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Xu D, Leister D, Kleine T. Identification of a highly drought-resistant pp7l hda6 mutant. FRONTIERS IN PLANT SCIENCE 2024; 15:1341576. [PMID: 38887464 PMCID: PMC11180769 DOI: 10.3389/fpls.2024.1341576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/09/2024] [Indexed: 06/20/2024]
Abstract
Plants have developed efficient strategies to counteract drought stress, including stomata closure, significant changes in nuclear gene expression, and epigenetic mechanisms. Previously, we identified Arabidopsis thaliana PROTEIN PHOSPHATASE7-LIKE (PP7L) as an extrachloroplastic protein that promotes chloroplast development. In addition, it was shown that PP7L is involved in high light and salt tolerance. Here, we demonstrate that the pp7l mutant can withstand prolonged periods of drought stress. Interestingly, despite impaired growth under standard growth conditions, photosynthetic efficiency recovers in pp7l mutant plants experiencing drought conditions. To assess the (post)transcriptional changes occurring in the pp7l mutant under different durations of drought exposure, we used an RNA-sequencing technique that allows the simultaneous detection of organellar and nuclear transcripts. Compared with the previously reported drought-responsive changes in the wild type, the drought-responsive changes in organellar and nuclear transcripts detected in the pp7l mutant were negligible. Our analysis of the data generated in this study and review and analysis of previous literature motivated us to create a pp7l hda6 (histone deacetylase 6) mutant, which exhibits remarkable drought resistance. Notably, the growth penalty associated with pp7l was alleviated in the double mutant, ruling out a dwarf effect on the drought-tolerant trait of this genotype. Future studies may consider that multiple loci and factors are involved in stress resistance and explore combinations of these factors to create even more resilient plants.
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Affiliation(s)
| | | | - Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
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2
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Alves RM, de Abreu VAC, Oliveira RP, Almeida JVDA, de Oliveira MDM, Silva SR, Paschoal AR, de Almeida SS, de Souza PAF, Ferro JA, Miranda VFO, Figueira A, Domingues DS, Varani AM. Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation. Gigascience 2024; 13:giae027. [PMID: 38837946 PMCID: PMC11152179 DOI: 10.1093/gigascience/giae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/21/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family. FINDINGS The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species. CONCLUSIONS The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.
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Affiliation(s)
| | - Vinicius A C de Abreu
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Rafaely Pantoja Oliveira
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - João Victor dos Anjos Almeida
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Mauro de Medeiros de Oliveira
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Saura R Silva
- Departamento de Biologia, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Alexandre R Paschoal
- Departamento de Ciência da Computação (DACOM), Grupo de e Bioinformática e Reconhecimento de Padrões (bioinfo-cp), Universidade Tecnológica Federal do Paraná (UTFPR), 80230-901 Cornélio Procópio, PR, Brazil
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, OX110QX Didcot, UK
| | - Sintia S de Almeida
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Pedro A F de Souza
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Jesus A Ferro
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Vitor F O Miranda
- Departamento de Biologia, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, 13416-000 Piracicaba, SP, Brazil
| | - Douglas S Domingues
- Departamento de Genética, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), 13418-900 Piracicaba, SP, Brazil
| | - Alessandro M Varani
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
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3
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Suo A, Yang J, Mao C, Li W, Wu X, Xie W, Yang Z, Guo S, Zheng B, Zheng Y. Phased secondary small interfering RNAs in Camellia sinensis var. assamica. NAR Genom Bioinform 2023; 5:lqad103. [PMID: 38025046 PMCID: PMC10673657 DOI: 10.1093/nargab/lqad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Phased secondary small interfering RNAs (phasiRNAs) in plants play important roles in regulating genome stability, plant development and stress adaption. Camellia sinensis var. assamica has immense economic, medicinal and cultural significance. However, there are still no studies of phasiRNAs and their putative functions in this valuable plant. We identified 476 and 43 PHAS loci which generated 4290 twenty one nucleotide (nt) and 264 twenty four nt phasiRNAs, respectively. Moreover, the analysis of degradome revealed more than 35000 potential targets for these phasiRNAs. We identified several conserved 21 nt phasiRNA generation pathways in tea plant, including miR390 → TAS3, miR482/miR2118 → NB-LRR, miR393 → F-box, miR828 → MYB/TAS4, and miR7122 → PPR in this study. Furthermore, we found that some transposase and plant mobile domain genes could generate phasiRNAs. Our results show that phasiRNAs target genes in the same family in cis- or trans-manners, and different members of the same gene family may generate the same phasiRNAs. The phasiRNAs, generated by transposase and plant mobile domain genes, and their targets, suggest that phasiRNAs may be involved in the inhibition of transposable elements in tea plant. To summarize, these results provide a comprehensive view of phasiRNAs in Camellia sinensis var. assamica.
