@article{fdi:010076131,
  title = {{E}valuation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species},
  author = {{G}uyeux, {C}. and {C}harr, {J}. {C}. and {T}ran, {H}. {T}. {M}. and {F}urtado, {A}. and {H}enry, {R}. {J}. and {C}rouzillat, {D}. and {G}uyot, {R}omain and {H}amon, {P}erla},
  editor = {},
  language = {{ENG}},
  abstract = {{C}hloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. {W}hole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution {H}owever new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. {I}n this study, the two main tools for chloroplast genome annotation were compared. {M}ore consistent detection and annotation of genes were produced with {G}e{S}eq when compared to the currently used {D}ogma. {T}his suggests that the annotation of most of the previously annotated chloroplast genomes should now be updated. {G}e{S}eq was applied to species related to coffee, including 16 species of the {C}offea and {P}silanthus genera to reconstruct the ancestral chloroplast genomes and to evaluate their phylogenetic relationships. {E}ight genes in the plant chloroplast pan genome (consisting of 92 genes) were always absent in the coffee species analyzed. {N}otably, the two main cultivated coffee species (i.e. {A}rabica and {R}obusta) did not group into the same clade and differ in their pattern of gene evolution. {W}hile {A}rabica coffee ({C}offea arabica) belongs to the {C}offea genus, {R}obusta coffee ({C}offea canephora) is associated with the {P}silanthus genus. {A} more extensive survey of related species is required to determine if this is a unique attribute of {R}obusta coffee or a more widespread feature of coffee tree species.},
  keywords = {},
  booktitle = {},
  journal = {{PLOS} {O}ne},
  volume = {14},
  numero = {6},
  pages = {e0216347 [20 p.]},
  ISSN = {1932-6203},
  year = {2019},
  DOI = {10.1371/journal.pone.0216347},
  URL = {https://www.documentation.ird.fr/hor/fdi:010076131},
}