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Edula SR, Hand LC, Roberts PM, Beasley E, Snider JL, Kemerait RC, Chee PW, Bag S. Characterization of Caulimovirid-like Sequences from Upland Cotton ( Gossypium hirsutum L.) Exhibiting Terminal Abortion in Georgia, USA. Viruses 2024; 16:1111. [PMID: 39066273 PMCID: PMC11281623 DOI: 10.3390/v16071111] [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: 06/21/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
In this study, we investigated the potential involvement of endogenous viral elements (EVEs) in the development of apical tissue necrosis, resulting in the terminal abortion of upland cotton (Gossypium hirsutum L.) in Georgia. The high-throughput sequence analysis of symptomatic and asymptomatic plant tissue samples revealed near-complete EVE-Georgia (EVE-GA) sequences closely related to caulimoviruses. The analysis of EVE-GA's putative open reading frames (ORFs) compared to cotton virus A and endogenous cotton pararetroviral elements (eCPRVE) revealed their similarity in putative ORFs 1-4. However, in the ORF 5 and ORF 6 encoding putative coat protein and reverse transcriptase, respectively, the sequences from EVE-GA have stop codons similar to eCPRVE sequences from Mississippi. In silico mining of the cotton genome database using EVE-GA as a query uncovered near-complete viral sequence insertions in the genomes of G. hirsutum species (~7 kb) but partial in G. tomentosum (~5.3 kb) and G. mustelinum (~5.1 kb) species. Furthermore, cotton EVEs' episomal forms and messenger RNA (mRNA) transcripts were detected in both symptomatic and asymptomatic plants collected from cotton fields. No significant yield difference was observed between symptomatic and asymptomatic plants of the two varieties evaluated in the experimental plot. Additionally, EVEs were also detected in cotton seeds and seedlings. This study emphasizes the need for future research on EVE sequences, their coding capacity, and any potential role in host immunity or pathogenicity.
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Affiliation(s)
- Surendra R. Edula
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
| | - Lavesta C. Hand
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA 31793, USA
| | | | - Edward Beasley
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA 31793, USA
| | - John L. Snider
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA 31793, USA
| | - Robert C. Kemerait
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
| | - Peng W. Chee
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA 31793, USA
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
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2
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Gao D. Introduction of Plant Transposon Annotation for Beginners. BIOLOGY 2023; 12:1468. [PMID: 38132293 PMCID: PMC10741241 DOI: 10.3390/biology12121468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate transposons, especially for beginners, as transposon prediction requires necessary expertise in both transposon biology and bioinformatics. Moreover, the complexity of plant genomes and the dynamic evolution of transposons also bring difficulties for genome-wide transposon discovery. This review summarizes the three major strategies for transposon detection including repeat-based, structure-based, and homology-based annotation, and introduces the transposon superfamilies identified in plants thus far, and some related bioinformatics resources for detecting plant transposons. Furthermore, it describes transposon classification and explains why the terms 'autonomous' and 'non-autonomous' cannot be used to classify the superfamilies of transposons. Lastly, this review also discusses how to identify misannotated transposons and improve the quality of the transposon database. This review provides helpful information about plant transposons and a beginner's guide on annotating these repetitive sequences.
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Affiliation(s)
- Dongying Gao
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210, USA
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3
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Saito N, Chen S, Kitajima K, Zhou Z, Koide Y, Encabo JR, Diaz MGQ, Choi IR, Koyanagi KO, Kishima Y. Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species. FRONTIERS IN PLANT SCIENCE 2023; 14:1261705. [PMID: 37965031 PMCID: PMC10641527 DOI: 10.3389/fpls.2023.1261705] [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: 07/19/2023] [Accepted: 09/29/2023] [Indexed: 11/16/2023]
Abstract
Introduction Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. These viral elements, known as endogenous RTBV-like sequences (eRTBVLs), comprise five subfamilies, eRTBVL-A, -B, -C, -D, and -X. Four subfamilies (A, B, C, and X) are present to a limited degree in the genomes of the Asian cultivated rice Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon. Methods The eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (Nipponbare) genome occur mostly at orthologous chromosomal positions in other AA-genome species. The eRTBVL-D sequences were inserted into the genomes just before speciation of the AA-genome species. Results and discussion Ten eRTBVL-D segments are located at six loci, which were used for our evolutionary analyses during the speciation of the AA-genome species. The degree of genetic differentiation varied among the eRTBVL-D segments. Of the six loci, three showed phylogenetic trees consistent with the standard speciation pattern (SSP) of the AA-genome species (Type A), and the other three represented phylogenies different from the SSP (Type B). The atypical phylogenetic trees for the Type B loci revealed chromosome region-specific evolution among the AA-genome species that is associated with phylogenetic incongruences: complex genome rearrangements between eRTBVL-D segments, an introgression between the distant species, and low genetic diversity of a shared eRTBVL-D segment. Using eRTBVL-D as an indicator, this study revealed the phylogenetic incongruence of local chromosomal regions with different topologies that developed during speciation.
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Affiliation(s)
- Nozomi Saito
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing, China
| | - Katsuya Kitajima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Zhitong Zhou
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Jaymee R. Encabo
- Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines, Los Baños, Laguna, Philippines
| | - Maria Genaleen Q. Diaz
- Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines, Los Baños, Laguna, Philippines
| | - Il-Ryong Choi
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Kanako O. Koyanagi
- Faculty of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Aboughanem-Sabanadzovic N, Allen TW, Frelichowski J, Scheffler J, Sabanadzovic S. Discovery and Analyses of Caulimovirid-like Sequences in Upland Cotton ( Gossypium hirsutum). Viruses 2023; 15:1643. [PMID: 37631986 PMCID: PMC10458927 DOI: 10.3390/v15081643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Analyses of Illumina-based high-throughput sequencing data generated during characterization of the cotton leafroll dwarf virus population in Mississippi (2020-2022) consistently yielded contigs varying in size (most frequently from 4 to 7 kb) with identical nucleotide content and sharing similarities with reverse transcriptases (RTases) encoded by extant plant pararetroviruses (family Caulimoviridiae). Initial data prompted an in-depth study involving molecular and bioinformatic approaches to characterize the nature and origins of these caulimovirid-like sequences. As a result, here, we report on endogenous viral elements (EVEs) related to extant members of the family Caulimoviridae, integrated into a genome of upland cotton (Gossypium hirsutum), for which we propose the provisional name "endogenous cotton pararetroviral elements" (eCPRVE). Our investigations pinpointed a ~15 kbp-long locus on the A04 chromosome consisting of head-to-head orientated tandem copies located on positive- and negative-sense DNA strands (eCPRVE+ and eCPRVE-). Sequences of the eCPRVE+ comprised nearly complete and slightly decayed genome information, including ORFs coding for the viral movement protein (MP), coat protein (CP), RTase, and transactivator/viroplasm protein (TA). Phylogenetic analyses of major viral proteins suggest that the eCPRVE+ may have been initially derived from a genome of a cognate virus belonging to a putative new genus within the family. Unexpectedly, an identical 15 kb-long locus composed of two eCPRVE copies was also detected in a newly recognized species G. ekmanianum, shedding some light on the relatively recent evolution within the cotton family.
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Affiliation(s)
- Nina Aboughanem-Sabanadzovic
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, 2 Research Park, Mailstop 9627, Mississippi, MS 39762, USA;
| | - Thomas W. Allen
- Delta Research and Extension Center, Mississippi State University, 82 Stoneville Road, P.O. Box 197, Stoneville, MS 38776, USA;
| | | | - Jodi Scheffler
- USDA-ARS Mid-South Area, 141 Experiment Station Road, Stoneville, MS 38776, USA;
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Twelve Lane, Mail Stop 9775, Mississippi, MS 39762, USA
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Vassilieff H, Geering ADW, Choisne N, Teycheney PY, Maumus F. Endogenous Caulimovirids: Fossils, Zombies, and Living in Plant Genomes. Biomolecules 2023; 13:1069. [PMID: 37509105 PMCID: PMC10377300 DOI: 10.3390/biom13071069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The Caulimoviridae is a family of double-stranded DNA viruses that infect plants. The genomes of most vascular plants contain endogenous caulimovirids (ECVs), a class of repetitive DNA elements that is abundant in some plant genomes, resulting from the integration of viral DNA in the chromosomes of germline cells during episodes of infection that have sometimes occurred millions of years ago. In this review, we reflect on 25 years of research on ECVs that has shown that members of the Caulimoviridae have occupied an unprecedented range of ecological niches over time and shed light on their diversity and macroevolution. We highlight gaps in knowledge and prospects of future research fueled by increased access to plant genome sequence data and new tools for genome annotation for addressing the extent, impact, and role of ECVs on plant biology and the origin and evolutionary trajectories of the Caulimoviridae.
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Affiliation(s)
| | - Andrew D W Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, F-97410 Saint-Pierre de La Réunion, France
- UMR PVBMT, Université de la Réunion, F-97410 Saint-Pierre de La Réunion, France
| | - Florian Maumus
- INRAE, URGI, Université Paris-Saclay, 78026 Versailles, France
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6
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Kuriyama K, Tabara M, Moriyama H, Takahashi H, Fukuhara T. The essential role of the quasi-long terminal repeat sequence for replication and gene expression of an endogenous pararetrovirus, petunia vein clearing virus. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:405-414. [PMID: 37283613 PMCID: PMC10240922 DOI: 10.5511/plantbiotechnology.22.1017a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/17/2022] [Indexed: 06/08/2023]
Abstract
Petunia vein clearing virus (PVCV) is a type member of the genus Petuvirus within the Caulimoviridae family and is defined as one viral unit consisting of a single open reading frame (ORF) encoding a viral polyprotein and one quasi-long terminal repeat (QTR) sequence. Since some full-length PVCV sequences are found in the petunia genome and a vector for horizontal transmission of PVCV has not been identified yet, PVCV is referred to as an endogenous pararetrovirus. Molecular mechanisms of replication, gene expression and horizontal transmission of endogenous pararetroviruses in plants are elusive. In this study, agroinfiltration experiments using various PVCV infectious clones indicated that the replication (episomal DNA synthesis) and gene expression of PVCV were efficient when the QTR sequences are present on both sides of the ORF. Whereas replacement of the QTR with another promoter and/or terminator is possible for gene expression, it is essential for QTR sequences to be on both sides for viral replication. Although horizontal transmission of PVCV by grafting and biolistic inoculation was previously reported, agroinfiltration is a useful and convenient method for studying its replication and gene expression.