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Affiliation(s)
- Angbaji Suo
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Jun Yang
- School of Criminal Investigation, Yunnan Police College, No. 249 North Jiaochang Road, 650223 Yunnan, China
| | - Chunyi Mao
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Wanran Li
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Xingwang Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Wenping Xie
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Zhengan Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Shiyong Guo
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, No. 220 Handan Road, 200433 Shanghai, China
| | - Yun Zheng
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
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Olivier M, Hesketh A, Pouch-Pélissier MN, Pélissier T, Huang Y, Latrasse D, Benhamed M, Mathieu O. RTEL1 is required for silencing and epigenome stability. Nucleic Acids Res 2023; 51:8463-8479. [PMID: 37471026 PMCID: PMC10484728 DOI: 10.1093/nar/gkad610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/13/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Transcriptional silencing is an essential mechanism for controlling the expression of genes, transgenes and heterochromatic repeats through specific epigenetic marks on chromatin that are maintained during DNA replication. In Arabidopsis, silenced transgenes and heterochromatic sequences are typically associated with high levels of DNA methylation, while silenced genes are enriched in H3K27me3. Reactivation of these loci is often correlated with decreased levels of these repressive epigenetic marks. Here, we report that the DNA helicase REGULATOR OF TELOMERE ELONGATION 1 (RTEL1) is required for transcriptional silencing. RTEL1 deficiency causes upregulation of many genes enriched in H3K27me3 accompanied by a moderate decrease in this mark, but no loss of DNA methylation at reactivated heterochromatic loci. Instead, heterochromatin exhibits DNA hypermethylation and increased H3K27me3 in rtel1. We further find that loss of RTEL1 suppresses the release of heterochromatin silencing caused by the absence of the MOM1 silencing factor. RTEL1 is conserved among eukaryotes and plays a key role in resolving DNA secondary structures during DNA replication. Inducing such aberrant DNA structures using DNA cross-linking agents also results in a loss of transcriptional silencing. These findings uncover unappreciated roles for RTEL1 in transcriptional silencing and in stabilizing DNA methylation and H3K27me3 patterns.
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Affiliation(s)
- Margaux Olivier
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000 Clermont-Ferrand, France
| | - Amy Hesketh
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000 Clermont-Ferrand, France
| | - Marie-Noëlle Pouch-Pélissier
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000 Clermont-Ferrand, France
| | - Thierry Pélissier
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000 Clermont-Ferrand, France
| | - Ying Huang
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université d’Évry, F-91405 Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université d’Évry, F-91405 Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université d’Évry, F-91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, F-75006 Paris, France
- Institut Universitaire de France (IUF), France
| | - Olivier Mathieu
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000 Clermont-Ferrand, France
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5
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Mineri L, Cerise M, Giaume F, Vicentini G, Martignago D, Chiara M, Galbiati F, Spada A, Horner D, Fornara F, Brambilla V. Rice florigens control a common set of genes at the shoot apical meristem including the F-BOX BROADER TILLER ANGLE 1 that regulates tiller angle and spikelet development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1647-1660. [PMID: 37285314 DOI: 10.1111/tpj.16345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023]
Abstract
Rice flowering is triggered by transcriptional reprogramming at the shoot apical meristem (SAM) mediated by florigenic proteins produced in leaves in response to changes in photoperiod. Florigens are more rapidly expressed under short days (SDs) compared to long days (LDs) and include the HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) phosphatidylethanolamine binding proteins. Hd3a and RFT1 are largely redundant at converting the SAM into an inflorescence, but whether they activate the same target genes and convey all photoperiodic information that modifies gene expression at the SAM is currently unclear. We uncoupled the contribution of Hd3a and RFT1 to transcriptome reprogramming at the SAM by RNA sequencing of dexamethasone-inducible over-expressors of single florigens and wild-type plants exposed to photoperiodic induction. Fifteen highly differentially expressed genes common to Hd3a, RFT1, and SDs were retrieved, 10 of which still uncharacterized. Detailed functional studies on some candidates revealed a role for LOC_Os04g13150 in determining tiller angle and spikelet development and the gene was renamed BROADER TILLER ANGLE 1 (BRT1). We identified a core set of genes controlled by florigen-mediated photoperiodic induction and defined the function of a novel florigen target controlling tiller angle and spikelet development.
