@article{fdi:010065385,
  title = {{G}enome-wide analysis of {LTR}-retrotransposons in oil palm},
  author = {{B}eul{\'e}, {T}. and {A}gbessi, {M}. {D}. {T}. and {D}ussert, {S}t{\'e}phane and {J}aligot, {E}. and {G}uyot, {R}omain},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {T}he oil palm ({E}laeis guineensis {J}acq.) is a major cultivated crop and the world's largest source of edible vegetable oil. {T}he genus {E}laeis comprises two species {E}. guineensis, the commercial {A}frican oil palm and {E}. oleifera, which is used in oil palm genetic breeding. {T}he recent publication of both the {A}frican oil palm genome assembly and the first draft sequence of its {L}atin {A}merican relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences. {M}ethods: {I}n this study, we identified, annotated and compared {T}ransposable {E}lements ({TE}) from the {A}frican and {L}atin {A}merican oil palms. {I}n a first step, {T}ransposable {E}lement databases were built through de novo detection in both genome sequences then the {TE} content of both genomes was estimated. {T}hen putative full-length retrotransposons with {L}ong {T}erminal {R}epeats ({LTR}s) were further identified in the {E}. guineensis genome for characterization of their structural diversity, copy number and chromosomal distribution. {F}inally, their relative expression in several tissues was determined through in silico analysis of publicly available transcriptome data. {R}esults: {O}ur results reveal a congruence in the transpositional history of {LTR} retrotransposons between {E}. oleifera and {E}. guineensis, especially the {S}to-4 family. {A}lso, we have identified and described 583 full-length {LTR}-retrotransposons in the {E}laeis guineensis genome. {O}ur work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred. {M}oreover, the analysis of chromosomal distribution suggests a preferential insertion of {C}opia elements in gene-rich regions, whereas {G}ypsy elements appear to be evenly distributed throughout the genome. {C}onclusions: {C}onsidering the high proportion of {LTR} retrotransposon in the oil palm genome, our work will contribute to a greater understanding of their impact on genome organization and evolution. {M}oreover, the knowledge gained from this study constitutes a valuable resource for both the improvement of genome annotation and the investigation of the evolutionary history of palms.},
  keywords = {{O}il palm ; {T}ransposable elements ; {R}etrotransposons ; {LTR}},
  booktitle = {},
  journal = {{B}mc {G}enomics},
  volume = {16},
  numero = {},
  pages = {795},
  ISSN = {1471-2164},
  year = {2015},
  DOI = {10.1186/s12864-015-2023-1},
  URL = {https://www.documentation.ird.fr/hor/fdi:010065385},
}