@article{fdi:010068137,
  title = {{P}artial sequencing reveals the transposable element composition of {C}offea genomes and provides evidence for distinct evolutionary stories},
  author = {{G}uyot, {R}omain and {D}arre, {T}. and {D}upeyron, {M}. and {K}ochko, {A}lexandre de and {H}amon, {S}erge and {C}outuron, {E}mmanuel and {C}rouzillat, {D}. and {R}igoreau, {M}. and {R}akotomalala, {J}. {J}. and {R}aharimalala, {N}. {E}. and {A}kaffou, {S}. {D}. and {H}amon, {P}erla},
  editor = {},
  language = {{ENG}},
  abstract = {{T}he {C}offea genus, 124 described species, has a natural distribution spreading from inter-tropical {A}frica, to {W}estern {I}ndian {O}cean {I}slands, {I}ndia, {A}sia and up to {A}ustralasia. {T}wo cultivated species, {C}. arabica and {C}. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. {H}ere, we report the characterization and comparison of the highly repeated transposable elements content of 11 {C}offea species representatives of the natural biogeographic distribution. {A} total of 994 {M}b from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7 %. {T}he analyses showed that highly repeated transposable elements, mainly {LTR} retrotransposons ({LTR}-{RT}), represent between 32 and 53 % of {C}offea genomes depending on their biogeographic location and genome size. {S}pecies from {W}est and {C}entral {A}frica ({E}ucoffea) contained the highest {LTR}-{RT} content but with no strong variation relative to their genome size. {A}t the opposite, for the insular species ({M}ascarocoffea), a strong variation of {LTR}-{RT} was observed suggesting differential dynamics of these elements in this group. {T}wo {LTR}-{RT} lineages, {SIRE} and {D}el were clearly differentially accumulated between {A}frican and insular species, suggesting these lineages were associated to the genome divergence of {C}offea species in {A}frica. {A}ltogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild {C}offea genomes.},
  keywords = {{LTR} retrotransposons ; {P}artial genome sequencing ; {C}offea ; {G}enome size ; {G}eographic divergence ; {AFRIQUE} ; {ZONE} {TROPICALE} ; {ASIE} {DU} {SUD} ; {OCEAN} {INDIEN} {ILES} ; {MADAGASCAR} ; {INDE} ; {INDONESIE}},
  booktitle = {},
  journal = {{M}olecular {G}enetics and {G}enomics},
  volume = {291},
  numero = {5},
  pages = {1979--1990},
  ISSN = {1617-4615},
  year = {2016},
  DOI = {10.1007/s00438-016-1235-7},
  URL = {https://www.documentation.ird.fr/hor/fdi:010068137},
}