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Affiliation(s)
- Lorenzo Mineri
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Martina Cerise
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Francesca Giaume
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133, Milan, Italy
| | - Giulio Vicentini
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133, Milan, Italy
| | - Damiano Martignago
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Francesca Galbiati
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133, Milan, Italy
| | - David Horner
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Vittoria Brambilla
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133, Milan, Italy
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6
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Jarry L, Descombin J, Nicolau M, Dussutour A, Picault N, Moissiard G. Plant mobile domain proteins ensure Microrchidia 1 expression to fulfill transposon silencing. Life Sci Alliance 2023; 6:e202201539. [PMID: 36732020 PMCID: PMC9899485 DOI: 10.26508/lsa.202201539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
Silencing of transposable elements (TEs) is an essential process to maintain genomic integrity within the cell. In Arabidopsis, together with canonical epigenetic pathways such as DNA methylation and modifications of histone tails, the plant mobile domain (PMD) proteins MAINTENANCE OF MERISTEMS (MAIN) and MAIN-LIKE 1 (MAIL1) are involved in TE silencing. In addition, the MICRORCHIDIA (MORC) ATPases, including MORC1, are important cellular factors repressing TEs. Here, we describe the genetic interaction and connection between the PMD and MORC pathways by showing that MORC1 expression is impaired in main and mail1 mutants. Transcriptomic analyses of higher order mutant plants combining pmd and morc1 mutations, and pmd mutants in which MORC1 expression is restored, show that the silencing defects of a subset of TEs in pmd mutants are most likely the consequence of MORC1 down-regulation. Besides, a significant fraction of up-regulated TEs in pmd mutants are not targeted by the MORC1 pathway.
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Affiliation(s)
- Lucas Jarry
- LGDP-UMR5096, CNRS, Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Julie Descombin
- LGDP-UMR5096, CNRS, Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Melody Nicolau
- LGDP-UMR5096, CNRS, Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Ange Dussutour
- LGDP-UMR5096, CNRS, Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Nathalie Picault
- LGDP-UMR5096, CNRS, Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Guillaume Moissiard
- LGDP-UMR5096, CNRS, Perpignan, France
- LGDP-UMR5096, Université de Perpignan Via Domitia, Perpignan, France
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7
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Cui F, Ye X, Li X, Yang Y, Hu Z, Overmyer K, Brosché M, Yu H, Salojärvi J. Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis. PLANT COMMUNICATIONS 2022; 3:100307. [PMID: 35605198 PMCID: PMC9284290 DOI: 10.1016/j.xplc.2022.100307] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/09/2022] [Accepted: 02/24/2022] [Indexed: 05/25/2023]
Abstract
Vaccinium darrowii is a subtropical wild blueberry species that has been used to breed economically important southern highbush cultivars. The adaptive traits of V. darrowii to subtropical climates can provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assembled the V. darrowii genome into 12 pseudochromosomes using Oxford Nanopore long reads complemented with Hi-C scaffolding technologies, and we predicted 41 815 genes using RNA-sequencing evidence. Syntenic analysis across three Vaccinium species revealed a highly conserved genome structure, with the highest collinearity between V. darrowii and Vaccinium corymbosum. This conserved genome structure may explain the high fertility observed during crossbreeding of V. darrowii with other blueberry cultivars. Analysis of gene expansion and tandem duplication indicated possible roles for defense- and flowering-associated genes in the adaptation of V. darrowii to the subtropics. Putative SOC1 genes in V. darrowii were identified based on phylogeny and expression analysis. Blueberries are covered in a thick cuticle layer and contain anthocyanins, which confer their powdery blue color. Using RNA sequencing, we delineated the cuticle biosynthesis pathways of Vaccinium species in V. darrowii. This result can serve as a reference for breeding berries whose colors are appealing to customers. The V. darrowii reference genome, together with the unique traits of this species, including its diploid genome, short vegetative phase, and high compatibility in hybridization with other blueberries, make V. darrowii a potential research model for blueberry species.
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Affiliation(s)
- Fuqiang Cui
- College of Forestry and Biotechnology, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
| | - Xiaoxue Ye
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiaoxiao Li
- College of Forestry and Biotechnology, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Yifan Yang
- College of Forestry and Biotechnology, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Zhubing Hu
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, Kaifeng, China
| | - Kirk Overmyer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and the Viikki Plant Science Centre, University of Helsinki, PO Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
| | - Mikael Brosché
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and the Viikki Plant Science Centre, University of Helsinki, PO Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
| | - Hong Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and the Viikki Plant Science Centre, University of Helsinki, PO Box 65 (Viikinkaari 1), 00014 Helsinki, Finland.
