@article{fdi:010053620,
  title = {{O}rganization and molecular evolution of a disease-resistance gene cluster in coffee trees},
  author = {{R}ibas, {A}lessandra and {C}enci, {A}lberto and {C}ombes, {M}arie-{C}hristine and {E}tienne, {H}. and {L}ashermes, {P}hilippe},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {M}ost 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. {H}owever, the specific evolutionary routes of {NBS}-{LRR} encoding genes remain elusive. {R}ecently in coffee tree ({C}offea arabica), a region spanning the {S}({H})3 locus that confers resistance to coffee leaf rust, one of the most serious coffee diseases, was identified and characterized. {U}sing comparative sequence analysis, the purpose of the present study was to gain insight into the genomic organization and evolution of the {S}({H})3 locus. {R}esults: {S}equence analysis of the {S}({H})3 region in three coffee genomes, {E}-a and {C}-a subgenomes from the allotetraploid {C}. arabica and {C}-c genome from the diploid {C}. canephora, revealed the presence of 5, 3 and 4 {R} genes in {E}-a, {C}-a, and {C}-c genomes, respectively. {A}ll these {R}-gene sequences appeared to be members of a {CC}-{NBS}-{LRR} ({CNL}) gene family that was only found at the {S}({H})3 locus in {C}. arabica. {F}urthermore, 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. {T}he orthology relationship among the {S}({H})3-{CNL} copies in the three analyzed genomes was determined and the duplication/deletion events that shaped the {S}({H})3 locus were traced back. {G}ene conversion events were detected between paralogs in all three genomes and also between the two sub-genomes of {C}. arabica. {S}ignificant positive selection was detected in the solvent-exposed residues of the {S}({H})3-{CNL} copies. {C}onclusion: {T}he ancestral {S}({H})3-{CNL} copy was inserted in the {S}({H})3 locus after the divergence between {S}olanales and {R}ubiales lineages. {M}oreover, the origin of most of the {S}({H})3-{CNL} copies predates the divergence between {C}offea species. {T}he {S}({H})3-{CNL} family appeared to evolve following the birth-and-death model, since duplications and deletions were inferred in the evolution of the {S}({H})3 locus. {G}ene conversion between paralog members, inter-subgenome sequence exchanges and positive selection appear to be the major forces acting on the evolution of {S}({H})3-{CNL} in coffee trees.},
  keywords = {},
  booktitle = {},
  journal = {{B}mc {G}enomics},
  volume = {12},
  numero = {},
  pages = {240},
  ISSN = {1471-2164},
  year = {2011},
  DOI = {10.1186/1471-2164-12-240},
  URL = {https://www.documentation.ird.fr/hor/fdi:010053620},
}