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Affiliation(s)
- Kazunori Kuriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Midori Tabara
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
| | - Hideki Takahashi
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aza-Aoba, Sendai, Miyagi 980-0845, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
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de Tomás C, Vicient CM. Genome-wide identification of Reverse Transcriptase domains of recently inserted endogenous plant pararetrovirus ( Caulimoviridae). FRONTIERS IN PLANT SCIENCE 2022; 13:1011565. [PMID: 36589050 PMCID: PMC9794742 DOI: 10.3389/fpls.2022.1011565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
Endogenous viral elements (EVEs) are viral sequences that have been integrated into the nuclear chromosomes. Endogenous pararetrovirus (EPRV) are a class of EVEs derived from DNA viruses of the family Caulimoviridae. Previous works based on a limited number of genome assemblies demonstrated that EPRVs are abundant in plants and are present in several species. The availability of genome sequences has been immensely increased in the recent years and we took advantage of these resources to have a more extensive view of the presence of EPRVs in plant genomes. We analyzed 278 genome assemblies corresponding to 267 species (254 from Viridiplantae) using tBLASTn against a collection of conserved domains of the Reverse Transcriptases (RT) of Caulimoviridae. We concentrated our search on complete and well-conserved RT domains with an uninterrupted ORF comprising the genetic information for at least 300 amino acids. We obtained 11.527 sequences from the genomes of 202 species spanning the whole Tracheophyta clade. These elements were grouped in 57 clusters and classified in 13 genera, including a newly proposed genus we called Wendovirus. Wendoviruses are characterized by the presence of four open reading frames and two of them encode for aspartic proteinases. Comparing plant genomes, we observed important differences between the plant families and genera in the number and type of EPRVs found. In general, florendoviruses are the most abundant and widely distributed EPRVs. The presence of multiple identical RT domain sequences in some of the genomes suggests their recent amplification.
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8
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Valli AA, Gonzalo-Magro I, Sanchez DH. Rearranged Endogenized Plant Pararetroviruses as Evidence of Heritable RNA-based Immunity. Mol Biol Evol 2022; 40:6794085. [PMID: 36322467 PMCID: PMC9868043 DOI: 10.1093/molbev/msac240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/05/2022] [Accepted: 10/25/2022] [Indexed: 01/24/2023] Open
Abstract
Eukaryotic genomics frequently revealed historical spontaneous endogenization events of external invading nucleic acids, such as viral elements. In plants, an extensive occurrence of endogenous plant pararetroviruses (EPRVs) is usually believed to endow hosts with an additional layer of internal suppressive weaponry. However, an actual demonstration of this activity remains speculative. We analyzed the EPRV component and accompanying silencing effectors of Solanum lycopersicum, documenting that intronic/intergenic pararetroviral integrations bearing inverted-repeats fuel the plant's RNA-based immune system with suitable transcripts capable of evoking a silencing response. A surprisingly small set of rearrangements explained a substantial fraction of pararetroviral-derived endogenous small-interfering (si)RNAs, enriched in 22-nt forms typically associated with anti-viral post-transcriptional gene silencing. We provide preliminary evidence that such genetic and immunological signals may be found in other species outside the genus Solanum. Based on molecular dating, bioinformatics, and empirical explorations, we propose that homology-dependent silencing emerging from particular immuno-competent rearranged chromosomal areas that constitute an adaptive heritable trans-acting record of past infections, with potential impact against the unlocking of plant latent EPRVs and cognate-free pararetroviruses.
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Affiliation(s)
| | - Irene Gonzalo-Magro
- Centro Nacional de Biotecnología (CNB-CSIC), Calle Darwin 3, 28049 Madrid, Spain
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9
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Kalyankumar KK, Malathi VG, Renukadevi P, S MK, Manivannan N, Patil SG, Karthikeyan G. Molecular epidemiology on seasonal variation of yellow mosaic disease incidence in blackgram (Vigna mungo L. Hepper) with its vector Bemisia tabaci. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2022; 66:1985-1995. [PMID: 35930085 DOI: 10.1007/s00484-022-02334-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
The yellow mosaic disease (YMD) of blackgram caused by Mungbean yellow mosaic virus has emerged as a serious threat to grain legume production, especially in Southeastern Asia. Seasonal incidence of YMD with its vector population was assessed in three different agroclimatic zones of Tamil Nadu in India for three consecutive cropping seasons namely, Rabi 2018 (October-December), Summer 2019 (March-May), and Kharif 2019 (June-August) at three different time intervals viz., 20, 40, and 60 days after sowing (DAS). For all three seasons, disease incidence and whitefly count were recorded for a resistant and susceptible variety of blackgram in fields without any vector control intervention. The highest disease incidence (87%) was observed in the Panpozhi location during the summer season followed by Vamban and Coimbatore locations. The whitefly count was made through both visual count and yellow sticky traps. The whitefly population was highest at 20 DAS and decreased with the increasing age of crop for all the three locations assessed. Molecular epidemiology was analyzed by determining latent infection of mungbean yellow mosaic virus (MYMV) using molecular diagnosis. Latent infection was found to be well pronounced in the Coimbatore location during the Kharif season, where the crop was asymptomatic in both the resistant and susceptible varieties for all the three time periods assessed. The latent infection of MYMV observed in Coimbatore and Vamban ranged from 16.6 to 83.3% in both resistant and susceptible varieties for all three seasons. In Panpozhi, the latent infection of MYMV ranged from 16.6 to 66.6% for the susceptible variety (CO-5) for all three seasons observed. However, in the Panpozhi location, the resistant variety (VBN-8) failed to record any latent infection.
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Affiliation(s)
| | - V G Malathi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - P Renukadevi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Mohan Kumar S
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - N Manivannan
- National Pulses Research Centre, Tamil Nadu Agricultural University, Vamban, 622303, Pudukkottai, India
| | - S G Patil
- Department of Physical Sciences and Information Technology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - G Karthikeyan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
- Department of Physical Sciences and Information Technology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
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10
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Interspecific hybridization in tomato influences endogenous viral sRNAs and alters gene expression. Genome Biol 2022; 23:120. [PMID: 35597968 PMCID: PMC9124383 DOI: 10.1186/s13059-022-02685-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background Hybridization is associated with the activation of transposable elements and changes in the patterns of gene expression leading to phenotypic changes. However, the underlying mechanisms are not well understood. Results Here, we describe the changes to the gene expression in interspecific Solanum hybrids that are associated with small RNAs derived from endogenous (para)retroviruses (EPRV). There were prominent changes to sRNA profiles in these hybrids involving 22-nt species produced in the DCL2 biogenesis pathway, and the hybridization-induced changes to the gene expression were similar to those in a dcl2 mutant. Conclusions These findings indicate that hybridization leads to activation of EPRV, perturbation of small RNA profiles, and, consequently, changes in the gene expression. Such hybridization-induced variation in the gene expression could increase the natural phenotypic variation in natural evolution or in breeding for agriculture. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02685-z.
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Silva G, Bömer M, Turaki AA, Nkere CK, Kumar PL, Seal SE. Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:846989. [PMID: 35620696 PMCID: PMC9127665 DOI: 10.3389/fpls.2022.846989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Viruses of the genus Badnavirus (family Caulimoviridae) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically important plant species. Infection due to activation of replication-competent integrated copies of the genera Badnavirus, Petuvirus and Cavemovirus has been described. Such endogenous badnaviral elements pose challenges to the development of nucleic acid-based diagnostic methods for episomal virus infections and decisions on health certification for international movement of germplasm and seed. One major food security crop affected is yam (Dioscorea spp.). A diverse range of Dioscorea bacilliform viruses (DBVs), and endogenous DBV (eDBV) sequences have been found to be widespread in yams cultivated in West Africa and other parts of the world. This study outlines the development of multiplex PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE) to assist in the detection and analysis of eDBVs, through the example of analysing yam germplasm from Nigeria and Ghana. Primers targeting the three most prevalent DBV monophyletic species groups in West Africa were designed to improve DGGE resolution of complex eDBV sequence fingerprints. Multiplex PCR-DGGE with the addition of a tailor-made DGGE sequence marker enables rapid comparison of endogenous badnaviral sequence diversity across germplasm, as illustrated in this study for eDBV diversity in yam.
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Affiliation(s)
- Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Moritz Bömer
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Aliyu A. Turaki
- Kebbi State University of Science and Technology Aliero, Birnin Kebbi, Nigeria
| | - Chukwuemeka K. Nkere
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Crop Protection and Environmental Biology (CPEB), University of Ibadan, Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - P. Lava Kumar
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Susan E. Seal
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
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Bhat AI, Mohandas A, Sreenayana B, Archana TS, Jasna K. Piper DNA virus 1 and 2 are endogenous pararetroviruses integrated into chromosomes of black pepper ( Piper nigrum L). Virusdisease 2022; 33:114-118. [PMID: 35493754 PMCID: PMC9005556 DOI: 10.1007/s13337-021-00752-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/18/2021] [Indexed: 11/26/2022] Open
Abstract
A previous study named 7178 and 892 bp contigs obtained through high-throughput sequencing (HTS) of black pepper as Piper DNA virus 1 (PDV-1) and PDV-2 respectively. In the present study, HTS results were confirmed through polymerase chain reaction and Sanger sequencing. The sequenced region of both PDV-1 and PDV-2 contained partial genomes with motifs characteristic of pararetroviruses. BLAST analysis of PDV-1 and PDV-2 against the whole genome sequence of the black pepper showed integration of the PDV-1 at 22 loci in chromosome number 14, and PDV-2 at two loci in chromosome number 12 of black pepper. The integration was confirmed through amplification and sequencing of the junction regions. The present study suggests that both PDV-1 and PDV-2 occur as endogenous viruses in black pepper. Further studies are needed to determine whether these endogenous viruses occur in episomal forms, their complete genome sequence and whether they are activable under abiotic stress conditions. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-021-00752-w.
