@article{fdi:010068256,
  title = {{I}nter-genomic {DNA} exchanges and homeologous gene silencing shaped the nascent allopolyploid coffee genome ({C}offea arabica {L}.)},
  author = {{L}ashermes, {P}hilippe and {H}ueber, {Y}ann and {C}ombes, {M}arie-{C}hristine and {S}everac, {D}. and {D}ereeper, {A}lexis},
  editor = {},
  language = {{ENG}},
  abstract = {{A}llopolyploidization is a biological process that has played a major role in plant speciation and evolution. {G}enomic changes are common consequences of polyploidization, but their dynamics over time are still poorly understood. {C}offea arabica, a recently formed allotetraploid, was chosen to study genetic changes that accompany allopolyploid formation. {B}oth {RNA}-seq and {DNA}-seq data were generated from two genetically distant {C}. arabica accessions. {G}enomic structural variation was investigated using {C}. canephora, one of its diploid progenitors, as reference genome. {T}he fate of 9047 duplicate homeologous genes was inferred and compared between the accessions. {T}he pattern of {SNP} density along the reference genome was consistent with the allopolyploid structure. {L}arge genomic duplications or deletions were not detected. {T}wo homeologous copies were retained and expressed in 96% of the genes analyzed. {N}evertheless, duplicated genes were found to be affected by various genomic changes leading to homeolog loss or silencing. {G}enetic and epigenetic changes were evidenced that could have played a major role in the stabilization of the unique ancestral allotetraploid and its subsequent diversification. {W}hile the early evolution of {C}. arabica mainly involved homeologous crossover exchanges, the later stage appears to have relied on more gradual evolution involving gene conversion and homeolog silencing.},
  keywords = {polyploidy ; evolution ; gene conversion ; homoeologous recombination ; genome dominance},
  booktitle = {},
  journal = {{G}3 : {G}enes {G}enomes {G}enetics},
  volume = {6},
  numero = {9},
  pages = {2937--2948},
  ISSN = {2160-1836},
  year = {2016},
  DOI = {10.1534/g3.116.030858},
  URL = {https://www.documentation.ird.fr/hor/fdi:010068256},
}