@article{fdi:010078132,
  title = {{C}hloroplast genomes of {R}ubiaceae : comparative genomics and molecular phylogeny in subfamily {I}xoroideae},
  author = {{L}y, {S}. {N}. and {G}aravito, {A}. and {D}e {B}lock, {P}. and {A}sselman, {P}. and {G}uyeux, {C}. and {C}harr, {J}. {C}. and {J}anssens, {S}. and {M}ouly, {A}. and {H}amon, {P}erla and {G}uyot, {R}omain},
  editor = {},
  language = {{ENG}},
  abstract = {{I}n {R}ubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. {A} robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. {A}dvances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. {D}ue to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast {DNA} sequences have long been used as choice markers for plant phylogeny reconstruction. {T}he main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the {R}ubiaceae ({I}xoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining {SNP}s in the nuclear genome of {I}xoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. {W}e assembled whole chloroplast genome sequences for 27 species of the {R}ubiaceae subfamily {I}xoroideae using next-generation sequences. {A}nalysis of the plastid genome structure reveals a relatively good conservation of gene content and order. {G}enerally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. {A}n average of 79% of the {SNP} determined in the {C}offea genus are transferable to {I}xoroideae, with variation ranging from 35% to 96%. {I}n general, the plastid and the nuclear genome phylogenies are congruent with each other. {T}hey are well-resolved with well-supported branches. {G}enerally, the tribes form well-identified clades but the tribe {S}herbournieae is shown to be polyphyletic. {T}he results are discussed relative to the methodology used and the chloroplast genome features in {R}ubiaceae and compared to previous {R}ubiaceae phylogenies.},
  keywords = {},
  booktitle = {},
  journal = {{PL}o{S} {O}ne},
  volume = {15},
  numero = {4},
  pages = {art. e0232295 [21 p.]},
  ISSN = {1932-6203},
  year = {2020},
  DOI = {10.1371/journal.pone.0232295},
  URL = {https://www.documentation.ird.fr/hor/fdi:010078132},
}