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Affiliation(s)
- A. I. Bhat
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673012 India
| | - A. Mohandas
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673012 India
| | - B. Sreenayana
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673012 India
| | - T. S. Archana
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673012 India
| | - K. Jasna
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673012 India
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Zakeel MCM, Geering ADW, Thomas JE, Akinsanmi OA. Characterisation of novel endogenous geminiviral elements in macadamia. BMC Genomics 2021; 22:858. [PMID: 34837949 PMCID: PMC8626973 DOI: 10.1186/s12864-021-08174-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/11/2021] [Indexed: 11/11/2022] Open
Abstract
Background The presence of geminivirus sequences in a preliminary analysis of sRNA sequences from the leaves of macadamia trees with abnormal vertical growth (AVG) syndrome was investigated. Results A locus of endogenous geminiviral elements (EGE) in the macadamia genome was analysed, and the sequences revealed a high level of deletions and/or partial integrations, thus rendering the EGE transcriptionally inactive. The replication defective EGE in the macadamia genome indicates its inability to be the source of new viral infections and thus cause AVG or any other disease in macadamia. The EGE sequences were detected in two edible Macadamia species that constitute commercial cultivars and the wild germplasm of edible and inedible species of Macadamia. This strongly suggests that the integration preceded speciation of the genus Macadamia. A draft genome of a locus of EGE in Macadamia was developed. The findings of this study provide evidence to suggest the endogenization of the geminiviral sequences in the macadamia genome and the ancestral relationship of EGE with Macadamia in the Proteaceae family. Random mutations accumulating in the EGE inform that the sequence is evolving. Conclusions The EGE in Macadamia is inactive and thus not a direct cause of any diseases or syndromes including AVG in macadamia. The insertion of the EGE in the macadamia genome preceded speciation of the genus Macadamia. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08174-0.
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Affiliation(s)
- Mohamed C M Zakeel
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, GPO Box 267, Brisbane, QLD, 4001, Australia.
| | - Andrew D W Geering
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, GPO Box 267, Brisbane, QLD, 4001, Australia
| | - John E Thomas
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, GPO Box 267, Brisbane, QLD, 4001, Australia
| | - Olufemi A Akinsanmi
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, GPO Box 267, Brisbane, QLD, 4001, Australia.
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14
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Schmidt N, Seibt KM, Weber B, Schwarzacher T, Schmidt T, Heitkam T. Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). ANNALS OF BOTANY 2021; 128:281-299. [PMID: 33729490 PMCID: PMC8389469 DOI: 10.1093/aob/mcab042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Endogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence. METHODS Using next- and third-generation sequencing data and genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRVs (beetEPRVs) in the B. vulgaris genome. Focusing on the endogenous caulimovirid beetEPRV3, we investigated its chromosomal localization, abundance and distribution by fluorescent in situ and Southern hybridization. KEY RESULTS Full-length beetEPRVs range between 7.5 and 10.7 kb in size, are heterogeneous in structure and sequence, and occupy about 0.3 % of the beet genome. Although all three beetEPRVs were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that specifically target the individual beetEPRVs, indicating stringent epigenetic suppression. BeetEPRV3 sequences occur along all sugar beet chromosomes, preferentially in the vicinity of each other and are associated with heterochromatic, centromeric and intercalary satellite DNAs. BeetEPRV3 members also exist in genomes of related wild species, indicating an initial beetEPRV3 integration 13.4-7.2 million years ago. CONCLUSIONS Our study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing implies possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.
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Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kathrin M Seibt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Beatrice Weber
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou, PR China
| | - Thomas Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
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15
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Kovarik A, Hemleben V. A commentary on: 'Broken, silent and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris)'. ANNALS OF BOTANY 2021; 128:iii-iv. [PMID: 34350938 PMCID: PMC8389174 DOI: 10.1093/aob/mcab068] [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] [Indexed: 06/13/2023]
Abstract
This article comments on: Nicola Schmidt, Kathrin M. Seibt, Beatrice Weber, Trude Schwarzacher, Thomas Schmidt, and Tony Heitkam, Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris), Annals of Botany Volume 128, Issue 3, 26 August 2021, Pages 281–291, https://doi.org/10.1093/aob/mcab042
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Affiliation(s)
- Ales Kovarik
- Laboratory of Molecular Epigenetics, Intitute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, Czech Republic
| | - Vera Hemleben
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle, Tübingen, Germany
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16
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Ahamedemujtaba V, Atheena PV, Bhat AI, Krishnamurthy KS, Srinivasan V. Symptoms of piper yellow mottle virus in black pepper as influenced by temperature and relative humidity. Virusdisease 2021; 32:305-313. [PMID: 34423100 DOI: 10.1007/s13337-021-00686-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/26/2021] [Indexed: 11/26/2022] Open
Abstract
Masking of symptoms in winter and their re-appearance in black pepper (Piper nigrum L.) infected with piper yellow mottle virus (PYMoV) in summer is common, especially on new flushes that appear after pre-monsoon showers. Plants of nineteen cultivars of black pepper infected with PYMoV but without any visible symptoms were grown in a polyhouse under natural conditions and in a greenhouse under controlled conditions from January 2019 to January 2020. The number of plants expressing symptoms in the polyhouse increased gradually from 1% during the 3rd standard meteorological week (SMW) (16 January) to 41% during the 21st SMW (22 May), when the afternoon temperature was 30-40 °C and relative humidity (RH) was 75-93%, but began declining thereafter until the 53rd SMW (1 January), when the afternoon temperature was 30-36 °C and RH was 65-86%. The proportion of plants expressing symptoms varied with the cultivar. However, in the greenhouse, in which temperature and RH were maintained at approximately 26 °C and 80%, respectively, not more than 2% of the plants expressed symptoms. The number of symptomatic plants was positively correlated to maximum temperature (T Max) and maximum relative humidity (RH Max) in the afternoon. Based on this observation, a model for predicting the percentage of symptomatic plants was developed using stepwise regression analysis. Plants at the two sites did not differ significantly in the concentration of virus (virus titre) but differed significantly in the content of total carbohydrates, lipid peroxidase, and phenols. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-021-00686-3.
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Affiliation(s)
- V Ahamedemujtaba
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673 012 India
| | - P V Atheena
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673 012 India
| | - A I Bhat
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673 012 India
| | - K S Krishnamurthy
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673 012 India
| | - V Srinivasan
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala 673 012 India
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Chabannes M, Gabriel M, Aksa A, Galzi S, Dufayard J, Iskra‐Caruana M, Muller E. Badnaviruses and banana genomes: a long association sheds light on Musa phylogeny and origin. MOLECULAR PLANT PATHOLOGY 2021; 22:216-230. [PMID: 33231927 PMCID: PMC7814968 DOI: 10.1111/mpp.13019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/07/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Badnaviruses are double-stranded DNA pararetroviruses of the family Caulimoviridae. Badnaviral sequences found in banana are distributed over three main clades of the genus Badnavirus and exhibit wide genetic diversity. Interestingly, the nuclear genome of many plants, including banana, is invaded by numerous badnaviral sequences although badnaviruses do not require an integration step to replicate, unlike animal retroviruses. Here, we confirm that banana streak viruses (BSVs) are restricted to clades 1 and 3. We also show that only BSVs from clade 3 encompassing East African viral species are not integrated into Musa genomes, unlike BSVs from clade 1. Finally, we demonstrate that sequences from clade 2 are definitively integrated into Musa genomes with no evidence of episomal counterparts; all are phylogenetically distant from BSVs known to date. Using different molecular approaches, we dissected the coevolution between badnaviral sequences of clade 2 and banana by comparing badnavirus integration patterns across a banana sampling representing major Musa speciation events. Our data suggest that primary viral integrations occurred millions of years ago in banana genomes under different possible scenarios. Endogenous badnaviral sequences can be used as powerful markers to better characterize the Musa phylogeny, narrowing down the likely geographical origin of the Musa ancestor.
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Affiliation(s)
- Matthieu Chabannes
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Marc Gabriel
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Abderrahmane Aksa
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Serge Galzi
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Jean‐François Dufayard
- CIRAD, UMR AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | | | - Emmanuelle Muller
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
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18
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Serfraz S, Sharma V, Maumus F, Aubriot X, Geering ADW, Teycheney PY. Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant ( Solanum melongena). FRONTIERS IN PLANT SCIENCE 2021; 12:683681. [PMID: 34367211 PMCID: PMC8346255 DOI: 10.3389/fpls.2021.683681] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/30/2021] [Indexed: 05/20/2023]
Abstract
Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene (R1) of brinjal eggplant (Solanum melongena) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena, whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum, the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum.
