and C4 , and C3 +C4 and C4 genotypes to determine whether the acquisition of C4 characteristics increases photosynthetic performance. The hybrids have leaf anatomical characters and C4 gene expression profiles that are largely intermediate between those of their parents. Carbon isotope ratios are similarly intermediate, which suggests that a partial C4 cycle coexists with C3 carbon fixation in the hybrids. This partial C4 phenotype is associated with C4 -like photosynthetic efficiency in C3 +C4 × C4 , but not in C3 × C4 hybrids, which are overall less efficient than both parents. Our results support the hypothesis that the photosynthetic gains from the upregulation of C4 characteristics depend on coordinated changes in anatomy and biochemistry. The order of acquisition of C4 components is thus constrained, with C3 +C4 species providing an essential step for C4 evolution.
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Affiliation(s)
- Matheus E Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Emma V Curran
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Vanja Milenkovic
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Emanuela Samaritani
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Lígia T Bertolino
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
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24
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Bianconi ME, Sotelo G, Curran EV, Milenkovic V, Samaritani E, Dunning LT, Bertolino LT, Osborne CP, Christin P. Upregulation of C 4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass. PLANT, CELL & ENVIRONMENT 2022; 45:1398-1411. [PMID: 35201618 PMCID: PMC9314825 DOI: 10.1111/pce.14301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/20/2021] [Accepted: 11/21/2021] [Indexed: 06/14/2023]
Abstract
C4 photosynthesis is thought to have evolved via intermediate stages, with changes towards the C4 phenotype gradually enhancing photosynthetic performance. This hypothesis is widely supported by modelling studies, but experimental tests are missing. Mixing of C4 components to generate artificial intermediates can be achieved via crossing, and the grass Alloteropsis semialata represents an outstanding study system since it includes C4 and non-C4 populations. Here, we analyse F1 hybrids between C3 and C4 , and C3 +C4 and C4 genotypes to determine whether the acquisition of C4 characteristics increases photosynthetic performance. The hybrids have leaf anatomical characters and C4 gene expression profiles that are largely intermediate between those of their parents. Carbon isotope ratios are similarly intermediate, which suggests that a partial C4 cycle coexists with C3 carbon fixation in the hybrids. This partial C4 phenotype is associated with C4 -like photosynthetic efficiency in C3 +C4 × C4 , but not in C3 × C4 hybrids, which are overall less efficient than both parents. Our results support the hypothesis that the photosynthetic gains from the upregulation of C4 characteristics depend on coordinated changes in anatomy and biochemistry. The order of acquisition of C4 components is thus constrained, with C3 +C4 species providing an essential step for C4 evolution.
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Affiliation(s)
- Matheus E. Bianconi
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Emma V. Curran
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Vanja Milenkovic
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Emanuela Samaritani
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Luke T. Dunning
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Lígia T. Bertolino
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Colin P. Osborne
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Pascal‐Antoine Christin
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
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25
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Delmont TO, Gaia M, Hinsinger DD, Frémont P, Vanni C, Fernandez-Guerra A, Eren AM, Kourlaiev A, d'Agata L, Clayssen Q, Villar E, Labadie K, Cruaud C, Poulain J, Da Silva C, Wessner M, Noel B, Aury JM, de Vargas C, Bowler C, Karsenti E, Pelletier E, Wincker P, Jaillon O, Acinas SG, Bork P, Karsenti E, Bowler C, Sardet C, Stemmann L, de Vargas C, Wincker P, Lescot M, Babin M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Jaillon O, Kandels S, Iudicone D, Ogata H, Pesant S, Sullivan MB, Not F, Lee KB, Boss E, Cochrane G, Follows M, Poulton N, Raes J, Sieracki M, Speich S. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean. CELL GENOMICS 2022; 2:100123. [PMID: 36778897 PMCID: PMC9903769 DOI: 10.1016/j.xgen.2022.100123] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 12/10/2021] [Accepted: 04/04/2022] [Indexed: 12/20/2022]
Abstract
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
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Affiliation(s)
- Tom O. Delmont
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Corresponding author
| | - Morgan Gaia
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Damien D. Hinsinger
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Chiara Vanni
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - A. Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity at Oldenburg, Germany
| | - Artem Kourlaiev
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Leo d'Agata
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Quentin Clayssen
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Emilie Villar
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Corinne Cruaud
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Marc Wessner
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Tara Oceans CoordinatorsSunagawaShinichi12AcinasSilvia G.13BorkPeer141516KarsentiEric171819BowlerChris1718SardetChristian1720StemmannLars1720de VargasColomban1721WinckerPatrick1722LescotMagali1723BabinMarcel1724GorskyGabriel1720GrimsleyNigel172526GuidiLionel1720HingampPascal1723JaillonOlivier1722KandelsStefanie1417IudiconeDaniele27OgataHiroyuki28PesantStéphane2930SullivanMatthew B.313233NotFabrice21LeeKarp-Boss34BossEmmanuel34CochraneGuy35FollowsMichael36PoultonNicole37RaesJeroen383940SierackiMike37SpeichSabrina4142Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, EtH Zürich, Zürich, SwitzerlandDepartment of Marine Biology and Oceanography, Institute of Marine Sciences–CsiC, Barcelona, SpainStructural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, GermanyMax Delbrück Center for Molecular Medicine, Berlin, GermanyDepartment of Bioinformatics, Biocenter, University of