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8
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Alvarado-Marchena L, Martínez-Pérez M, Aparicio F, Pallas V, Maumus F. Recent Acquisition of Functional m6A RNA Demethylase Domain in Orchid Ty3/Gypsy Elements. FRONTIERS IN PLANT SCIENCE 2022; 13:939843. [PMID: 35860540 PMCID: PMC9289625 DOI: 10.3389/fpls.2022.939843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Long terminal repeats (LTR) retrotransposons are transposable elements (TEs) representing major components of most plant genomes. The fixation of additional conserved protein domains in their genomes is considered a rare event in the course of their evolution. Such changes can bring novel functions and increase their fitness by playing a role in the regulation of their replicative cycle or by affecting their integration landscape so that the detection of new domains can in turn reveal important aspects of host-TE interactions. We have mined angiosperm genomes for the presence of additional domains in LTR retrotransposons. We report a lineage of large (25 kbp) Gypsy-type elements in the genomes of Phalaenopsis orchids that contain an additional open reading frame containing a 2-ODD domain with close similarity to those responsible for m6A RNA demethylase activity in AlkB proteins. By performing in vitro assays, we demonstrate the RNA binding capability and the demethylase activity of the Gypsy-encoded AlkB protein, suggesting it could be functional against cognate TE mRNA or any cellular RNA in planta. In line with recent literature, we propose that the fixation of an RNA demethylase in this lineage of LTR retrotransposons may reflect an important role for epitranscriptomic control in host surveillance against TEs.
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Affiliation(s)
- Luis Alvarado-Marchena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Mireya Martínez-Pérez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Frederic Aparicio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Florian Maumus
- INRAE, URGI, Université Paris-Saclay, Versailles, France
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9
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Nicolau M, Picault N, Moissiard G. The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation. Cells 2021; 10:cells10112952. [PMID: 34831175 PMCID: PMC8616336 DOI: 10.3390/cells10112952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.
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Affiliation(s)
- Melody Nicolau
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Nathalie Picault
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Guillaume Moissiard
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Correspondence:
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Niu F, Jiang Q, Sun X, Hu Z, Wang L, Zhang H. Large DNA fragment deletion in lncRNA77580 regulates neighboring gene expression in soybean (Glycine max). FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:1139-1147. [PMID: 34585661 DOI: 10.1071/fp20400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) affect gene expressions via a wide range of mechanisms and are considered important regulators of numerous essential biological processes, including abiotic stress responses. However, the biological functions of most lncRNAs are yet to be determined. Moreover, to date, no effective methods have been developed to study the function of plant lncRNAs. We previously discovered a salt stress-related lncRNA, lncRNA77580 in soybean (Glycine max L.). In this study, we cloned the full-length lncRNA77580 and found that it shows nuclear-specific localisation. Furthermore, we employed CRISPR/Cas9 technology to induce large DNA fragment deletions in lncRNA77580 in soybean using a dual-single guide RNA/Cas9 design. As a result, we obtained deletion mutant soybean roots with targeted genomic fragment deletion in lncRNA77580. Deletion and overexpression of lncRNA77580 were found to alter the expression of several neighboring protein-coding genes associated with the response to salt stress. The longer the deleted DNA fragment in lncRNA77580, the greater the influence on the expression of lncRNA77580 itself and neighboring genes. Collectively, the findings of this study revealed that large DNA fragment deletion in lncRNAs using the CRISPR/Cas9 system is a powerful method to obtain functional mutations of soybean lncRNAs that could benefit future research on lncRNA function in soybean.
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Affiliation(s)
- Fengjuan Niu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | | | - Xianjun Sun
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zheng Hu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Lixia Wang
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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Hummel G, Berr A, Graindorge S, Cognat V, Ubrig E, Pflieger D, Molinier J, Drouard L. Epigenetic silencing of clustered tRNA genes in Arabidopsis. Nucleic Acids Res 2020; 48:10297-10312. [PMID: 32941623 PMCID: PMC7544208 DOI: 10.1093/nar/gkaa766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/21/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. This work demonstrates that both genomic and epigenomic contexts are key players in the regulation of tDNAs transcription. The conservation of most of these regulatory processes suggests that this pioneering work in Arabidopsis can provide new insights into the regulation of RNA Pol III transcription in other organisms, including vertebrates.
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Affiliation(s)
- Guillaume Hummel
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Alexandre Berr
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Stéfanie Graindorge
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Elodie Ubrig
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Jean Molinier
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
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