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Affiliation(s)
- Saad Serfraz
- CIRAD, UMR AGAP Institut, F-97130, Capesterre-Belle-Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, France
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Vikas Sharma
- URGI, INRAE, Université Paris-Saclay, Versailles, France
| | - Florian Maumus
- URGI, INRAE, Université Paris-Saclay, Versailles, France
| | - Xavier Aubriot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Andrew D. W. Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP Institut, F-97130, Capesterre-Belle-Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, France
- *Correspondence: Pierre-Yves Teycheney,
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19
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Richert-Pöggeler KR, Vijverberg K, Alisawi O, Chofong GN, Heslop-Harrison JS(P, Schwarzacher T. Participation of Multifunctional RNA in Replication, Recombination and Regulation of Endogenous Plant Pararetroviruses (EPRVs). FRONTIERS IN PLANT SCIENCE 2021; 12:689307. [PMID: 34234799 PMCID: PMC8256270 DOI: 10.3389/fpls.2021.689307] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/19/2021] [Indexed: 05/11/2023]
Abstract
Pararetroviruses, taxon Caulimoviridae, are typical of retroelements with reverse transcriptase and share a common origin with retroviruses and LTR retrotransposons, presumably dating back 1.6 billion years and illustrating the transition from an RNA to a DNA world. After transcription of the viral genome in the host nucleus, viral DNA synthesis occurs in the cytoplasm on the generated terminally redundant RNA including inter- and intra-molecule recombination steps rather than relying on nuclear DNA replication. RNA recombination events between an ancestral genomic retroelement with exogenous RNA viruses were seminal in pararetrovirus evolution resulting in horizontal transmission and episomal replication. Instead of active integration, pararetroviruses use the host DNA repair machinery to prevail in genomes of angiosperms, gymnosperms and ferns. Pararetrovirus integration - leading to Endogenous ParaRetroViruses, EPRVs - by illegitimate recombination can happen if their sequences instead of homologous host genomic sequences on the sister chromatid (during mitosis) or homologous chromosome (during meiosis) are used as template. Multiple layers of RNA interference exist regulating episomal and chromosomal forms of the pararetrovirus. Pararetroviruses have evolved suppressors against this plant defense in the arms race during co-evolution which can result in deregulation of plant genes. Small RNAs serve as signaling molecules for Transcriptional and Post-Transcriptional Gene Silencing (TGS, PTGS) pathways. Different populations of small RNAs comprising 21-24 nt and 18-30 nt in length have been reported for Citrus, Fritillaria, Musa, Petunia, Solanum and Beta. Recombination and RNA interference are driving forces for evolution and regulation of EPRVs.
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Affiliation(s)
- Katja R. Richert-Pöggeler
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- *Correspondence: Katja R. Richert-Pöggeler,
| | - Kitty Vijverberg
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Leiden, Netherlands
- Radboud University, Institute for Water and Wetland Research (IWWR), Nijmegen, Netherlands
| | - Osamah Alisawi
- Department of Plant Protection, Faculty of Agriculture, University of Kufa, Najaf, Iraq
| | - Gilbert N. Chofong
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - J. S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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20
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Dolja VV, Krupovic M, Koonin EV. Deep Roots and Splendid Boughs of the Global Plant Virome. ANNUAL REVIEW OF PHYTOPATHOLOGY 2020; 58:23-53. [PMID: 32459570 DOI: 10.1146/annurev-phyto-030320-041346] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Land plants host a vast and diverse virome that is dominated by RNA viruses, with major additional contributions from reverse-transcribing and single-stranded (ss) DNA viruses. Here, we introduce the recently adopted comprehensive taxonomy of viruses based on phylogenomic analyses, as applied to the plant virome. We further trace the evolutionary ancestry of distinct plant virus lineages to primordial genetic mobile elements. We discuss the growing evidence of the pivotal role of horizontal virus transfer from invertebrates to plants during the terrestrialization of these organisms, which was enabled by the evolution of close ecological associations between these diverse organisms. It is our hope that the emerging big picture of the formation and global architecture of the plant virome will be of broad interest to plant biologists and virologists alike and will stimulate ever deeper inquiry into the fascinating field of virus-plant coevolution.
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Affiliation(s)
- Valerian V Dolja
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331-2902, USA;
| | - Mart Krupovic
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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21
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Kuriyama K, Tabara M, Moriyama H, Kanazawa A, Koiwa H, Takahashi H, Fukuhara T. Disturbance of floral colour pattern by activation of an endogenous pararetrovirus, petunia vein clearing virus, in aged petunia plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:497-511. [PMID: 32100385 PMCID: PMC7496347 DOI: 10.1111/tpj.14728] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 05/22/2023]
Abstract
White areas of star-type bicolour petals of petunia (Petunia hybrida) are caused by post-transcriptional gene silencing (PTGS) of the key enzyme of anthocyanin biosynthesis. We observed blotched flowers and a vein-clearing symptom in aged petunia plants. To determine the cause of blotched flowers, we focused on an endogenous pararetrovirus, petunia vein clearing virus (PVCV), because this virus may have a suppressor of PTGS (VSR). Transcripts and episomal DNAs derived from proviral PVCVs accumulated in aged plants, indicating that PVCV was activated as the host plant aged. Furthermore, DNA methylation of CG and CHG sites in the promoter region of proviral PVCV decreased in aged plants, suggesting that poor maintenance of DNA methylation activates PVCV. In parallel, de novo DNA methylation of CHH sites in its promoter region was also detected. Therefore, both activation and inactivation of PVCV occurred in aged plants. The accumulation of PVCV transcripts and episomal DNAs in blotched regions and the detection of VSR activity support a mechanism in which suppression of PTGS by PVCV causes blotched flowers.
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Affiliation(s)
- Kazunori Kuriyama
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Midori Tabara
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Akira Kanazawa
- Research Faculty of AgricultureHokkaido UniversityKita 9, Nishi 9, Kita‐kuSapporo060‐8589Japan
| | - Hisashi Koiwa
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Department of Horticultural SciencesTexas A&M UniversityCollege StationTX77843USA
| | - Hideki Takahashi
- Graduate School of Agricultural ScienceTohoku University468‐1, Aramaki‐Aza‐AobaSendai980‐0845Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
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Takahashi H, Fukuhara T, Kitazawa H, Kormelink R. Virus Latency and the Impact on Plants. Front Microbiol 2019; 10:2764. [PMID: 31866963 PMCID: PMC6908805 DOI: 10.3389/fmicb.2019.02764] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/12/2019] [Indexed: 11/15/2022] Open
Abstract
Plant viruses are thought to be essentially harmful to the lives of their cultivated crop hosts. In most cases studied, the interaction between viruses and cultivated crop plants negatively affects host morphology and physiology, thereby resulting in disease. Native wild/non-cultivated plants are often latently infected with viruses without any clear symptoms. Although seemingly non-harmful, these viruses pose a threat to cultivated crops because they can be transmitted by vectors and cause disease. Reports are accumulating on infections with latent plant viruses that do not cause disease but rather seem to be beneficial to the lives of wild host plants. In a few cases, viral latency involves the integration of full-length genome copies into the host genome that, in response to environmental stress or during certain developmental stages of host plants, can become activated to generate and replicate episomal copies, a transition from latency to reactivation and causation of disease development. The interaction between viruses and host plants may also lead to the integration of partial-length segments of viral DNA genomes or copy DNA of viral RNA genome sequences into the host genome. Transcripts derived from such integrated viral elements (EVEs) may be beneficial to host plants, for example, by conferring levels of virus resistance and/or causing persistence/latency of viral infections. Studies on viral latency in wild host plants might help us to understand and elucidate the underlying mechanisms of latency and provide insights into the raison d’être for viruses in the lives of plants.
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Affiliation(s)
- Hideki Takahashi
- Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Plant Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences and Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University, Wageningen, Netherlands
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23
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Genetic differences between Korean and American isolates of Petunia vein clearing virus. Virus Genes 2019; 56:78-86. [PMID: 31705264 DOI: 10.1007/s11262-019-01711-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
Petunia plants are used for urban landscaping in many parts of the world, including South Korea. In this study, we aimed to investigate the occurrence of petunia vein clearing virus (PVCV) infection in petunia plants in Seoul, South Korea. PVCV was detected from 23 of 79 petunia samples collected from Seoul. We obtained the complete genome sequences of the Korean isolates in this study (called PVCV-Kr, Kr2, and Kr3), which were compared with the genome sequence of the USA isolate of the virus (PVCV-USA). The genomic DNA of the three PVCV isolates was found to comprise 7210-7267 nucleotides (nts), which is 4-15 nts longer than the PVCV-USA genome. The genomes of the Kr and Kr2 isolates encode a large polyprotein of 252 kDa (2180 amino acids (aa)). The genome of the Kr3 isolate encodes a large polyprotein of 255 kDa (2203 aa). The polyprotein has six protein domains: a movement protein (MP; 72 aa), a coiled-coil domain (CC; 33 aa), an RNA-binding domain (RB; 18 aa), a protease (PR; 21 aa), a reverse transcriptase (RT; 196 aa), and an RNase H (RH; 121 aa). The large polyprotein and six domains of the three isolates showed 93.9-100.0% sequence homology with those of PVCV-USA. Furthermore, the polymerase polyprotein gene (PR, RT, and RH) of the four PVCV isolates containing the USA isolate grouped with those of Rice tungro bacilliform virus and Soybean chlorotic mottle virus, which belong to the same family (Caulimoviridae). Our findings suggested that the Korean isolates represent a new isolate of PVCV. To our knowledge, this is the first report of PVCV detection in South Korea.