Würzburg, Würzburg, GermanyResearch Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOsee, Paris, FranceInstitut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, FranceDirectors’ Research, European Molecular Biology Laboratory, Heidelberg, GermanySorbonne Université, CNRS, Laboratoire D’Océanographie de Villefranche, Villefranche- sur- Mer, FranceSorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, FranceGénomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l’Énergie Atomique, CNrs, Université Evry, Université Paris- Saclay, Evry, FranceAix Marseille Universit/e, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, FranceDépartement de Biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)–CNRS (France), Université Laval, Quebec, QC, CanadaCNRS UMR 7232, Biologie Intégrative des Organismes Marins, Banyuls- sur- Mer, FranceSorbonne Universités Paris 06, OOB UPMC, Banyuls- sur- Mer, FranceStazione Zoologica Anton Dohrn, Naples, ItalyInstitute for Chemical Research, Kyoto University, Kyoto, JapanPaNGaea, University of Bremen, Bremen, GermanyMaruM, Center for Marine Environmental Sciences, University of Bremen, Bremen, GermanyDepartment of Microbiology, The Ohio State University, Columbus, OH, USADepartment of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USACenter for RNA Biology, The Ohio State University, Columbus, OH, USASchool of Marine Sciences, University of Maine, Orono, ME, USAEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UKDepartment of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USABigelow Laboratory for Ocean Sciences, East Boothbay, ME, USADepartment of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, BelgiumCenter for the Biology of Disease, VIB KU Leuven, Leuven, BelgiumDepartment of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, BelgiumDepartment of Geosciences, Laboratoire de Météorologie Dynamique, École Normale Supérieure, Paris, FranceOcean Physics Laboratory, University of Western Brittany, Brest, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Karsenti
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France,Directors’ Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
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26
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Huang W, Zhang L, Columbus JT, Hu Y, Zhao Y, Tang L, Guo Z, Chen W, McKain M, Bartlett M, Huang CH, Li DZ, Ge S, Ma H. A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C 4 photosynthesis. MOLECULAR PLANT 2022; 15:755-777. [PMID: 35093593 DOI: 10.1016/j.molp.2022.01.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/09/2021] [Accepted: 01/24/2022] [Indexed: 05/11/2023]
Abstract
Poaceae (the grasses) includes rice, maize, wheat, and other crops, and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11 000 species with a global distribution that contributes to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong phylogenetic support for their monophyly. However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain. To better resolve the Poaceae phylogeny, we generated 342 transcriptomic and seven genomic datasets; these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1200 low-copy nuclear genes were retrieved from these datasets, with several subsets obtained using additional criteria, and used for coalescent analyses to reconstruct a Poaceae phylogeny. Our results strongly support the monophyly of 11 subfamilies; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. Molecular clock analyses estimated the crown age of Poaceae to be ∼101 million years old. Ancestral character reconstruction of C3/C4 photosynthesis supports the hypothesis of multiple independent origins of C4 photosynthesis. These origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which suggests that members of three paralogous subclades (ppc-aL1a, ppc-aL1b, and ppc-B2) were recruited as functional C4ppc genes. This study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.
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Affiliation(s)
- Weichen Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - J Travis Columbus
- Rancho Santa Ana Botanic Garden and Claremont Graduate University, 1500 North College Avenue, Claremont, CA 91711, USA
| | - Yi Hu
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Yiyong Zhao
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Lin Tang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhenhua Guo
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Wenli Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Michael McKain
- Department of Biological Sciences, University of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL 35487, USA
| | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, 611 North Pleasant Street, 221 Morrill 3, Amherst, MA 01003 USA
| | - Chien-Hsun Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA.
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27
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Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int J Mol Sci 2022; 23:2671. [PMID: 35269811 PMCID: PMC8910360 DOI: 10.3390/ijms23052671] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (C.G.T.F.); (B.J.N.); (M.F.D.); (M.G.); (J.P.); (P.E.B.); (P.M.F.); (J.B.)
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28
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Curran EV, Scott MS, Olofsson JK, Nyirenda F, Sotelo G, Bianconi ME, Manzi S, Besnard G, Pereira L, Christin PA. Hybridization boosts dispersal of two contrasted ecotypes in a grass species. Proc Biol Sci 2022; 289:20212491. [PMID: 35078363 PMCID: PMC8790336 DOI: 10.1098/rspb.2021.2491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and influence rates of hybridization. How these dynamics affect the emergence and spread of novel phenotypes remains only partially understood. Here, we use phylogenomics and population genomics to retrace the origin and spread of two geographically overlapping ecotypes of the African grass Alloteropsis angusta. In addition to an ecotype inhabiting wetlands, we report the existence of a previously undescribed ecotype inhabiting Miombo woodlands and grasslands. The two ecotypes are consistently associated with different nuclear groups, which represent an advanced stage of divergence with secondary low-level gene flow. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can enter the seeds of the other via occasional pollen movements with sorting of nuclear groups in subsequent generations. The contrasting ecotypes of A. angusta can thus use each other as a gateway to new locations across a large part of Africa, showing that hybridization can facilitate the geographical dispersal of distinct ecotypes of the same grass species.
