5 results on '"Rdr1 gene"'
Search Results
2. Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily
- Author
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Menz, Ina, Lakhwani, Deepika, Clotault, Jérémy, Linde, Marcus, Foucher, Fabrice, Debener, Thomas, Leibniz University Hannover, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Open Access fund of Leibniz Universität Hannover.
- Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,Plant Science ,Plant Genetics ,Database and Informatics Methods ,Homologous Chromosomes ,rosa ,ressource génétique végétale ,Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik) ,Plant Genomics ,cartographie chromosomique ,Flowering Plants ,Roses ,Phylogeny ,Data Management ,Plant Proteins ,Vegetal Biology ,Chromosome Biology ,Eukaryota ,Phylogenetic Analysis ,Genomics ,Plants ,[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics ,Agricultural sciences ,Botanique ,Phylogenetics ,ddc:580 ,Multigene Family ,Medicine ,Engineering and Technology ,Sequence Analysis ,Research Article ,Biotechnology ,Rose ,Botanics ,Computer and Information Sciences ,Bioinformatics ,Science ,Bioengineering ,Biotechnologies ,Research and Analysis Methods ,Chromosomes ,Chromosomes, Plant ,Evolution, Molecular ,horticulture ornementale ,Amino Acid Sequence Analysis ,Genomic Medicine ,malus ,Genetics ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Evolutionary Systematics ,diversité phylogénétique ,Rosaceae ,Taxonomy ,Evolutionary Biology ,Organisms ,Biology and Life Sciences ,Computational Biology ,cluster de gènes ,Cell Biology ,Genome Analysis ,RNA-Dependent RNA Polymerase ,rosoideae ,Rdr1 gene ,cartographie du génome ,Plant Biotechnology ,Sequence Alignment ,Biologie végétale ,Sciences agricoles ,analyse génétique ,amélioration des plantes - Abstract
International audience; The Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis ‘Old Blush’ genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae. Members of the Rdr1 gene family are organized into two major clusters in R. chinensis and at a syntenic location in the Fragaria genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional Rdr1 gene muRdr1A, were subject to a faster evolution than genes from cluster 1. As no Rdr1 homologs were found in syntenic positions for Prunus persica, Malus x domestica and Rubus occidentalis, a translocation of the Rdr1 clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70–80 million years ago during the Cretaceous period.
- Published
- 2020
3. Differential Symptom Development and Viral RNA Loads in 10 Nicotiana benthamiana Accessions Infected with the Tobamovirus Yellow Tailflower Mild Mottle Virus.
- Author
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Xu W, Guo Y, Li H, Sivasithamparam K, Jones MGK, Chen X, and Wylie SJ
- Subjects
- Plant Diseases, RNA, Viral genetics, RNA-Dependent RNA Polymerase, Nicotiana, Tobamovirus genetics
- Abstract
Yellow tailflower mild mottle virus (YTMMV, genus Tobamovirus ) was identified from wild plants of solanaceous species in Australia. Nicotiana benthamiana is a species indigenous to the arid north of Australia. N. benthamiana accession RA-4 (the lab type), which has a mutant, functionally defective, RNA-dependent RNA polymerase 1 ( Rdr1 ) gene ( Nb-Rdr1m ), has played a significant role in plant virology, but little study has been done regarding responses to virus infection by other accessions of N. benthamiana . All wild-collected N. benthamiana accessions used in this study harbored wild-type Rdr1 genes ( Nb-Rdr1 ). We compared symptoms of YTMMV infection and viral RNA load on RA-4 and nine wild-collected accessions of N. benthamiana from mainland Western Australia, an island, and the Northern Territory. After inoculation with YTMMV, RA-4 plants responded with systemic hypersensitivity and all individuals were dead 35 days postinoculation (dpi). Plants of wild-collected accessions exhibited a range of symptoms, from mild to severe, and some, but not all, died in the same period. Quantitative reverse transcription PCR revealed that the Rdr1 mutation was not a predictor of viral RNA load or symptom severity. For example, wild-collected A019412 plants carried more than twice the viral RNA load of RA-4 plants, but symptom expression was moderate. For plants of most accessions, viral RNA load did not increase after 10 dpi. The exception was plants of accession Barrow-1, in which viral RNA load was low until 15 dpi, after which it increased more than 29-fold. This study revealed differential responses by N. benthamiana accessions to infection by an isolate of YTMMV. The Rdr1 gene, whether mutant or wild-type, did not appear to influence viral RNA load or disease expression. Genetic diversity of the 10 N. benthamiana accessions in some cases reflected geographical location, but in other accessions this was not so.