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24
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Development of expressed sequenced tags (EST) to identify some pathogen resistance genes expressed in Gossypium arboreum. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Liu Q, Li X, Zhou X, Li M, Zhang F, Schwarzacher T, Heslop-Harrison JS. The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads. BMC PLANT BIOLOGY 2019; 19:226. [PMID: 31146681 PMCID: PMC6543597 DOI: 10.1186/s12870-019-1769-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/09/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Repetitive DNA motifs - not coding genetic information and repeated millions to hundreds of times - make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the repetitive DNA families in oats (Avena sativa, 2n = 6x = 42, AACCDD), a recognized health-food, and its wild relatives. RESULTS Whole-genome sequencing followed by k-mer and RepeatExplorer graph-based clustering analyses enabled assessment of repetitive DNA composition in common oat and its wild relatives' genomes. Fluorescence in situ hybridization (FISH)-based karyotypes are developed to understand chromosome and repetitive sequence evolution of common oat. We show that some 200 repeated DNA motifs make up 70% of the Avena genome, with less than 20 families making up 20% of the total. Retroelements represent the major component, with Ty3/Gypsy elements representing more than 40% of all the DNA, nearly three times more abundant than Ty1/Copia elements. DNA transposons are about 5% of the total, while tandemly repeated, satellite DNA sequences fit into 55 families and represent about 2% of the genome. The Avena species are monophyletic, but both bioinformatic comparisons of repeats in the different genomes, and in situ hybridization to metaphase chromosomes from the hexaploid species, shows that some repeat families are specific to individual genomes, or the A and D genomes together. Notably, there are terminal regions of many chromosomes showing different repeat families from the rest of the chromosome, suggesting presence of translocations between the genomes. CONCLUSIONS The relatively small number of repeat families shows there are evolutionary constraints on their nature and amplification, with mechanisms leading to homogenization, while repeat characterization is useful in providing genome markers and to assist with future assemblies of this large genome (c. 4100 Mb in the diploid). The frequency of inter-genomic translocations suggests optimum strategies to exploit genetic variation from diploid oats for improvement of the hexaploid may differ from those used widely in bread wheat.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xiaoyu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangying Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingzhi Li
- Genepioneer Biotechnologies Co. Ltd., Nanjing, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
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Zhang F, Yang Z, Hong N, Wang G, Wang A, Wang L. Identification and characterization of water chestnut Soymovirus-1 (WCSV-1), a novel Soymovirus in water chestnuts (Eleocharis dulcis). BMC PLANT BIOLOGY 2019; 19:159. [PMID: 31023231 PMCID: PMC6482551 DOI: 10.1186/s12870-019-1761-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND A disease of unknown etiology in water chestnut plants (Eleocharis dulcis) was reported in China between 2012 and 2014. High throughput sequencing of small RNA (sRNA) combined with bioinformatics, and molecular identification based on PCR detection with virus-specific primers and DNA sequencing is a desirable approach to identify an unknown infectious agent. In this study, we employed this approach to identify viral sequences in water chestnut plants and to explore the molecular interaction of the identified viral pathogen and its natural plant host. RESULTS Based on high throughput sequencing of virus-derived small RNAs (vsRNA), we identified the sequence a new-to-science double-strand DNA virus isolated from water chestnut cv. 'Tuanfeng' samples, a widely grown cultivar in Hubei province, China, and analyzed its genomic organization. The complete genomic sequence is 7535 base-pairs in length, and shares 42-52% nucleotide sequence identity with viruses in the Caulimoviridae family. The virus contains nine predicated open reading frames (ORFs) encoding nine hypothetical proteins, with conserved domains characteristic of caulimoviruses. Phylogenetic analyses at the nucleotide and amino acid levels indicated that the virus belongs to the genus Soymovirus. The virus is tentatively named Water chestnut soymovirus-1 (WCSV-1). Phylogenetic analysis of the putative viral polymerase protein suggested that WCSV-1 is distinct to other well established species in the Soymovirus genus. This conclusion was supported by phylogenetic analyses of the amino acid sequences encoded by ORFs I, IV, VI, or VII. The sRNA bioinformatics showed that the majority of the vsRNAs are 22-nt in length with a preference for U at the 5'-terminal nucleotide. The vsRNAs are unevenly distributed over both strands of the entire WCSV-1 circular genome, and are clustered into small defined regions. In addition, we detected WCSV-1 in asymptomatic and symptomatic water chestnut samples collected from different regions of China by using PCR. RNA-seq assays further confirmed the presence of WCSV-1-derived viral RNA in infected plants. CONCLUSIONS This is the first discovery of a dsDNA virus in the genus Soymovirus infecting water chestnuts. Data presented also add new information towards a better understanding of the co-evolutionary mechanisms between the virus and its natural plant host.
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Affiliation(s)
- Fangpeng Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
- Lab of Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
| | - Zuokun Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
- Lab of Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
- Lab of Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
- Lab of Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 Canada
| | - Liping Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
- Lab of Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
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27
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Pooggin MM. Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization. Front Microbiol 2018; 9:2779. [PMID: 30524398 PMCID: PMC6256188 DOI: 10.3389/fmicb.2018.02779] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.
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Affiliation(s)
- Mikhail M. Pooggin
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
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28
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Chu H, Jo Y, Choi H, Lee BC, Cho WK. Identification of viral domains integrated into Arabidopsis proteome. Mol Phylogenet Evol 2018; 128:246-257. [PMID: 30125655 DOI: 10.1016/j.ympev.2018.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 08/05/2018] [Accepted: 08/15/2018] [Indexed: 10/28/2022]
Abstract
Horizontal gene transfer (HGT) contributes to the genome evolution of living organisms. In particular, several recent studies provide convincing data on the integration of viral sequences into diverse organisms. Here, we identified 101 viral domains integrated into the model plant Arabidopsis proteome. Functional analysis based on gene ontology (GO) terms indicates that viral domains in the Arabidopsis proteome were involved in various stress responses with binding functions. Protein interaction networks support the strong protein interactions of viral domains with other Arabidopsis proteins. A proteome-wide analysis gave a comprehensive evolutionary view of viral domains integrated into 41 plant proteomes, revealing the specific and conserved integration of viral domains into plant proteomes. Phylogenetic analyses revealed the possible HGT between viral domains and plant proteomes. Our results provide an overview of the integration of viral domains into plant proteomes and their possible functional roles associated with plant defense mechanisms.
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Affiliation(s)
- Hyosub Chu
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonhwa Jo
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hoseong Choi
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bong Choon Lee
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju 55365, Republic of Korea
| | - Won Kyong Cho
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; The Taejin Genome Institute, Gadam-gil 61, Hoeongseong 25239, Republic of Korea.
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29
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Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, Gifford R, Harrach B, Hull R, Johnson W, Kreuze JF, Lindemann D, Llorens C, Lockhart B, Mayer J, Muller E, Olszewski NE, Pappu HR, Pooggin MM, Richert-Pöggeler KR, Sabanadzovic S, Sanfaçon H, Schoelz JE, Seal S, Stavolone L, Stoye JP, Teycheney PY, Tristem M, Koonin EV, Kuhn JH. Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses. J Virol 2018; 92:e00515-18. [PMID: 29618642 PMCID: PMC5974489 DOI: 10.1128/jvi.00515-18] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris, France
| | - Jonas Blomberg
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Hung Fan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Andrew D Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Robert Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Roger Hull
- Child Okeford, Blandford Forum, Dorset, United Kingdom
| | - Welkin Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts, USA
| | - Jan F Kreuze
- Crop and System Sciences Division, International Potato Center (CIP), Lima, Peru
| | - Dirk Lindemann
- Institute of Virology, Technische Universität Dresden, Dresden, Germany
| | - Carlos Llorens
- Biotechvana, Parc Cientific, Universitat de Valencia, Valencia, Spain
| | - Ben Lockhart
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jens Mayer
- Institute of Human Genetics, University of Saarland, Homburg, Germany
| | - Emmanuelle Muller
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Neil E Olszewski
- Department of Microbial and Plant Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | | | - Katja R Richert-Pöggeler
- Julius Kühn-Institut, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Hélène Sanfaçon
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, BC, Canada
| | - James E Schoelz
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Chatham, Kent, United Kingdom
| | - Livia Stavolone
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Jonathan P Stoye
- The Francis Crick Institute and Department of Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP, Capesterre Belle Eau, Guadeloupe, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Michael Tristem
- Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
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30
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Yu H, Wang X, Lu Z, Xu Y, Deng X, Xu Q. Endogenous pararetrovirus sequences are widely present in Citrinae genomes. Virus Res 2018; 262:48-53. [PMID: 29792903 DOI: 10.1016/j.virusres.2018.05.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 05/20/2018] [Accepted: 05/20/2018] [Indexed: 01/04/2023]
Abstract
Endogenous pararetroviruses (EPRVs) are characterized in several plant genomes and their biological effects have been reported. In this study, hundreds of EPRV segments were identified in six Citrinae genomes. A total of 1034 EPRV segments were identified in the genomes of sweet orange, 2036 in pummelo, 598 in clementine mandarin, 752 in Ichang papeda, 2060 in citron and 245 in atalantia. Genomic analysis indicated that EPRV segments tend to cluster as hot spots in the genomes, particularly on chromosome 2 and 5. Large numbers of simple repeats and transposable elements were identified in the 2-kb flanking regions of the EPRV segments. Comparative genomic analysis and PCR experiments showed that there are highly conserved EPRV segments and species-specific EPRV segments between the Citrinae genomes. Phylogenetic analysis suggested that the integration events of EPRVs could initiate in a common progenitor of Citrinae species and repeatedly occur during the Citrinae divergence.
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Affiliation(s)
- Huiwen Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhihao Lu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuantao Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.