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Affiliation(s)
- Emma V. Curran
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Matilda S. Scott
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jill K. Olofsson
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Matheus E. Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Sophie Manzi
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III – Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III – Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmF C genes. BMC Genomics 2021; 22:816. [PMID: 34772334 PMCID: PMC8588681 DOI: 10.1186/s12864-021-08105-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Background The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08105-z.
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Artur MAS, Kajala K. Convergent evolution of gene regulatory networks underlying plant adaptations to dry environments. PLANT, CELL & ENVIRONMENT 2021; 44:3211-3222. [PMID: 34196969 PMCID: PMC8518057 DOI: 10.1111/pce.14143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 06/25/2021] [Indexed: 05/21/2023]
Abstract
Plants transitioned from an aquatic to a terrestrial lifestyle during their evolution. On land, fluctuations on water availability in the environment became one of the major problems they encountered. The appearance of morpho-physiological adaptations to cope with and tolerate water loss from the cells was undeniably useful to survive on dry land. Some of these adaptations, such as carbon concentrating mechanisms (CCMs), desiccation tolerance (DT) and root impermeabilization, appeared in multiple plant lineages. Despite being crucial for evolution on land, it has been unclear how these adaptations convergently evolved in the various plant lineages. Recent advances on whole genome and transcriptome sequencing are revealing that co-option of genes and gene regulatory networks (GRNs) is a common feature underlying the convergent evolution of these adaptations. In this review, we address how the study of CCMs and DT has provided insight into convergent evolution of GRNs underlying plant adaptation to dry environments, and how these insights could be applied to currently emerging understanding of evolution of root impermeabilization through different barrier cell types. We discuss examples of co-option, conservation and innovation of genes and GRNs at the cell, tissue and organ levels revealed by recent phylogenomic (comparative genomic) and comparative transcriptomic studies.
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Affiliation(s)
- Mariana A. S. Artur
- Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Kaisa Kajala
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
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31
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Park M, Sarkhosh A, Tsolova V, El-Sharkawy I. Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity of Vitis. Int J Mol Sci 2021; 22:ijms221910446. [PMID: 34638784 PMCID: PMC8508631 DOI: 10.3390/ijms221910446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/20/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022] Open
Abstract
While horizontally transferred transposable elements (TEs) have been reported in several groups of plants, their importance for genome evolution remains poorly understood. To understand how horizontally transferred TEs contribute to plant genome evolution, we investigated the composition and activity of horizontally transferred TEs in the genomes of four Vitis species. A total of 35 horizontal transfer (HT) events were identified between the four Vitis species and 21 other plant species belonging to 14 different families. We determined the donor and recipient species for 28 of these HTs, with the Vitis species being recipients of 15 of them. As a result of HTs, 8–10 LTR retrotransposon clusters were newly formed in the genomes of the four Vitis species. The activities of the horizontally acquired LTR retrotransposons differed among Vitis species, showing that the consequences of HTs vary during the diversification of the recipient lineage. Our study provides the first evidence that the HT of TEs contributes to the diversification of plant genomes by generating additional TE subfamilies and causing their differential proliferation in host genomes.
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Affiliation(s)
- Minkyu Park
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32308, USA; (M.P.); (V.T.)
| | - Ali Sarkhosh
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
| | - Violeta Tsolova
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32308, USA; (M.P.); (V.T.)
| | - Islam El-Sharkawy
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL 32308, USA; (M.P.); (V.T.)
- Correspondence: ; Tel.: +1-850-599-8685
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32
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Watanabe Y, Spangenberg GC, Shinozuka H. Fungus-originated glucanase and monooxygenase genes in creeping bent grass (Agrostis stolonifera L.). PLoS One 2021; 16:e0257173. [PMID: 34506557 PMCID: PMC8432771 DOI: 10.1371/journal.pone.0257173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/24/2021] [Indexed: 11/24/2022] Open
Abstract
Recent studies have revealed presence of fungus-originated genes in genomes of cool-season grasses, suggesting occurrence of multiple ancestral gene transfer events between the two distant lineages. The current article describes identification of glucanase-like and monooxygenase-like genes from creeping bent grass, as lateral gene transfer candidates. An in silico analysis suggested presence of the glucanase-like gene in Agrostis, Deyeuxia, and Polypogon genera, but not in other species belonging to the clade 1 of the Poeae tribe. Similarly, the monooxygenase-like gene was confined to Agrostis and Deyeuxia genera. A consistent result was obtained from PCR-based screening. The glucanase-like gene was revealed to be ubiquitously expressed in young seedlings of creeping bent grass. Although expression of the monooxygenase-like gene was suggested in plant tissues, the levels were considerably lower than those of the glucanase-like gene. A phylogenetic analysis revealed close relationships of the two genes between the corresponding genes in fungal endophyte species of the Epichloë genus, suggesting that the genes originated from the Epichloë lineage.
