Improvement of the BPK282/0cl4 (2011) reference by PacBio sequencing and aneuploidy analysis in different environments.

Leishmania is an intracellular protistan parasite affecting macrophages and dendritic cells. The parasite Leishmania donovani causes a disease called visceral leishmaniasis that affects many of the world's poorest people. Up to 80% of these cases occur in the Indian subcontinent. This was sequenced to improve the BPK282/0cl4 reference (Downing and Imamura et al. 2011) using PacBio sequencing by the Institute of Tropical Medicine, Antwerp. Illumina reads were used for aneuploidy analysis (see below). Aneuploidy is usually detrimental in multicellular organisms, but in several micro-organisms (fungi being the best-studied) it can be tolerated and even beneficial. Leishmania – a protozoan parasite killing more than 30,000 persons each year – is emerging as a new model for aneuploidy studies: unexpectedly high levels of aneuploidy are found in clinical isolates. Leishmania lacks classical regulation of transcription through inducible promoters, so aneuploidy could represent a major adaptive strategy of this parasite to modulate gene dosage in response to stressful environments. For the first time, we document the dynamics of aneuploidy throughout the life cycle of the parasite, in vitro and in vivo. Pacbio reference assembly: 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. 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. For detail, please see "Modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments, and its impact on gene expression." mbio