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31
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Jeger M, Bragard C, Caffier D, Chatzivassiliou E, Dehnen-Schmutz K, Gilioli G, Gregoire JC, Jaques Miret JA, MacLeod A, Navajas Navarro M, Niere B, Parnell S, Potting R, Rafoss T, Rossi V, Urek G, Van Bruggen A, Van der Werf W, West J, Winter S, Catara AF, Duran-Vila N, Hollo G, Kaluski T, Candresse T. Pest categorisation of 'Blight and blight-like' diseases of citrus. EFSA J 2018; 16:e05248. [PMID: 32625880 PMCID: PMC7009572 DOI: 10.2903/j.efsa.2018.5248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The EFSA Panel on Plant Health performed a pest categorisation of 'Blight and blight-like' for the EU territory. Blight is a major disease of citrus. Similar 'blight-like' diseases are also known (e.g. declinio, declinamiento) and are addressed simultaneously with Blight in the present categorisation. The causal agent(s) remain(s) unknown and the potential role of a recently identified citrus endogenous pararetrovirus (Citrus Blight-associated pararetrovirus, CBaPRV) remains to be established. Transmissibility and ability to produce consistent (although poorly specific) symptoms have been demonstrated and a combination of indirect approaches is used, with limits, for diagnosis. There are large uncertainties on the biology of the causal agent(s) and on the epidemiology of the disease, including the transmission mechanism(s) responsible for the observed field spread. Blight has been reported from North, Central and South America, Africa and Oceania but is not known to occur in the EU. It is listed in Annex IIA of Directive 2000/29EC. It has the potential to enter, establish and spread in the EU territory. The main entry pathway (citrus plants for planting) is closed by existing legislation and entry is only possible on minor pathways (such as illegal import). Blight is a severe disease and a negative impact is expected should it be introduced in the EU, but the magnitude of this negative impact is very difficult to estimate. 'Blight and blight like' satisfies all criteria evaluated by EFSA to qualify as a Union quarantine pest. It does not meet the criterion of being present in the EU to qualify as a Union regulated non-quarantine pest (RNQP). Since the identity of the causal agent(s) of the Blight and blight-like disease(s) and the existence and efficiency of natural spread mechanism(s) remain unknown, large uncertainties affect all aspects of the present pest categorisation.
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32
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Carrasco JL, Sánchez-Navarro JA, Elena SF. Exploring the role of cellular homologous of the 30K-superfamily of plant virus movement proteins. Virus Res 2018; 262:54-61. [PMID: 29475053 DOI: 10.1016/j.virusres.2018.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 12/22/2022]
Abstract
Genes orthologous to the 30K-superfamily of movement proteins (MP) from plant viruses have been recently discovered by bioinformatics analyses as integrated elements in the genome of most vascular plants. However, their functional relevance for plants is still unclear. Here, we undertake some preliminary steps into the functional characterization of one of these putative MP genes found in Arabidopsis thaliana. We found that the AtMP gene is expressed at different stages of the plant development, with accumulation being highest in flowers but lowest in mature siliques. We also found down-regulation of the gene may result in a small delay in plant development and in an exacerbation of the negative effect of salinity in germination efficiency. We have also explored whether changes in expression of the endogenous AtMP have any effect on susceptibility to infection with several viruses, and found that the infectivity of tobacco rattle tobravirus was strongly dependent on the expression of the endogenous AtMP. Finally, we have cloned the endogenous MP from four different plant species into an expression vector that allows for specifically assessing their activity as cell-to-cell movement proteins and have shown that though some may still retain the ancestral activity, they do so in a quite inefficient manner, thus suggesting they have acquired a novel function during adaptation to the host genome.
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Affiliation(s)
- José L Carrasco
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain
| | - Jesús A Sánchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain; Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Parc Científic UV, Catedrático Agustín Escardino 9, 46980, Paterna, València, Spain; The Santa Fe Institute,1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
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33
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Shrestha A, Khan A, Mishra DR, Bhuyan K, Sahoo B, Maiti IB, Dey N. RETRACTED: WRKY71 and TGA1a physically interact and synergistically regulate the activity of a novel promoter isolated from Petunia vein-clearing virus. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:133-146. [PMID: 29413896 DOI: 10.1016/j.bbagrm.2018.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/28/2017] [Accepted: 01/12/2018] [Indexed: 11/23/2022]
Abstract
Caulimoviral promoters have become excellent tools for efficient transgene expression in plants. However, the transcriptional framework controlling their systematic regulation is poorly understood. To understand this regulatory mechanism, we extensively studied a novel caulimoviral promoter, PV8 (-163 to +138, 301 bp), isolated from Petunia vein-clearing virus (PVCV). PVCV was found to be Salicylic acid (SA)-inducible and 2.5-3.0 times stronger than the widely used CaMV35S promoter. In silico analysis of the PV8 sequence revealed a unique clustering of two stress-responsive cis-elements, namely, as-11 and W-box1-2, located within a span of 31 bp (-74 to -47) that bound to the TGA1a and WRKY71 plant transcription factors (TFs), respectively. We found that as-1 (TTACG) and W-box (TGAC) elements occupied both TGA1a and WRKY71 on the PV8 backbone. Mutational studies demonstrated that the combinatorial influence of as-1 (-57) and W-box1-2 (-74 and -47) on the PV8 promoter sequence largely modulated its activity. TGA1a and WRKY71 physically interacted and cooperatively enhanced the transcriptional activity of the PV8 promoter. Biotic stress stimuli induced PV8 promoter activity by ~1.5 times. We also established the possible pathogen-elicitor function of AtWRKY71 and NtabWRKY71 TFs. Altogether, this study elucidates the interplay between TFs, biotic stress and caulimoviral promoter function.
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Affiliation(s)
- Ankita Shrestha
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Ahamed Khan
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Dipti Ranjan Mishra
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Kashyap Bhuyan
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Bhabani Sahoo
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Indu B Maiti
- Department of Molecular Plant Virology and Plant Genetic Engineering, KTRDC, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546-0236, United States
| | - Nrisingha Dey
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
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34
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Bömer M, Rathnayake AI, Visendi P, Silva G, Seal SE. Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Arch Virol 2017; 163:533-538. [PMID: 29134336 PMCID: PMC5799344 DOI: 10.1007/s00705-017-3605-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/27/2017] [Indexed: 11/03/2022]
Abstract
Yams (Dioscorea spp.) host a diverse range of badnaviruses (genus Badnavirus, family Caulimoviridae). The first complete genome sequence of Dioscorea bacilliform RT virus 3 (DBRTV3), which belongs to the monophyletic species group K5, is described. This virus is most closely related to Dioscorea bacilliform SN virus (DBSNV, group K4) based on a comparison of genome sequences. Recombination analysis identified a unique recombination event in DBRTV3, with DBSNV likely to be the major parent and Dioscorea bacilliform AL virus (DBALV) the minor parent, providing the first evidence for recombination in yam badnaviruses. This has important implications for yam breeding programmes globally.
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Affiliation(s)
- Moritz Bömer
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK.
| | - Ajith I Rathnayake
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Visendi
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
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PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm. Viruses 2017; 9:v9070181. [PMID: 28696406 PMCID: PMC5537673 DOI: 10.3390/v9070181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 12/19/2022] Open
Abstract
Badnaviruses (family Caulimoviridae, genus Badnavirus) have emerged as serious pathogens especially affecting the cultivation of tropical crops. Badnavirus sequences can be integrated in host genomes, complicating the detection of episomal infections and the assessment of viral genetic diversity in samples containing a complex mixture of sequences. Yam (Dioscorea spp.) plants are hosts to a diverse range of badnavirus species, and recent findings have suggested that mixed infections occur frequently in West African yam germplasm. Historically, the determination of the diversity of badnaviruses present in yam breeding lines has been achieved by cloning and sequencing of polymerase chain reaction (PCR) products. In this study, the molecular diversity of partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences from yam badnaviruses was analysed using PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE). This resulted in the identification of complex ‘fingerprints’ composed of multiple sequences of Dioscorea bacilliform viruses (DBVs). Many of these sequences show high nucleotide identities to endogenous DBV (eDBV) sequences deposited in GenBank, and fall into six monophyletic species groups. Our findings highlight PCR-DGGE as a powerful tool in badnavirus diversity studies enabling a rapid indication of sequence diversity as well as potential candidate integrated sequences revealed by their conserved nature across germplasm.
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Shahid MS, Aboughanem-Sabanadzovic N, Sabanadzovic S, Tzanetakis IE. Genomic Characterization and Population Structure of a Badnavirus Infecting Blackberry. PLANT DISEASE 2017; 101:110-115. [PMID: 30682310 DOI: 10.1094/pdis-04-16-0527-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Blackberry viruses are pervasive, decreasing growth, yield, and plant longevity. In a quest to identify viruses associated with blackberry yellow vein, a disease caused by virus complexes, a new double-stranded DNA virus, referred to as blackberry virus F (BVF), a putative member of the genus Badnavirus, family Caulimoviridae, was identified. The virus was found in both cultivated and wild blackberry samples collected from several states in the southern United States. Population structure, host range, and association with disease symptoms were assessed. As BVF integrates into the plant genome, it affects the production of virus-free propagation material, the cornerstone for certification programs.
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Affiliation(s)
- Muhammad Shafiq Shahid
- Department of Plant Pathology, Division of Agriculture, University of Arkansas, Fayetteville 72701
| | | | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State 39762
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Chen S, Kishima Y. Endogenous pararetroviruses in rice genomes as a fossil record useful for the emerging field of palaeovirology. MOLECULAR PLANT PATHOLOGY 2016; 17:1317-1320. [PMID: 27870389 PMCID: PMC6638417 DOI: 10.1111/mpp.12490] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 07/03/2016] [Accepted: 08/03/2016] [Indexed: 05/26/2023]
Affiliation(s)
- Sunlu Chen
- Laboratory of Plant Breeding, Research Faculty of AgricultureHokkaido UniversitySapporo060‐8589Japan
| | - Yuji Kishima
- Laboratory of Plant Breeding, Research Faculty of AgricultureHokkaido UniversitySapporo060‐8589Japan
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Bhat AI, Hohn T, Selvarajan R. Badnaviruses: The Current Global Scenario. Viruses 2016; 8:E177. [PMID: 27338451 PMCID: PMC4926197 DOI: 10.3390/v8060177] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/18/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022] Open
Abstract
Badnaviruses (Family: Caulimoviridae; Genus: Badnavirus) are non-enveloped bacilliform DNA viruses with a monopartite genome containing about 7.2 to 9.2 kb of dsDNA with three to seven open reading frames. They are transmitted by mealybugs and a few species by aphids in a semi-persistent manner. They are one of the most important plant virus groups and have emerged as serious pathogens affecting the cultivation of several horticultural crops in the tropics, especially banana, black pepper, cocoa, citrus, sugarcane, taro, and yam. Some badnaviruses are also known as endogenous viruses integrated into their host genomes and a few such endogenous viruses can be awakened, e.g., through abiotic stress, giving rise to infective episomal forms. The presence of endogenous badnaviruses poses a new challenge for the fool-proof diagnosis, taxonomy, and management of the diseases. The present review aims to highlight emerging disease problems, virus characteristics, transmission, and diagnosis of badnaviruses.