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Affiliation(s)
- Yugo Watanabe
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Hiroshi Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
- * E-mail:
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33
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Park M, Christin PA, Bennetzen JL. Sample Sequence Analysis Uncovers Recurrent Horizontal Transfers of Transposable Elements among Grasses. Mol Biol Evol 2021; 38:3664-3675. [PMID: 33964159 PMCID: PMC8382918 DOI: 10.1093/molbev/msab133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Limited genome resources are a bottleneck in the study of horizontal transfer (HT) of DNA in plants. To solve this issue, we tested the usefulness of low-depth sequencing data generated from 19 previously uncharacterized panicoid grasses for HT investigation. We initially searched for horizontally transferred LTR-retrotransposons by comparing the 19 sample sequences to 115 angiosperm genome sequences. Frequent HTs of LTR-retrotransposons were identified solely between panicoids and rice (Oryza sativa). We consequently focused on additional Oryza species and conducted a nontargeted investigation of HT involving the panicoid genus Echinochloa, which showed the most HTs in the first set of analyses. The comparison of nine Echinochloa samples and ten Oryza species identified recurrent HTs of diverse transposable element (TE) types at different points in Oryza history, but no confirmed cases of HT for sequences other than TEs. One case of HT was observed from one Echinochloa species into one Oryza species with overlapping geographic distributions. Variation among species and data sets highlights difficulties in identifying all HT, but our investigations showed that sample sequence analyses can reveal the importance of HT for the diversification of the TE repertoire of plants.
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Affiliation(s)
- Minkyu Park
- Department of Genetics, University of Georgia, Athens, GA, USA
| | | | - Jeffrey L Bennetzen
- Department of Genetics, University of Georgia, Athens, GA, USA
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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34
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Aubin E, El Baidouri M, Panaud O. Horizontal Gene Transfers in Plants. Life (Basel) 2021; 11:life11080857. [PMID: 34440601 PMCID: PMC8401529 DOI: 10.3390/life11080857] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
In plants, as in all eukaryotes, the vertical transmission of genetic information through reproduction ensures the maintenance of the integrity of species. However, many reports over the past few years have clearly shown that horizontal gene transfers, referred to as HGTs (the interspecific transmission of genetic information across reproductive barriers) are very common in nature and concern all living organisms including plants. The advent of next-generation sequencing technologies (NGS) has opened new perspectives for the study of HGTs through comparative genomic approaches. In this review, we provide an up-to-date view of our current knowledge of HGTs in plants.
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35
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Huang Y, Huang W, Meng Z, Braz GT, Li Y, Wang K, Wang H, Lai J, Jiang J, Dong Z, Jin W. Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation. Genome Biol 2021; 22:237. [PMID: 34416918 PMCID: PMC8377971 DOI: 10.1186/s13059-021-02448-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/02/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation. RESULTS In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement. CONCLUSIONS These findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the "fossil" structure variations during genome evolution and speciation.
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Affiliation(s)
- Yumin Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Wei Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Zhuang Meng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Guilherme Tomaz Braz
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yunfei Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Kai Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hai Wang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Zhaobin Dong
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China.
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China.
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36
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Kloub L, Gosselin S, Fullmer M, Graf J, Gogarten JP, Bansal MS. Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes. Mol Biol Evol 2021; 38:2639-2659. [PMID: 33565580 PMCID: PMC8136488 DOI: 10.1093/molbev/msab043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multigene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale data set of over 22,000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multigene transfer. Among other insights, we find that 1) the observed relative frequency of HMGT increases as divergence between genomes increases, 2) HMGTs often have conserved gene functions, and 3) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.
