Leishmania donovani BPK282/0/cl4 reference based on PacBio. Leishmania donovani BPK282/0/cl4 PacBio reference 2017

This was sequenced to improve the BPK282/0cl4 reference (LdBPKv1: Downing and Imamura et al. 2011) using PacBio sequencing by the Institute of Tropical Medicine, Antwerp and it is a part of the publication "Modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments, and its impact on gene expression. mbio". To increase the quality of our genomic and transcriptomic studies we generated an updated version of the BPK282A1 reference genome using Pacific Biosciences SMRT technology (median 131 fold coverage). 130 contigs generated from PacBio sequences were aligned, mapped against the L. major genome LmjF to produce a beta version of the new reference genome. Companion annotated 8,681 genes. It contains a larger number of genes, has only 20 large gaps, and includes an annotated kDNA maxi-circle sequence. The long PacBio reads improved the accuracy of multi-copy genes and tandem repeats; they also allowed assembly and annotation of subtelomeric and telomeric regions which were mostly missed in LdBPKv1. In addition, inversions and miss-assemblies in LdBPKv1 were corrected, substantially reducing the number of false-positive base and copy number variations.