@article{PAR00013207,
  title = {{D}e novo assembly and annotation of the {A}sian tiger mosquito ({A}edes albopictus) repeatome with dna{P}ipe{TE} from raw genomic reads and comparative analysis with the yellow fever mosquito ({A}edes aegypti)},
  author = {{G}oubert, {C}. and {M}odolo, {L}. and {V}ieira, {C}. and {V}aliente{M}oro, {C}. and {M}avingui, {P}atrick and {B}oulesteix, {M}.},
  editor = {},
  language = {{ENG}},
  abstract = {{R}epetitive {DNA}, including transposable elements ({TE}s), is found throughout eukaryotic genomes. {A}nnotating and assembling the "repeatome" during genome-wide analysis often poses a challenge. {T}o address this problem, we present dna{P}ipe{TE}-a new bioinformatics pipeline that uses a sample of raw genomic reads. {I}t produces precise estimates of repeated {DNA} content and {TE} consensus sequences, as well as the relative ages of {TE} families. {W}e shows that dna{P}ipe{TE} performs well using very low coverage sequencing in different genomes, losing accuracy only with old {TE} families. {W}e applied this pipeline to the genome of the {A}sian tiger mosquito {A}edes albopictus, an invasive species of human health interest, for which the genome size is estimated to be over 1 {G}bp. {U}sing dna{P}ipe{TE}, we showed that this species harbors a large (50% of the genome) and potentially active repeatome with an overall {TE} class and order composition similar to that of {A}edes aegypti, the yellow fever mosquito. {H}owever, intraorder dynamics show clear distinctions between the two species, with differences at the {TE} family level. {O}ur pipeline's ability to manage the repeatome annotation problem will make it helpful for new or ongoing assembly projects, and our results will benefit future genomic studies of {A}. albopictus.},
  keywords = {transposable elements ; repeated {DNA} ; {TE} analysis ; {A}edes albopictus ; {T}rinity ; bioinformatic pipeline},
  booktitle = {},
  journal = {{G}enome {B}iology and {E}volution},
  volume = {7},
  numero = {4},
  pages = {1192--1205},
  ISSN = {1759-6653},
  year = {2015},
  DOI = {10.1093/gbe/evv050},
  URL = {https://www.documentation.ird.fr/hor/{PAR}00013207},
}