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Affiliation(s)
- Lina Kloub
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
| | - Sean Gosselin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Matthew Fullmer
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,Bioinformatics Institute, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,The Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,The Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Mukul S Bansal
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.,The Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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37
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Pu Q, Fan XT, Sun AQ, Pan T, Li H, Bo Lassen S, An XL, Su JQ. Co-effect of cadmium and iron oxide nanoparticles on plasmid-mediated conjugative transfer of antibiotic resistance genes. ENVIRONMENT INTERNATIONAL 2021; 152:106453. [PMID: 33798824 DOI: 10.1016/j.envint.2021.106453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Conjunctive transfer of antibiotic resistance genes (ARGs) among bacteria driven by plasmids facilitated the evolution and spread of antibiotic resistance. Heavy metal exposure accelerated the plasmid-mediated conjunctive transfer of ARGs. Nanomaterials are well-known adsorbents for heavy metals removal, with the capability of combatting resistant bacteria/facilitating conjunctive transfer of ARGs. However, co-effect of heavy metals and nanomaterials on plasmid-mediated conjunctive transfer of ARGs was still unknown. In this study, we investigated the effect of the simultaneous exposure of Cd2+ and nano Fe2O3 on conjugative transfer of plasmid RP4 from Pseudomonas putida KT2442 to water microbial community. The permeability of bacterial cell membranes, antioxidant enzyme activities and conjugation gene expression were also investigated. The results suggested that the combination of Cd2+ and high concentration nano Fe2O3 (10 mg/L and 100 mg/L) significantly increased conjugative transfer frequencies of RP4 plasmid (p < 0.05). The most transconjugants were detected in the treatment of co-exposure to Cd2+ and nano Fe2O3, the majority of which were identified to be human pathogens. The mechanisms of the exacerbated conjugative transfer of ARGs were involved in the enhancement of cell membrane permeability, antioxidant enzyme activities, and mRNA expression levels of the conjugation genes by the co-effect of Cd2+ and nano Fe2O3. This study confirmed that the simultaneous exposure to Cd2+and nano Fe2O3 exerted a synergetic co-effect on plasmid-mediated conjunctive transfer of ARGs, emphasizing that the co-effect of nanomaterials and heavy metals should be prudently evaluated when combating antibiotic resistance.
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Affiliation(s)
- Qiang Pu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xiao-Ting Fan
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - An-Qi Sun
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Ting Pan
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Simon Bo Lassen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Sino-Danish Center of Education and Research, Beijing, China
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
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Hedenäs L, Larsson P, Cronholm B, Bisang I. Evidence of horizontal gene transfer between land plant plastids has surprising conservation implications. ANNALS OF BOTANY 2021; 127:903-908. [PMID: 33608721 PMCID: PMC8225274 DOI: 10.1093/aob/mcab021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/13/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Horizontal gene transfer (HGT) is an important evolutionary mechanism because it transfers genetic material that may code for traits or functions between species or genomes. It is frequent in mitochondrial and nuclear genomes but has not been demonstrated between plastid genomes of different green land plant species. METHODS We Sanger-sequenced the nuclear internal transcribed spacers (ITS1 and 2) and the plastid rpl16 G2 intron (rpl16). In five individuals with foreign rpl16 we also sequenced atpB-rbcL and trnLUAA-trnFGAA. KEY RESULTS We discovered 14 individuals of a moss species with typical nuclear ITSs but foreign plastid rpl16 from a species of a distant lineage. None of the individuals with three plastid markers sequenced contained all foreign markers, demonstrating the transfer of plastid fragments rather than the entire plastid genome, i.e. entire plastids were not transferred. The two lineages diverged 165-185 Myr BP. The extended time interval since lineage divergence suggests that the foreign rpl16 is more likely explained by HGT than by hybridization or incomplete lineage sorting. CONCLUSIONS We provide the first conclusive evidence of interspecific plastid-to-plastid HGT among land plants. Two aspects are critical: it occurred at several localities during the massive colonization of recently disturbed open habitats that were created by large-scale liming as a freshwater biodiversity conservation measure; and it involved mosses whose unique life cycle includes spores that first develop a filamentous protonema phase. We hypothesize that gene transfer is facilitated when protonema filaments of different species intermix intimately when colonizing disturbed early succession habitats.
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Affiliation(s)
- Lars Hedenäs
- Department of Botany, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
- For correspondence. E-mail
| | - Petter Larsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Bodil Cronholm
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Irene Bisang
- Department of Botany, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
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Hibdige SGS, Raimondeau P, Christin PA, Dunning LT. Widespread lateral gene transfer among grasses. THE NEW PHYTOLOGIST 2021; 230:2474-2486. [PMID: 33887801 DOI: 10.1111/nph.17328] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Lateral gene transfer (LGT) occurs in a broad range of prokaryotes and eukaryotes, occasionally promoting adaptation. LGT of functional nuclear genes has been reported among some plants, but systematic studies are needed to assess the frequency and facilitators of LGT. We scanned the genomes of a diverse set of 17 grass species that span more than 50 Ma of divergence and include major crops to identify grass-to-grass protein-coding LGT. We identified LGTs in 13 species, with significant variation in the amount each received. Rhizomatous species acquired statistically more genes, probably because this growth habit boosts opportunities for transfer into the germline. In addition, the amount of LGT increases with phylogenetic relatedness, which might reflect genomic compatibility among close relatives facilitating successful transfers. However, genetic exchanges among highly divergent species indicates that transfers can occur across almost the entire family. Overall, we showed that LGT is a widespread phenomenon in grasses that has moved functional genes across the grass family into domesticated and wild species alike. Successful LGTs appear to increase with both opportunity and compatibility.
