Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast

Simon Dittami (1) , Erwan Corre (2, 3)

1 LBI2M - Laboratoire de Biologie Intégrative des Modèles Marins
2 SBR - Station biologique de Roscoff [Roscoff]
3 FR2424 - Fédération de recherche de Roscoff

Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).

Mots clés: Bioinformatics; Genomics; Plant Science; Basic local alignment search tool (BLAST); Horizontal gene transfer; Contaminating; sequences; Genome assembly; Brown algae

Domaines: Sciences du Vivant [q-bio]

Simon Dittami, Erwan Corre. Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast. PeerJ, 2017, 5, pp.e4073. ⟨10.7717/peerj.4073⟩. ⟨hal-01654700⟩