@article{fdi:010062061,
  title = {{G}enome rearrangements derived from homoeologous recombination following allopolyploidy speciation in coffee},
  author = {{L}ashermes, {P}hilippe and {C}ombes, {M}arie-{C}hristine and {H}ueber, {Y}ann and {S}everac, {D}. and {D}ereeper, {A}lexis},
  editor = {},
  language = {{ENG}},
  abstract = {{A}llopolyploidization is widespread and has played a major role in flowering plant diversification. {G}enomic changes are common consequences of allopolyploidization, but their mechanisms of occurrence and dynamics over time are still poorly understood. {C}offea arabica, a recently formed allotetraploid, was chosen as a model to investigate genetic changes in allopolyploid using an approach that exploits next-generation sequencing technologies. {G}enes affected by putative homoeolog loss were inferred by comparing the numbers of single-nucleotide polymorphisms detected using {RNA}-seq in individual accessions of {C}.arabica, and between accessions of its two diploid progenitor species for common sequence positions. {T}heir physical locations were investigated and clusters of genes exhibiting homoeolog loss were identified. {T}o validate these results, genome sequencing data were generated from one accession of {C}.arabica and further analyzed. {G}enomic rearrangements involving homoeologous exchanges appear to occur in {C}.arabica and to be a major source of genetic diversity. {A}t least 5% of the {C}.arabica genes were inferred to have undergone homoeolog loss. {T}he detection of a large number of homoeologous exchange events ({HEE}s) shared by all accessions of {C}.arabica strongly reinforces the assumption of a single allopolyploidization event. {F}urthermore, {HEE}s were specific to one or a few accessions, suggesting that {HEE} accumulates gradually. {O}ur results provide evidence for the important role of {HEE} in allopolyploid genome evolution.},
  keywords = {polyploidy ; genome evolution ; homoeologous recombination ; {C}offea arabica ; {RNA} sequencing ; single-nucleotide polymorphisms ; next-generation sequencing},
  booktitle = {},
  journal = {{P}lant {J}ournal},
  volume = {78},
  numero = {4},
  pages = {674--685},
  ISSN = {0960-7412},
  year = {2014},
  DOI = {10.1111/tpj.12505},
  URL = {https://www.documentation.ird.fr/hor/fdi:010062061},
}