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Affiliation(s)
- Samuel G S Hibdige
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Pauline Raimondeau
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | | | - Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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40
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Izuegbunam CL, Wijewantha N, Wone B, Ariyarathne MA, Sereda G, Wone BWM. A nano-biomimetic transformation system enables in planta expression of a reporter gene in mature plants and seeds. NANOSCALE ADVANCES 2021; 3:3240-3250. [PMID: 36133668 PMCID: PMC9417712 DOI: 10.1039/d1na00107h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/16/2021] [Indexed: 05/08/2023]
Abstract
Plant genetic engineering will be essential to decipher the genomic basis of complex traits, optimize crop genomics, and enable plant-based production of recombinant proteins. However, established plant transformation approaches for bioengineering are fraught with limitations. Although nanoparticle-mediated methods show great promise for advancing plant biotechnology, many engineered nanomaterials can have cytotoxic and ecological effects. Here, we demonstrate the efficient uptake of a nano-biomimetic carrier of plasmid DNA and transient expression of a reporter gene in leaves of Arabidopsis, common ice plant and tobacco, as well as in the developing seed tissues of Arabidopsis, field mustard, barley, and wheat. The nano-biomimetic transformation system described here has all the advantages of other nanoparticle-mediated approaches for passive delivery of genetic cargo into a variety of plant species and is also nontoxic to cells and to the environment for diverse biotechnological applications in plant biology and crop science.
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Affiliation(s)
| | | | - Beate Wone
- Department of Biology, University of South Dakota SD USA
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41
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Filip E, Skuza L. Horizontal Gene Transfer Involving Chloroplasts. Int J Mol Sci 2021; 22:ijms22094484. [PMID: 33923118 PMCID: PMC8123421 DOI: 10.3390/ijms22094484] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 02/04/2023] Open
Abstract
Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.
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Affiliation(s)
- Ewa Filip
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland;
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
- Correspondence:
| | - Lidia Skuza
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland;
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
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Phansopa C, Dunning LT, Reid JD, Christin PA. Lateral Gene Transfer Acts As an Evolutionary Shortcut to Efficient C4 Biochemistry. Mol Biol Evol 2021; 37:3094-3104. [PMID: 32521019 PMCID: PMC7751175 DOI: 10.1093/molbev/msaa143] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The adaptation of proteins for novel functions often requires changes in their kinetics via amino acid replacement. This process can require multiple mutations, and therefore extended periods of selection. The transfer of genes among distinct species might speed up the process, by providing proteins already adapted for the novel function. However, this hypothesis remains untested in multicellular eukaryotes. The grass Alloteropsis is an ideal system to test this hypothesis due to its diversity of genes encoding phosphoenolpyruvate carboxylase, an enzyme that catalyzes one of the key reactions in the C4 pathway. Different accessions of Alloteropsis either use native isoforms relatively recently co-opted from other functions or isoforms that were laterally acquired from distantly related species that evolved the C4 trait much earlier. By comparing the enzyme kinetics, we show that native isoforms with few amino acid replacements have substrate KM values similar to the non-C4 ancestral form, but exhibit marked increases in catalytic efficiency. The co-option of native isoforms was therefore followed by rapid catalytic improvements, which appear to rely on standing genetic variation observed within one species. Native C4 isoforms with more amino acid replacements exhibit additional changes in affinities, suggesting that the initial catalytic improvements are followed by gradual modifications. Finally, laterally acquired genes show both strong increases in catalytic efficiency and important changes in substrate handling. We conclude that the transfer of genes among distant species sharing the same physiological novelty creates an evolutionary shortcut toward more efficient enzymes, effectively accelerating evolution.
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Affiliation(s)
- Chatchawal Phansopa
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - James D Reid
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
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Nowak MD, Birkeland S, Mandáková T, Roy Choudhury R, Guo X, Gustafsson ALS, Gizaw A, Schrøder‐Nielsen A, Fracassetti M, Brysting AK, Rieseberg L, Slotte T, Parisod C, Lysak MA, Brochmann C. The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. Mol Ecol Resour 2021; 21:661-676. [PMID: 33058468 PMCID: PMC7983928 DOI: 10.1111/1755-0998.13280] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/26/2020] [Accepted: 10/09/2020] [Indexed: 01/04/2023]
Abstract
The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome-scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.
