@article{fdi:010066167,
  title = {{A}ctive transposable elements recover species boundaries and geographic structure in {M}adagascan coffee species},
  author = {{R}oncal, {J}. and {G}uyot, {R}omain and {H}amon, {P}erla and {C}rouzillat, {D}. and {R}igoreau, {M}. and {K}onan, {O}. {N}. and {R}akotomalala, {J}. {J}. and {N}owak, {M}. {D}. and {D}avis, {A}. {P}. and {K}ochko, {A}lexandre de},
  editor = {},
  language = {{ENG}},
  abstract = {{T}he completion of the genome assembly for the economically important coffee plant {C}offea canephora ({R}ubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements ({TE}s), which can be used in evolutionary studies of the genus. {A}n overview of the copy number and location within the {C}. canephora genome of four {TE}s is presented. {T}hese are tested for their use as molecular markers to unravel the evolutionary history of the {M}illotii {C}omplex, a group of six wild coffee ({C}offea) species native to {M}adagascar. {T}wo {TE}s from the {G}ypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a {TE} from the {C}opia superfamily did not. {N}otably, species occurring in evergreen moist forests of eastern and southeastern {M}adagascar were divergent with respect to species in other habitats and regions. {O}ur results suggest that the peak of transpositional activity of the {G}ypsy and {C}opia {TE}s occurred, respectively, before and after the speciation events of the tested {M}adagascan species. {W}e conclude that the utilization of active {TE}s has considerable potential to unravel the evolutionary history and delimitation of closely related {C}offea species. {H}owever, the selection of {TE} needs to be experimentally tested, since each element has its own evolutionary history. {D}ifferent {TE}s with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.},
  keywords = {{C}offea canephora ; {D}iversification ; {LTR} retrotransposons ; {M}adagascar ; {REMAP} ; {MADAGASCAR}},
  booktitle = {},
  journal = {{M}olecular {G}enetics and {G}enomics},
  volume = {291},
  numero = {1},
  pages = {155--168},
  ISSN = {1617-4615},
  year = {2016},
  DOI = {10.1007/s00438-015-1098-3},
  URL = {https://www.documentation.ird.fr/hor/fdi:010066167},
}