Transcriptomics is currently the approach of choice to analyse species without available genomes, as is often the case for algae. Beyond functionally-oriented gene-expression analysis, the increasingly common investigation of multiple, closely-related genomes (or transcriptomes) unveils precious but hitherto under-exploited information on gene variants and gene evolution. This project is aiming to apply tools for genome/transcriptome-wide variant identification and subsequent analysis of gene evolution (e.g. positive selection) across orthologues, whilst using them to address questions on pathogen perception and the evolution of pathogenicity on a model algal-pathogen interaction.
This project, which is based at VIB – a life sciences research institute in Belgium, starts from the interaction between the genome model seaweed Ectocarpus siliculosus and its oomycete pathogen Eurychasma dicksonii. Initial analysis of the Ectocarpus genome sequence has revealed two gene families (so-called LRR-ROCO and NB-ARC-TPR) that display unique structural, regulatory and evolutionary features, making them excellent candidates pathogen receptors. An extensive RNAseq dataset, obtained on three clonal, haploid Ectocarpus strains belonging to two species, and either resistant or susceptible to infection by two Eurychasma strains is now available. Additional RNAseq data on related brown algal species are available within the consortium. Via the analysis of polymorphism of LRR-ROCO and NB-ARC-TPR genes across Ectocarpus strains and species, the existence of rapid, original evolutionary mechanisms will be tested. Likewise, oomycete pathogenicity effectors are typically both highly expressed during infection and highly variable between strains.
Looking for genes exhibiting such features across Eurychasma strains will directly inform our ongoing investigation of Eurychasma pathogenicity effectors and virulence mechanisms. Considering the benefit of a genome sequence to facilitate gene copy number and orthologue gene identification, obtaining and annotating a draft genome sequence for Eurychasma will be attempted (VIB). It is expected to have a haploid genome of 50-100 Mb, with ca. 10,000 genes. Axenic cultures and RNAseq data on two strains are available to facilitata assembly and annotation (C. Gachon). Tools used for variant analysis will be implemented in ORCAE, in close collaboration with ESR 14. Their portability into or interoperability with BioNumerics will be explored during a secondment at APPLIED MATHS NV. The Eurychasma genome (or failing this, transcriptome) annotation will further focus on gene family evolution and synteny analysis with other oomycete genomes.
The key results we expect to achieve from this research are:
- Insights into the mechanisms of pathogen detection, especially the evolution of LRRROCO and NB-ARC-TPR genes in Ectocarpus;
- De novo prediction of Eurychasma pathogenicity effectors based on their expression and evolutionary signatures; and
- Eurychasma genome sequence integrated in ORCAE.