- Published
- 2022
- Full Text
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4. Evolution of the Rdr1 TNL-cluster in roses and other Rosaceous species
- Abstract
Background: The resistance of plants to pathogens relies on two lines of defense: a basal defense response and a pathogen-specific system, in which resistance (R) genes induce defense reactions after detection of pathogen-associated molecular patterns (PAMPS). In the specific system, a so-called arms race has developed in which the emergence of new races of a pathogen leads to the diversification of plant resistance genes to counteract the pathogens' effect. The mechanism of resistance gene diversification has been elucidated well for short-lived annual species, but data are mostly lacking for long-lived perennial and clonally propagated plants, such as roses. We analyzed the rose black spot resistance gene, Rdr1, in five members of the Rosaceae: Rosa multiflora, Rosa rugosa, Fragaria vesca (strawberry), Malus x domestica (apple) and Prunus persica (peach), and we present the deduced possible mechanism of R-gene diversification.Results: We sequenced a 340.4-kb region from R. rugosa orthologous to the Rdr1 locus in R. multiflora. Apart from some deletions and rearrangements, the two loci display a high degree of synteny. Additionally, less pronounced synteny is found with an orthologous locus in strawberry but is absent in peach and apple, where genes from the Rdr1 locus are distributed on two different chromosomes. An analysis of 20 TIR-NBS-LRR (TNL) genes obtained from R. rugosa and R. multiflora revealed illegitimate recombination, gene conversion, unequal crossing over, indels, point mutations and transposable elements as mechanisms of diversification.A phylogenetic analysis of 53 complete TNL genes from the five Rosaceae species revealed that with the exception of some genes from apple and peach, most of the genes occur in species-specific clusters, indicating that recent TNL gene diversification began prior to the split of Rosa from Fragaria in the Rosoideae and peach from apple in the Spiraeoideae and continued after the split in individual species. Sequence s
- Published
- 2012
5. Evolution of the Rdr1 TNL-cluster in roses and other Rosaceous species
- Author
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Thomas Debener, Helgard Kaufmann, Diro Terefe-Ayana, and Marcus Linde
- Subjects
Unequal crossing over ,Rosoideae ,transposon ,Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften, Biologie ,Spiraeoideae ,phylogeny ,gene cluster ,peach ,Contig Mapping ,plant gene ,Fragaria vesca ,Gene cluster ,genetic variability ,Cluster Analysis ,R gene ,Dewey Decimal Classification::500 | Naturwissenschaften ,Phylogeny ,rose ,Plant Proteins ,Genetics ,genetic recombination ,gene conversion ,article ,chromosome analysis ,TNL gene ,Rosa rugosa ,Malus ,sequence alignment ,genetic similarity ,ddc:500 ,Prunus ,point mutation ,strawberry ,Black spot ,Biotechnology ,Research Article ,lcsh:QH426-470 ,gene locus ,lcsh:Biotechnology ,gene rearrangement ,apple ,Locus (genetics) ,gene sequence ,Biology ,Genes, Plant ,Rosa ,Fragaria ,Chromosomes ,Evolution, Molecular ,promoter region ,Rosa multiflora ,ddc:570 ,lcsh:TP248.13-248.65 ,controlled study ,Rosaceae ,Malus x domestica ,Synteny ,Prunus persica ,nonhuman ,gene deletion ,species difference ,gene duplication ,nucleotide sequence ,Gene rearrangement ,biology.organism_classification ,Rdr1 gene ,Repressor Proteins ,lcsh:Genetics ,Genetic Loci ,Fragaria x ananassa - Abstract
Background The resistance of plants to pathogens relies on two lines of defense: a basal defense response and a pathogen-specific system, in which resistance (R) genes induce defense reactions after detection of pathogen-associated molecular patterns (PAMPS). In the specific system, a so-called arms race has developed in which the emergence of new races of a pathogen leads to the diversification of plant resistance genes to counteract the pathogens’ effect. The mechanism of resistance gene diversification has been elucidated well for short-lived annual species, but data are mostly lacking for long-lived perennial and clonally propagated plants, such as roses. We analyzed the rose black spot resistance gene, Rdr1, in five members of the Rosaceae: Rosa multiflora, Rosa rugosa, Fragaria vesca (strawberry), Malus x domestica (apple) and Prunus persica (peach), and we present the deduced possible mechanism of R-gene diversification. Results We sequenced a 340.4-kb region from R. rugosa orthologous to the Rdr1 locus in R. multiflora. Apart from some deletions and rearrangements, the two loci display a high degree of synteny. Additionally, less pronounced synteny is found with an orthologous locus in strawberry but is absent in peach and apple, where genes from the Rdr1 locus are distributed on two different chromosomes. An analysis of 20 TIR-NBS-LRR (TNL) genes obtained from R. rugosa and R. multiflora revealed illegitimate recombination, gene conversion, unequal crossing over, indels, point mutations and transposable elements as mechanisms of diversification. A phylogenetic analysis of 53 complete TNL genes from the five Rosaceae species revealed that with the exception of some genes from apple and peach, most of the genes occur in species-specific clusters, indicating that recent TNL gene diversification began prior to the split of Rosa from Fragaria in the Rosoideae and peach from apple in the Spiraeoideae and continued after the split in individual species. Sequence similarity of up to 99% is obtained between two R. multiflora TNL paralogs, indicating a very recent duplication. Conclusions The mechanisms by which TNL genes from perennial Rosaceae diversify are mainly similar to those from annual plant species. However, most TNL genes appear to be of recent origin, likely due to recent duplications, supporting the hypothesis that TNL genes in woody perennials are generally younger than those from annuals. This recent origin might facilitate the development of new resistance specificities, compensating for longer generation times in woody perennials.
- Published
- 2012
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