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Affiliation(s)
| | | | | | | | - Xinyi Guo
- CEITECMasaryk UniversityBrnoCzech Republic
| | | | - Abel Gizaw
- Natural History MuseumUniversity of OsloOsloNorway
| | | | - Marco Fracassetti
- Science for Life Laboratory and Department of EcologyEnvironment and Plant ScienceStockholm UniversityStockholmSweden
| | - Anne K. Brysting
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
| | - Loren Rieseberg
- Department of BotanyThe University of British ColumbiaVancouverBCCanada
| | - Tanja Slotte
- Science for Life Laboratory and Department of EcologyEnvironment and Plant ScienceStockholm UniversityStockholmSweden
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Olofsson JK, Curran EV, Nyirenda F, Bianconi ME, Dunning LT, Milenkovic V, Sotelo G, Hidalgo O, Powell RF, Lundgren MR, Leitch IJ, Nosil P, Osborne CP, Christin PA. Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap. Mol Ecol 2021; 30:2116-2130. [PMID: 33682242 DOI: 10.1111/mec.15871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022]
Abstract
Geographical isolation facilitates the emergence of distinct phenotypes within a single species, but reproductive barriers or selection are needed to maintain the polymorphism after secondary contact. Here, we explore the processes that maintain intraspecific variation of C4 photosynthesis, a complex trait that results from the combined action of multiple genes. The grass Alloteropsis semialata includes C4 and non-C4 populations, which have coexisted as a polyploid series for more than 1 million years in the miombo woodlands of Africa. Using population genomics, we show that there is genome-wide divergence for the photosynthetic types, but the current geographical distribution does not reflect a simple habitat displacement scenario as the genetic clusters overlap, being occasionally mixed within a given habitat. Despite evidence of recurrent introgression between non-C4 and C4 groups, in both diploids and polyploids, the distinct genetic lineages retain their identity, potentially because of selection against hybrids. Coupled with strong isolation by distance within each genetic group, this selection created a geographical mosaic of photosynthetic types. Diploid C4 and non-C4 types never grew together, and the C4 type from mixed populations constantly belonged to the hexaploid lineage. By limiting reproductive interactions between photosynthetic types, the ploidy difference probably allows their co-occurrence, reinforcing the functional diversity within this species. Together, these factors enabled the persistence of divergent physiological traits of ecological importance within a single species despite gene flow and habitat overlap.
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Affiliation(s)
- Jill K Olofsson
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Emma V Curran
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Matheus E Bianconi
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Luke T Dunning
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Vanja Milenkovic
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Graciela Sotelo
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | | | | - Marjorie R Lundgren
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | | - Patrik Nosil
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Colin P Osborne
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
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Mahelka V, Krak K, Fehrer J, Caklová P, Nagy Nejedlá M, Čegan R, Kopecký D, Šafář J. A Panicum-derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress-related genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1141-1164. [PMID: 33484020 DOI: 10.1111/tpj.15167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Intra-specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper, we investigate the nature and evolution of a chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in the nuclear genomes of species of the barley genus Hordeum (Pooideae). The segment, spanning over 440 kb in the Asian Hordeum bogdanii and 219 kb in the South American Hordeum pubiflorum, resides on a pair of nucleolar organizer region (NOR)-bearing chromosomes. Conserved synteny and micro-collinearity of the segment in both species indicate a common origin of the segment, which was acquired before the split of the respective barley lineages 5-1.7 million years ago. A major part of the foreign DNA consists of several approximately 68 kb long repeated blocks containing five stress-related protein-coding genes and transposable elements (TEs). Whereas outside these repeats, the locus was invaded by multiple TEs from the host genome, the repeated blocks are rather intact and appear to be preserved. The protein-coding genes remained partly functional, as indicated by conserved reading frames, a low amount of non-synonymous mutations, and expression of mRNA. A screen across Hordeum species targeting the panicoid protein-coding genes revealed the presence of the genes in all species of the section Stenostachys. In summary, our study shows that grass genomes can contain large genomic segments obtained from distantly related species. These segments usually remain undetected, but they may play an important role in the evolution and adaptation of species.
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Affiliation(s)
- Václav Mahelka
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | - Karol Krak
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6, 16500, Czech Republic
| | - Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | - Petra Caklová
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | | | - Radim Čegan
- Institute of Biophysics, Czech Academy of Sciences, Brno, 61265, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
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Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1. Funct Integr Genomics 2021; 21:171-193. [PMID: 33547987 DOI: 10.1007/s10142-021-00768-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 09/30/2020] [Accepted: 01/19/2021] [Indexed: 12/11/2022]
Abstract
A pentachlorophenol degrading bacterium was isolated from effluent of a wastewater treatment plant in Durban, South Africa, and identified as Bacillus tropicus strain AOA-CPS1 (BtAOA). The isolate degraded 29% of pentachlorophenol (PCP) within 9 days at an initial PCP concentration of 100 mg L-1 and 62% of PCP when the initial concentration was set at 350 mg L-1. The whole-genome of BtAOA was sequenced using Pacific Biosciences RS II sequencer with the Single Molecule, Real-Time (SMRT) Link (version 7.0.1.66975) and analysed using the HGAP4-de-novo assembly application. The contigs were annotated at NCBI, RASTtk and PROKKA prokaryotic genome annotation pipelines. The BtAOA genome is comprised of a 5,246,860-bp chromosome and a 58,449-bp plasmid with a GC content of 35.4%. The metabolic reconstruction for BtAOA showed that the organism has been naturally exposed to various chlorophenolic compounds including PCP and other xenobiotics. The chromosome encodes genes for core processes, stress response and PCP catabolic genes. Analogues of PCP catabolic gene (cpsBDCAE, and p450) sequences were identified from the NCBI annotation data, PCR-amplified from the whole genome of BtAOA, cloned into pET15b expression vector, overexpressed in E. coli BL21 (DE3) expression host, purified and characterized. Sequence mining and comparative analysis of the metabolic reconstruction of the BtAOA genome with closely related strains suggests that the operon encoding the first two enzymes in the PCP degradation pathway were acquired from a pre-existing pterin-carbinolamine dehydratase subsystem. The other two enzymes were recruited via horizontal gene transfer (HGT) from the pool of hypothetical proteins with no previous specific function, while the last enzyme was recruited from pre-existing enzymes from the TCA or serine-glyoxalase cycle via HGT events. This study provides a comprehensive understanding of the role of BtAOA in PCP degradation and its potential exploitation for bioremediation of other xenobiotic compounds.
