ArticleBMC genomics2011
Organization and molecular evolution of a disease-resistance gene cluster in coffee trees.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 41 citations in OpenAlex.
- Genome-wide association study of powdery mildew resistance in cultivated soybean from Northeast China.Frontiers in plant science · 2023Article
- Genome-Wide Identification, Characterization, and Comparative Analysis ofFrontiers in plant science · 2022Article
- Article
- Development of an Efficient Protocol to Obtain Transgenic Coffee,International journal of molecular sciences · 2019Article
- The Hemileia vastatrix effector HvEC-016 suppresses bacterial blight symptoms in coffee genotypes with the SThe New phytologist · 2017Article
- Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2.Genetica · 2013Article
- A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci.BMC plant biology · 2013Article
- Perspectives of genomic diversification and molecular recombination towards R-gene evolution in plants.Physiology and molecular biology of plants : an international journal of functional plant biology · 2013Review
- Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments.Plant molecular biology · 2012Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMost disease-resistance (R) genes in plants encode NBS-LRR proteins and belong to one of the largest and most variable gene families among plant genomes. However, the specific evolutionary routes of NBS-LRR encoding genes remain elusive. Recently in coffee tree (Coffea arabica), a region spanning the SH3 locus that confers resistance to coffee leaf rust, one of the most serious coffee diseases, was identified and characterized. Using comparative sequence analysis, the purpose of the present study was to gain insight into the genomic organization and evolution of the SH3 locus.
resultsSequence analysis of the SH3 region in three coffee genomes, Ea and Ca subgenomes from the allotetraploid C. arabica and Cc genome from the diploid C. canephora, revealed the presence of 5, 3 and 4 R genes in Ea, Ca, and Cc genomes, respectively. All these R-gene sequences appeared to be members of a CC-NBS-LRR (CNL) gene family that was only found at the SH3 locus in C. arabica. Furthermore, while homologs were found in several dicot species, comparative genomic analysis failed to find any CNL R-gene in the orthologous regions of other eudicot species. The orthology relationship among the SH3-CNL copies in the three analyzed genomes was determined and the duplication/deletion events that shaped the SH3 locus were traced back. Gene conversion events were detected between paralogs in all three genomes and also between the two sub-genomes of C. arabica. Significant positive selection was detected in the solvent-exposed residues of the SH3-CNL copies.
conclusionThe ancestral SH3-CNL copy was inserted in the SH3 locus after the divergence between Solanales and Rubiales lineages. Moreover, the origin of most of the SH3-CNL copies predates the divergence between Coffea species. The SH3-CNL family appeared to evolve following the birth-and-death model, since duplications and deletions were inferred in the evolution of the SH3 locus. Gene conversion between paralog members, inter-subgenome sequence exchanges and positive selection appear to be the major forces acting on the evolution of SH3-CNL in coffee trees.
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