genomes & transcriptomes

de novo assembly of transcriptomes and genomes

We have been involved in a series of genome and transcriptome de novo sequencing projects.

de novo assembly of the Axolotl transcriptome

The mexican Axolotl (Ambystoma mexicanum) is able to regenerate entire body ports, such as limb or tail. Consequently, it is an important model organism for research on regeneration. For a long time, the lack of a completely sequenced genome has made genetic work in Axolotl difficult. Over the years, we have in close collaboration with the group of Elly Tanaka worked on the sequencing and assembly of the Axolotl transcriptome; first, based on standard Sanger EST sequencing (Habermann B, et al., Genome Biol. 2004;5(9):R67); with the advent of next-generation sequencing, we have focused on whole-transcriptome RNA-sequencing. We were able to sequence and assemble more than 1 billion NGS-reads from a various tissues of the Axolotl. In the course of this work and together with High-Performance Computing center in Dresden, we have moreover contributed to the parallelization and optimization of assembly algorithms within the BMBF project NGS goes HPC.

Our work has significantly contributed to the de novo sequencing of the Axolotl genome, the largest genome ever sequenced, which was recently published (Nowoshilow S, et al. Nature. 2018;554(7690):50-55. doi:10.1038/nature25458).

Genome rearrangements between A. salmonicida A449 and A. salmonicida pectinolytica 34mel

de novo assembly of complete genome of Aeromonas salmonicida pectinolytica

Aeromonads are wide-spread, mostly aquatic, gram-negative bacteria, which are pathogenic for animals. A. hydrophila for example is a human pathogen, A. salmonicida is pathogenic to fish. A subspecies of A. salmonicida called pectinolytica, however, shows no pathogenic potential, but is rather adapted to living in a highly polluted, aquatic environment.

Together with the lab of Stephan Gruber from the University of Lausanne, we have sequenced, assembled and annotated a high-quality, complete genome of A. salmonicida pectinolytica and compared this subspecies to fish- and human-pathogenic species (Pfeiffer, et al., BMC Genomics 2018;19(1):20. doi: 10.1186/s12864-017-4301-6.).

We have used PacBio, as well as Illumina sequencing and compared the two approaches, confirming the strength and precision of the rolling circle technology in bacterial genome sequencing. Another advantage of long-read sequencing is the easy generation of a complete, circular genome, making studies on genome plasticity possible.

de novo assembly of complete genome of Photorhabdus luminescens subsp. laumondii

A widely used lab strain of P. luminescens carrying a rifampicin resistance gene (TT01/rif) has shown substantial phenotypic differences to the type strain TT01 of this enteric bacterium.

We have sequenced the genomes of a widely used lab strain of P. luminescens that carries a rifampicin-resistance gene using PacBio sequencing and compared it to the published genome of TT01. Our genome comparison studies revealed a substantial number of mutations, frame shifts and strain-specific regions. Based on our analyses, strain TT01/rif, which we have renamed DJC, has to be considered an independent isolate, rather than a derivative of strain TT01 (Zamora-Lagos MA, et al. BMC Genomics.2018;19(1):854. doi:10.1186/s12864-018-5121-z.).