Guyeux C. auteur aut IRD Charr J. C. auteur aut IRD Tran H. T. M. auteur aut IRD Furtado A. auteur aut IRD Henry R. J. auteur aut IRD Crouzillat D. auteur aut IRD Guyot Romain auteur aut IRD Hamon Perla auteur aut IRD text journalArticle eng text/pdf reformatted digital access Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. In this study, the two main tools for chloroplast genome annotation were compared. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. This suggests that the annotation of most of the previously annotated chloroplast genomes should now be updated. GeSeq was applied to species related to coffee, including 16 species of the Coffea and Psilanthus genera to reconstruct the ancestral chloroplast genomes and to evaluate their phylogenetic relationships. Eight genes in the plant chloroplast pan genome (consisting of 92 genes) were always absent in the coffee species analyzed. Notably, the two main cultivated coffee species (i.e. Arabica and Robusta) did not group into the same clade and differ in their pattern of gene evolution. While Arabica coffee (Coffea arabica) belongs to the Coffea genus, Robusta coffee (Coffea canephora) is associated with the Psilanthus genus. A more extensive survey of related species is required to determine if this is a unique attribute of Robusta coffee or a more widespread feature of coffee tree species. specialized 076 14 6 e0216347 [20 p.] 2019 1932-6203 https://www.documentation.ird.fr/hor/fdi:010076131 10.1371/journal.pone.0216347 1932-6203 [F B010076131] https://www.documentation.ird.fr/hor/fdi:010076131 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers19-07/010076131.pdf IRD - Base Horizon / Pleins textes 2019-08-05 2025-02-24 fdi:010076131 fre