“High-quality genome sequences enable in-depth studies of the genomic structure and pathogenic potential of Aphanomyces astaci genotypes (7050)”

High-quality genome sequences enable in-depth studies of the genomic structure and pathogenic potential of Aphanomyces astaci genotypes

Aphanomyces astaci, the causal agent of crayfish plague, is a devastating oomycete pathogen that causes high mortalities in ecologically important European crayfish species such as noble crayfish, white-clawed crayfish, and stone crayfish. To date, at least five A.astaci genotype groups (A-E) with a pathogenic potential ranging from causing only chronic infections to rapid death have been identified. It is assumed that the differences in pathogenicity have a genomic component. It is also known from other oomycete pathogens that these organisms often have highly plastic genomes with a high percentage of repetitive elements. The A.astaci reference sequence is made from short-read data and thus quite fragmented (un-gapped length of 58Mb, N50 of 657kb).To study phenomena such as chromosomal rearrangements or effector expansion, high quality genome sequences are required, ideally with telomere to telomere (T2T) contigs.

To this end, we cultivated the five A.astaci genotype groups A-E in liquid culture and sequenced the extracted DNA with PacBio long reads. The data was assembled using Hifiasm and for gene prediction and functional annotation we made use of publicly available resources such as A.astaci transcriptomic data (PRJNA187375) and the Companion server (10.1093/nar/gkae378).

The resulting reference sequences show a high level of completeness and continuity. The assembly of genotype D for example includes all BUSCO genes of Stramenopiles (stramenopiles_odb10: C:100.0%[S:98.0%,D:2.0%], n:100), has an N50 and L50 of 3.7Mb and 12 contigs, respectively. More than 80Mb are contained in contigs with at least one telomer and the six T2T contigs comprise 30Mb. The high continuity of these genome assemblies allows comparative analyses of the five genotypes on the single nucleotide level, but more importantly also enables the assessment of the genomic structures, in particular long genomic or chromosomal re-arrangements. Differences in the genetic make-up of the genotypes, for example in the composition of effector genes, might help us to better understand the differences in pathogenicity. They are also a valuable resource for large scale gene expression studies in A.astaci aiming at shedding light on the mechanism of infection.

1. OBERHAENSLI, SIMONE, UNVERSITY OF BERN, Presenter
2. JEMMI, ELIANE, UNVERSITY OF BERN, Author
3. NICHOLSON, PAMELA, UNVERSITY OF BERN, Author
4. PISANO, SIMONE, UNVERSITY OF BERN, Author
5. SCHMIDT-POSTHAUS, HEIKE, UNVERSITY OF BERN, Author