@article{fdi:010053575,
  title = {{T}wo novel {T}y1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the {C}offea genus ({R}ubiaceae)},
  author = {{H}amon, {P}erla and {D}uroy, {P}ierre-{O}livier and {D}ubreuil {T}ranchant, {C}hristine and {M}afra {D}'{A}lmeida {C}osta, {P}aulo and {D}uret, {C}aroline and {R}azafinarivo, {N}orosoa and {C}outuron, {E}mmanuel and {H}amon, {S}erge and {K}ochko, {A}lexandre de and {P}oncet, {V}al{\'e}rie and {G}uyot, {R}omain},
  editor = {},
  language = {{ENG}},
  abstract = {{I}n the study, we developed new markers for phylogenetic relationships and intraspecies differentiation in {C}offea. {N}ana and {D}ivo, two novel {T}y1-copia {LTR}-retrotransposon families, were isolated through {C}. canephora {BAC} clone sequencing. {N}ana- and {D}ivo-based markers were used to test their: (1) ability to resolve recent phylogenetic relationships; (2) efficiency in detecting intra-species differentiation. {S}equence-specific amplification polymorphism ({SSAP}), retrotransposon-microsatellite amplified polymorphism ({REMAP}) and retrotransposon-based insertion polymorphism ({RBIP}) approaches were applied to 182 accessions (31 {C}offea species and one {P}silanthus accession). {N}ana- and {D}ivo-based markers revealed contrasted transpositional histories. {A}t the {BAC} clone locus, {RBIP} results on {C}. canephora demonstrated that {N}ana insertion took place prior to {C}. canephora differentiation, while {D}ivo insertion occurred after differentiation. {C}ombined {SSAP} and {REMAP} data showed that {N}ana could resolve {C}offea lineages, while {D}ivo was efficient at a lower taxonomic level. {T}he combined results indicated that the retrotransposon-based markers were useful in highlighting {C}offea genetic diversity and the chronological pattern of speciation/differentiation events. {O}ngoing complete sequencing of the {C}. canephora genome will soon enable exhaustive identification of {LTR}-{RTN} families, as well as more precise in-depth analyses on contributions to genome size variation and {C}offea evolution.},
  keywords = {{LTR}-retrotransposons ; {C}offea ; {G}enetic diversity ; {E}volution},
  booktitle = {},
  journal = {{M}olecular {G}enetics and {G}enomics},
  volume = {285},
  numero = {6},
  pages = {447--460},
  ISSN = {1617-4615},
  year = {2011},
  DOI = {10.1007/s00438-011-0617-0},
  URL = {https://www.documentation.ird.fr/hor/fdi:010053575},
}