title: De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti).
abstract: Repetitive DNA, including transposable elements (TEs), is found throughout eukaryotic genomes. Annotating and assembling the "repeatome" during genome-wide analysis often poses a challenge. To address this problem, we present dnaPipeTE-a new bioinformatics pipeline that uses a sample of raw genomic reads. It produces precise estimates of repeated DNA content and TE consensus sequences, as well as the relative ages of TE families. We shows that dnaPipeTE performs well using very low coverage sequencing in different genomes, losing accuracy only with old TE families. We applied this pipeline to the genome of the Asian tiger mosquito Aedes albopictus, an invasive species of human health interest, for which the genome size is estimated to be over 1 Gbp. Using dnaPipeTE, 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 Aedes aegypti, the yellow fever mosquito. However, intraorder dynamics show clear distinctions between the two species, with differences at the TE family level. Our 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.
authors.affiliation: Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France.
authors.forename: Clément
authors.initials: C
authors.lastname: Goubert
authors.affiliation: Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Modolo
authors.affiliation: Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France.
authors.forename: Cristina
authors.initials: C
authors.lastname: Vieira
authors.affiliation: Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France Ecologie Microbienne, UMR 5557, CNRS, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Villeurbanne, France.
authors.forename: Claire
authors.initials: C
authors.lastname: ValienteMoro
authors.affiliation: Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France Ecologie Microbienne, UMR 5557, CNRS, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Villeurbanne, France Université de La Réunion, UMR PIMIT, CNRS 9192, INSERM 1187, IRD 249.
authors.forename: Patrick
authors.initials: P
authors.lastname: Mavingui
authors.affiliation: Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France matthieu.boulesteix@univ-lyon1.f.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Boulesteix
mesh_terms: D000330:Aedes / Q000235:genetics*; D000818:Animals; D004247:DNA / Q000737:chemistry; D004251:DNA Transposable Elements; D049750:Genome, Insect; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid; D012984:Software
chemical_list: D004251:DNA Transposable Elements; D004247:DNA
keywords: Aedes albopictus; TE analysis; Trinity; bioinformatic pipeline; repeated DNA; transposable elements