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Affiliation(s)
| | - Thomas Hohn
- UNIBAS, Botanical Institute, 4056 Basel, Switzerland.
| | - Ramasamy Selvarajan
- ICAR-National Research Centre for Banana, Tiruchirapalli 620102, Tamil Nadu, India.
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Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D'Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus SL, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. NATURE PLANTS 2016; 2:16074. [PMID: 27255838 DOI: 10.1038/nplants.2016.74] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/22/2016] [Indexed: 05/21/2023]
Abstract
Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.
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Affiliation(s)
- Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, 490 West Campus Dr., Blacksburg, Virginia 24061, USA
| | - Michel Moser
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Avichai Amrad
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Manzhu Bao
- Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Laure Bapaume
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 6 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Mattijs Bliek
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Maaike R Boersma
- Department of Plant Physiology, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Lorenzo Borghi
- Institute of Plant and Microbiology, University of Zürich, Zollikerstr. 107, CH-8008 Zürich, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
| | - Marcel Bucher
- Cologne Biocenter, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zuelpicher Straße 47b, 50674 Cologne, Germany
| | - Nunzio D'Agostino
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per l'Orticoltura (CREA-ORT), via Cavalleggeri 25, 84098 Pontecagnano (Sa) Italy
| | - Kevin Davies
- Department of Breeding and Genomics, Plant and Food Research, Auckland, 120 Mt Albert Road, Mount Albert, Sandringham 1142, New Zealand
| | - Uwe Druege
- Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Kühnhäuserstr. 101, 99090 Erfurt, Germany
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-2063, USA
| | - Marcos Egea-Cortines
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Massimo Delledonne
- Dipartimento di Biotecnologie, Universita degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Noe Fernandez-Pozo
- Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, New York 14853, USA
| | - Philipp Franken
- Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Kühnhäuserstr. 101, 99090 Erfurt, Germany
| | - Laurie Grandont
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - J S Heslop-Harrison
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Jennifer Hintzsche
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Mitrick Johns
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Ronald Koes
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Xiaodan Lv
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, Arizona 85721, USA
| | - Diwa Malla
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Enrico Martinoia
- Institute of Plant and Microbiology, University of Zürich, Zollikerstr. 107, CH-8008 Zürich, Switzerland
| | - Neil S Mattson
- School of Integrative Plant Science, Cornell University, Cornell University, Ithaca, New York 14853, USA
| | - Patrice Morel
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, New York 14853, USA
| | - Joëlle Muhlemann
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-2063, USA
| | - Eva Nouri
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 4 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Valentina Passeri
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Mario Pezzotti
- Dipartimento di Biotecnologie, Universita degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Qinzhou Qi
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Didier Reinhardt
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 3 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Melanie Rich
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 5 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Katja R Richert-Pöggeler
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Tim P Robbins
- Department of Crop and Plant Sciences, University of Nottingham, Sutton Bonington, Leicestershire, UL LE12 5RD, UK
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Robert C Schuurink
- Department of Plant Physiology, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Trude Schwarzacher
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Kees Spelt
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Haibao Tang
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, Arizona 85721, USA
| | - Susan L Urbanus
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Kitty Vijverberg
- Radboud University, FNWI, IWWR, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Gonzalo H Villarino
- School of Integrative Plant Science, Cornell University, Cornell University, Ithaca, New York 14853, USA
| | - Ryan M Warner
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Julia Weiss
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Zhen Yue
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Jan Zethof
- Radboud University, FNWI, IWWR, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Francesca Quattrocchio
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Thomas L Sims
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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Duroy PO, Perrier X, Laboureau N, Jacquemoud-Collet JP, Iskra-Caruana ML. How endogenous plant pararetroviruses shed light on Musa evolution. ANNALS OF BOTANY 2016; 117:625-41. [PMID: 26971286 PMCID: PMC4817503 DOI: 10.1093/aob/mcw011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/06/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Banana genomes harbour numerous copies of viral sequences derived from banana streak viruses (BSVs) - dsDNA viruses belonging to the family Caulimoviridae.These viral integrants (eBSVs) are mostly defective, probably as a result of 'pseudogenization' driven by host genome evolution. However, some can give rise to infection by releasing a functional viral genome following abiotic stresses. These distinct infective eBSVs correspond to the three main widespread BSV species (BSOLV, BSGFV and BSIMV), fully described within the Musa balbisiana B genomes of the seedy diploid 'Pisang Klutuk Wulung' (PKW). METHODS We characterize eBSV distribution among a Musa sampling including seedy BB diploids and interspecific hybrids with Musa acuminate exhibiting different levels of ploidy for the B genome (ABB, AAB, AB). We used representative samples of the two areas of sympatry between M. acuminate and M. balbisiana species representing the native area of the most widely cultivated AAB cultivars (in India and in East Asia, ranging from the Philippines to New Guinea). Seventy-seven accessions were characterized using eBSV-related PCR markers and Southern hybridization approaches. We coded both sets of results to create a common dissimilarity matrix with which to interpret eBSV distribution. KEY RESULTS We propose a Musa phylogeny driven by the M. balbisiana genome based on a dendrogram resulting from a joint neighbour-joining analysis of the three BSV species, showing for the first time lineages between BB and ABB/AAB hybrids. eBSVs appear to be relevant phylogenetic markers that can illustrate theM. balbisiana phylogeography story. CONCLUSION The theoretical implications of this study for further elucidation of the historical and geographical process of Musa domestication are numerous. Discovery of banana plants with B genome non-infective for eBSV opens the way to the introduction of new genitors in programmes of genetic banana improvement.
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Villacreses J, Rojas-Herrera M, Sánchez C, Hewstone N, Undurraga SF, Alzate JF, Manque P, Maracaja-Coutinho V, Polanco V. Deep sequencing reveals the complete genome and evidence for transcriptional activity of the first virus-like sequences identified in Aristotelia chilensis (Maqui Berry). Viruses 2015; 7:1685-99. [PMID: 25855242 PMCID: PMC4411674 DOI: 10.3390/v7041685] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/12/2015] [Accepted: 03/25/2015] [Indexed: 01/01/2023] Open
Abstract
Here, we report the genome sequence and evidence for transcriptional activity of a virus-like element in the native Chilean berry tree Aristotelia chilensis. We propose to name the endogenous sequence as Aristotelia chilensis Virus 1 (AcV1). High-throughput sequencing of the genome of this tree uncovered an endogenous viral element, with a size of 7122 bp, corresponding to the complete genome of AcV1. Its sequence contains three open reading frames (ORFs): ORFs 1 and 2 shares 66%–73% amino acid similarity with members of the Caulimoviridae virus family, especially the Petunia vein clearing virus (PVCV), Petuvirus genus. ORF1 encodes a movement protein (MP); ORF2 a Reverse Transcriptase (RT) and a Ribonuclease H (RNase H) domain; and ORF3 showed no amino acid sequence similarity with any other known virus proteins. Analogous to other known endogenous pararetrovirus sequences (EPRVs), AcV1 is integrated in the genome of Maqui Berry and showed low viral transcriptional activity, which was detected by deep sequencing technology (DNA and RNA-seq). Phylogenetic analysis of AcV1 and other pararetroviruses revealed a closer resemblance with Petuvirus. Overall, our data suggests that AcV1 could be a new member of Caulimoviridae family, genus Petuvirus, and the first evidence of this kind of virus in a fruit plant.
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Affiliation(s)
- Javier Villacreses
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
| | - Marcelo Rojas-Herrera
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
| | - Carolina Sánchez
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
| | | | - Soledad F Undurraga
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica, Universidad de Antioquia, Medellín, Colombia.
| | - Patricio Manque
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
| | | | - Victor Polanco
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
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Mushegian AR, Elena SF. Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes. Virology 2015; 476:304-315. [DOI: 10.1016/j.virol.2014.12.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/04/2014] [Accepted: 12/06/2014] [Indexed: 12/01/2022]
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Becher H, Ma L, Kelly LJ, Kovarik A, Leitch IJ, Leitch AR. Endogenous pararetrovirus sequences associated with 24 nt small RNAs at the centromeres of Fritillaria imperialis L. (Liliaceae), a species with a giant genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:823-33. [PMID: 25230921 DOI: 10.1111/tpj.12673] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 05/25/2023]
Abstract
Endogenous pararetroviral sequences are the most commonly found virus sequences integrated into angiosperm genomes. We describe an endogenous pararetrovirus (EPRV) repeat in Fritillaria imperialis, a species that is under study as a result of its exceptionally large genome (1C = 42 096 Mbp, approximately 240 times bigger than Arabidopsis thaliana). The repeat (FriEPRV) was identified from Illumina reads using the RepeatExplorer pipeline, and exists in a complex genomic organization at the centromere of most, or all, chromosomes. The repeat was reconstructed into three consensus sequences that formed three interconnected loops, one of which carries sequence motifs expected of an EPRV (including the gag and pol domains). FriEPRV shows sequence similarity to members of the Caulimoviridae pararetrovirus family, with phylogenetic analysis indicating a close relationship to Petuvirus. It is possible that no complete EPRV sequence exists, although our data suggest an abundance that exceeds the genome size of Arabidopsis. Analysis of single nucleotide polymorphisms revealed elevated levels of C→T and G→A transitions, consistent with deamination of methylated cytosine. Bisulphite sequencing revealed high levels of methylation at CG and CHG motifs (up to 100%), and 15-20% methylation, on average, at CHH motifs. FriEPRV's centromeric location may suggest targeted insertion, perhaps associated with meiotic drive. We observed an abundance of 24 nt small RNAs that specifically target FriEPRV, potentially providing a signature of RNA-dependent DNA methylation. Such signatures of epigenetic regulation suggest that the huge genome of F. imperialis has not arisen as a consequence of a catastrophic breakdown in the regulation of repeat amplification.