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Bianconi ME, Hackel J, Vorontsova MS, Alberti A, Arthan W, Burke SV, Duvall MR, Kellogg EA, Lavergne S, McKain MR, Meunier A, Osborne CP, Traiperm P, Christin PA, Besnard G. Continued Adaptation of C4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses. Syst Biol 2020; 69:445-461. [PMID: 31589325 PMCID: PMC7672695 DOI: 10.1093/sysbio/syz066] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/18/2019] [Accepted: 09/26/2019] [Indexed: 11/29/2022] Open
Abstract
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}{}$_{4}$\end{document} photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} lineages is Andropogoneae, a group of \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}1200 grass species that includes some of the world’s most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} evolution in the group have compared a few model C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} plants to distantly related C\documentclass[12pt]{minimal}
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}{}$_{3}$\end{document} species so that changes directly responsible for the transition to C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} could not be distinguished from those that preceded or followed it. In this study, we analyze the genomes of 66 grass species, capturing the earliest diversification within Andropogoneae as well as their C\documentclass[12pt]{minimal}
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}{}$_{3}$\end{document} relatives. Phylogenomics combined with molecular dating and analyses of protein evolution show that many changes linked to the evolution of C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} photosynthesis in Andropogoneae happened in the Early Miocene, between 21 and 18 Ma, after the split from its C\documentclass[12pt]{minimal}
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}{}$_{3}$\end{document} sister lineage, and before the diversification of the group. This initial burst of changes was followed by an extended period of modifications to leaf anatomy and biochemistry during the diversification of Andropogoneae, so that a single C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} origin gave birth to a diversity of C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} phenotypes during 18 million years of speciation events and migration across geographic and ecological spaces. Our comprehensive approach and broad sampling of the diversity in the group reveals that one key transition can lead to a plethora of phenotypes following sustained adaptation of the ancestral state. [Adaptive evolution; complex traits; herbarium genomics; Jansenelleae; leaf anatomy; Poaceae; phylogenomics.]
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Affiliation(s)
- Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Jan Hackel
- Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Adriana Alberti
- CEA - Institut de Biologie Francois-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Watchara Arthan
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
- School of Biological Sciences, University of Reading, Reading RG6 6AH, UK
| | - Sean V Burke
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Melvin R Duvall
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MI 63132, USA
| | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, CNRS – Université Grenoble Alpes, UMR 5553, Grenoble, France
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, 500 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Alexandre Meunier
- Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Paweena Traiperm
- Department of Plant Science, Faculty of Science, Mahidol University, King Rama VI Road, Bangkok 10400, Thailand
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Guillaume Besnard
- Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France
- Correspondence to be sent to: Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France; E-mail:
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Chen R, Huangfu L, Lu Y, Fang H, Xu Y, Li P, Zhou Y, Xu C, Huang J, Yang Z. Adaptive innovation of green plants by horizontal gene transfer. Biotechnol Adv 2020; 46:107671. [PMID: 33242576 DOI: 10.1016/j.biotechadv.2020.107671] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
Horizontal gene transfer (HGT) refers to the movement of genetic material between distinct species by means other than sexual reproduction. HGT has contributed tremendously to the genome plasticity and adaptive evolution of prokaryotes and certain unicellular eukaryotes. The evolution of green plants from chlorophyte algae to angiosperms and from water to land represents a process of adaptation to diverse environments, which has been facilitated by acquisition of genetic material from other organisms. In this article, we review the occurrence of HGT in major lineages of green plants, including chlorophyte and charophyte green algae, bryophytes, lycophytes, ferns, and seed plants. In addition, we discuss the significance of horizontally acquired genes in the adaptive innovations of green plants and their potential applications to crop breeding and improvement.
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Affiliation(s)
- Rujia Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Liexiang Huangfu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yue Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Huimin Fang
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC 28590, USA; State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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Bianconi ME, Dunning LT, Curran EV, Hidalgo O, Powell RF, Mian S, Leitch IJ, Lundgren MR, Manzi S, Vorontsova MS, Besnard G, Osborne CP, Olofsson JK, Christin PA. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species. Proc Biol Sci 2020; 287:20201960. [PMID: 33171085 PMCID: PMC7735283 DOI: 10.1098/rspb.2020.1960] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C4 physiology away from its region of origin.
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Affiliation(s)
- Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Emma V Curran
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Oriane Hidalgo
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Robyn F Powell
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Sahr Mian
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Ilia J Leitch
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Sophie Manzi
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III - Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III - Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes. Trends Parasitol 2020; 36:927-941. [DOI: 10.1016/j.pt.2020.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
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