@article{fdi:010054234,
  title = {{G}enome evolution in diploid and tetraploid {C}offea species as revealed by comparative analysis of orthologous genome segments},
  author = {{C}enci, {A}lberto and {C}ombes, {M}arie-{C}hristine and {L}ashermes, {P}hilippe},
  editor = {},
  language = {{ENG}},
  abstract = {{S}equence comparison of orthologous regions enables estimation of the divergence between genomes, analysis of their evolution and detection of particular features of the genomes, such as sequence rearrangements and transposable elements. {D}espite the economic importance of {C}offea species, little genomic information is currently available. {C}offea is a relatively young genus that includes more than one hundred diploid species and a single tetraploid species. {T}hree {C}offea orthologous regions of 470-900 kb were analyzed and compared: both subgenomes of allotetraploid {C}offea arabica (contributed by the diploid species {C}offea eugenioides and {C}offea canephora) and the genome of diploid {C}. canephora. {S}equence divergence was calculated on global alignments or on coding and non-coding sequences separately. {A} search for transposable elements detected 43 retrotransposons and 198 transposons in the sequences analyzed. {C}omparative insertion analysis made it possible to locate 165 {TE} insertions in the phylogenetic tree of the three genomes/subgenomes. {I}n the tetraploid {C}. arabica, a homoeologous non-reciprocal transposition ({HNRT}) was detected and characterized: a 50 kb region of the {C}. eugenioides derived subgenome replaced the {C}. canephora derived counterpart. {C}omparative sequence analysis on three {C}offea genomes/subgenomes revealed almost perfect gene synteny, low sequence divergence and a high number of shared transposable elements. {C}ompared to the results of similar analysis in other genera ({A}egilops/{T}riticum and {O}ryza), {C}offea genomes/subgenomes appeared to be dramatically less diverged, which is consistent with the relatively recent radiation of the {C}offea genus. {B}ased on nucleotide substitution frequency, the {HNRT} was dated at 10,000-50,000 years {BP}, which is also the most recent estimation of the origin of {C}. arabica.},
  keywords = {{C}offea ; {P}olyploidy ; {C}omparative genomics ; {S}equence polymorphism ; {T}ransposable element ; {HNRT}},
  booktitle = {},
  journal = {{P}lant {M}olecular {B}iology},
  volume = {78},
  numero = {1-2},
  pages = {135--145},
  ISSN = {0167-4412},
  year = {2012},
  DOI = {10.1007/s11103-011-9852-3},
  URL = {https://www.documentation.ird.fr/hor/fdi:010054234},
}