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Affiliation(s)
- Hannes Becher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
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Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nat Commun 2014; 5:5269. [PMID: 25381880 PMCID: PMC4241990 DOI: 10.1038/ncomms6269] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/15/2014] [Indexed: 12/03/2022] Open
Abstract
The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of Caulimoviridae called ‘Florendovirus’, members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of Oryza is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20–34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In Vitis vinifera, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks. Endogenous viral elements have been extensively described in animals but their significance in plants is less well understood. Here, Geering et al. describe a new group of endogenous pararetroviruses, called florendoviruses, which have colonized the genomes of many important crop species.
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Umber M, Filloux D, Muller E, Laboureau N, Galzi S, Roumagnac P, Iskra-Caruana ML, Pavis C, Teycheney PY, Seal SE. The genome of African yam (Dioscorea cayenensis-rotundata complex) hosts endogenous sequences from four distinct Badnavirus species. MOLECULAR PLANT PATHOLOGY 2014; 15:790-801. [PMID: 24605894 PMCID: PMC6638810 DOI: 10.1111/mpp.12137] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Several endogenous viral elements (EVEs) have been identified in plant genomes, including endogenous pararetroviruses (EPRVs). Here, we report the first characterization of EPRV sequences in the genome of African yam of the Dioscorea cayenensis-rotundata complex. We propose that these sequences should be termed 'endogenous Dioscorea bacilliform viruses' (eDBVs). Molecular characterization of eDBVs shows that they constitute sequences originating from various parts of badnavirus genomes, resulting in a mosaic structure that is typical of most EPRVs characterized to date. Using complementary molecular approaches, we show that eDBVs belong to at least four distinct Badnavirus species, indicating multiple, independent, endogenization events. Phylogenetic analyses of eDBVs support and enrich the current taxonomy of yam badnaviruses and lead to the characterization of a new Badnavirus species in yam. The impact of eDBVs on diagnosis, yam germplasm conservation and movement, and breeding is discussed.
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Affiliation(s)
- Marie Umber
- INRA, UR1321 ASTRO Agrosystèmes tropicaux, F-97170, Petit-Bourg, (Guadeloupe), France
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Seal S, Turaki A, Muller E, Kumar PL, Kenyon L, Filloux D, Galzi S, Lopez-Montes A, Iskra-Caruana ML. The prevalence of badnaviruses in West African yams (Dioscorea cayenensis-rotundata) and evidence of endogenous pararetrovirus sequences in their genomes. Virus Res 2014; 186:144-54. [PMID: 24457074 DOI: 10.1016/j.virusres.2014.01.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/19/2013] [Accepted: 01/11/2014] [Indexed: 02/09/2023]
Abstract
Yam (Dioscorea spp.) is an important vegetatively-propagated staple crop in West Africa. Viruses are pervasive in yam worldwide, decreasing growth and yield, as well as hindering the international movement of germplasm. Badnaviruses have been reported to be the most prevalent in yam, and genomes of some other badnaviruses are known to be integrated in their host plant species. However, it was not clear if a similar scenario occurs in Dioscorea yam. This study was conducted to verify the prevalence of badnaviruses, and determine if badnavirus genomes are integrated in the yam genome. Leaf samples (n=58) representing eight species of yam from global yam collections kept at CIRAD, France, and 127 samples of D. rotundata breeding lines (n=112) and landraces (n=15) at IITA, Nigeria, were screened using generic badnavirus PCR primers. Positive amplification of an expected ca. 579bp fragment, corresponding to a partial RT-RNaseH region, was detected in 47 (81%) of 58 samples analysed from CIRAD collections, and 100% of the 127 IITA D. rotundata samples. All the D. cayenensis and D. rotundata samples from the CIRAD and IITA collections tested PCR-positive, and sequencing of a selection of the PCR products confirmed they were typical of the genus Badnavirus. A comparison of serological and nucleic acid techniques was used to investigate whether the PCR-positives were sequences amplified from badnavirus particles or putative endogenous badnavirus sequences in the yam genome. Protein A sandwich-enzyme-linked immunosorbent assay (PAS-ELISA) with badnavirus polyclonal antisera detected cross-reacting viral particles in only 60% (92 of 153) of the CIRAD collection samples analysed, in contrast to the aforementioned 81% by PCR. Immunosorbent electron microscopy (ISEM) of virus preparations of a select set of 16 samples, representing different combinations of positive and negative PCR and PAS-ELISA results, identified bacilliform particles in 11 of these samples. Three PCR-positive yam samples from Burkina Faso (cv. Pilimpikou) were identified in which no viral particles were detected by either PAS-ELISA or ISEM. Southern hybridisation results using a yam badnavirus RT-RNaseH sequence (Gn155Dr) as probe, supported a lack of badnavirus particles in the cv. Pilimpikou and identified their equivalent sequences to be of plant genome origin. Probe Gn155Dr, however, hybridised to viral particles and plant genomic DNA in three D. rotundata samples from Guinea. These results represent the first data demonstrating the presence of integrated sequences of badnaviruses in yam. The implications of this for virus-indexing, breeding and multiplication of seed yams are discussed.
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Affiliation(s)
- Susan Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK; CIRAD, UMR BGPI, F-34098 Montpellier, France.
| | - Aliyu Turaki
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | | | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Oyo Road PMB 5320, Ibadan, Nigeria
| | - Lawrence Kenyon
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | | | - Serge Galzi
- CIRAD, UMR BGPI, F-34098 Montpellier, France
| | - Antonio Lopez-Montes
- International Institute of Tropical Agriculture (IITA), Oyo Road PMB 5320, Ibadan, Nigeria
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Population of endogenous pararetrovirus genomes in carrizo citrange. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01063-13. [PMID: 24435856 PMCID: PMC3894270 DOI: 10.1128/genomea.01063-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete genome sequences of three related endogenous pararetroviruses (EPRVs) were obtained by 454 sequencing of nucleic acid extracts from Carrizo citrange, used as a citrus rootstock. Numerous homologous sequences have been found in the sweet orange genome. The new EPRVs are most closely related to petunia vein-clearing virus.
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48
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Hull R. Replication of Plant Viruses. PLANT VIROLOGY 2014. [PMCID: PMC7184227 DOI: 10.1016/b978-0-12-384871-0.00007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses co-infecting cells. Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses coinfecting cells.
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49
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Almeyda CV, Eid SG, Saar D, Samuitiene M, Pappu HR. Comparative analysis of endogenous plant pararetroviruses in cultivated and wild Dahlia spp. Virus Genes 2013; 48:140-52. [PMID: 24353027 DOI: 10.1007/s11262-013-0997-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/16/2013] [Indexed: 11/28/2022]
Abstract
Two distinct caulimoviruses, Dahlia mosaic virus (DMV) and Dahlia common mosaic virus, and an endogenous plant pararetroviral sequence (DvEPRS) were reported in Dahlia spp. DvEPRS, previously referred to as DMV-D10, was originally identified in the US from the cultivated Dahlia variabilis, and has also been found in New Zealand, Lithuania and Egypt, as well as in wild dahlia species growing in their natural habitats in Mexico. Sequence analysis of three new EPRSs from cultivated dahlias from Lithuania [D10-LT; 7,159 nucleotide level (nt)], New Zealand (D10-NZ, 7,156 nt), and the wild species, Dahlia rupicola, from Mexico (D10-DR, 7,133 nt) is reported in this study. The three EPRSs have the structure and organization typical of a caulimovirus species and showed identities among various open reading frames (ORFs) ranging between 71 and 97 % at the nt when compared to those or the known DvEPRS from the US. Examination of a dataset of seven full-length EPRSs obtained to date from cultivated and wild Dahlia spp. provided clues into genetic diversity of these EPRSs from diverse sources of dahlia. Phylogenetic analyses, mutation frequencies, potential recombination events, selection, and fitness were evaluated as evolutionary evidences for genetic variation. Assessment of all ORFs using phylogenomic and population genetics approaches suggests a wide genetic diversity of EPRSs occurring in dahlias. Phylogenetic analyses show that the EPRSs from various sources form one clade indicating a lack of clustering by geographical origin. Grouping of various EPRSs into two host taxa (cultivated vs. wild) shows little divergence with respect to their origin. Population genetic parameters demonstrate negative selection for all ORFs, with the reverse transcriptase region more variable than other ORFs. Recombination events were found which provide evolutionary evidence for genetic diversity among dahlia-associated EPRSs. This study contributes to an increased understanding of molecular population genetics and evolutionary pathways of these reverse transcribing viral elements.
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Affiliation(s)
- C V Almeyda
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
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50
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Endogenous pararetroviruses—a reservoir of virus infection in plants. Curr Opin Virol 2013; 3:615-20. [DOI: 10.1016/j.coviro.2013.08.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 07/30/2013] [Accepted: 08/22/2013] [Indexed: 12/12/2022]
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