| dc.description.abstract | Amphibian declines worldwide are a major threat to biodiversity and contribute to Earth’s sixth mass extinction. Amphibian extinctions and extirpations are caused by a variety of factors, including habitat loss and climate
change. However, the chytridiomycosis panzootic and its causative agents,
the batrachochytrids Batrachochytrium salamandrivorans (Bsal) and Batrachochytrium dendrobatidis (Bd), are major contributing factors and are together responsible for over 90 extinctions and more than 500 declines. Bsal
and Bd’s devastating impact reaches beyond amphibian populations into
ecosystem health including directly threatening human health, exemplified
by an increase in malaria incidence in Panama and Costa Rica linked to
collapses of local amphibian populations. Mitigation of this global threat to
biodiversity and human welfare is crucial. Gaining a deeper understanding
of the evolution and virulence of the batrachochytrids responsible for the
chytridomycosis panzootic is necessary to inform mitigation efforts and has
the potential to unveil deeper understanding of how pathogens adapt to a
wide range of hosts, how virulence evolves and how host-pathogen interactions shape genomes.
Until recently, the origins of Bsal’s virulence and the evolution of the batrachochytrids were largely unknown, owing in part to a lack of a high-quality
reference genome. Indeed, before 2022, only a highly fragmented shortread assembly of Bsal’s genome was available, mainly due to its repeatrichness.
After a literature review in chapter 1 and 2, outlining the motivation and aim
of the study in chapter 3, and detailing my research methodology in chapter
4, I describe my strategy and considerations for generating a new assembly
based on deep nanopore long-read sequencing in chapter 5. The resulting assembly provides a significant improvement in contiguity and completeness, as well as repeat resolution. I detail the road map to achieving
this high-quality assembly of an extremely repeat-rich genome with comprehensive descriptions of how I performed read quality control, trimming
and filtering, pre-assembly assessments, assembly benchmarking, polishing and further annotation. For benchmarking, I introduce a summary quality
score for easy comparison of different reference-free assemblies, which is
based on and adapted from the C-score for reference-based assemblies
(Zhang et al. 2022).
In chapter 6, I describe my analysis of this new assembly to discover that
Bsal has the most repeat-rich genome of the 22 Chytridiomycota investigated in this thesis, comprising 40.9% repetitive elements. The Bsal genome appears to have undergone a repeat-driven expansion to more than
3X the length of its closest relative Bd. Autonomous and fully functional
transposable elements of the LTR/Gypsy family appear to contribute significantly to the observed expansion. The M36 metalloprotease virulence
factors are highly expanded (n = 177) in Bsal, many of which are flanked by
transposable elements (TEs), suggesting they have contributed to a repeatassociated expansion of that protein family (described in detail in chapter
8). Three TE families belonging to the superfamily of LINEs, implicated with
gene copy number variations, are found to be enriched upstream of M36
metalloprotease genes. This highlights the role of TEs in actively and passively shaping genome architecture and evolution. Unlike other fungi, Bsal
and Bd have no RIP (Repeat Induced Point mutation) machinery to silence
TE activity, but appear to rely on i.a. RNAi silencing. I also present evidence
of increased methylation of TEs compared to other features of the genome,
which could represent another avenue for Bsal to control TE proliferation.
In chapter 7, I take a deeper dive into chytrid genome organization, and discover and describe for the first time Bsal’s highly compartmentalized
genome architecture, with virulence factors enriched in gene-sparse/repeatrich compartments, while core conserved genes are enriched in generich/repeat-poor compartments. Genes upregulated during infection are
primarily found in the gene-sparse/repeat-rich compartment in both Bd and
Bsal. Furthermore, genes with signatures of positive selection in Bd are enriched in repeat-rich regions, suggesting these regions are a cradle for the
evolution of chytrid pathogenicity. These are the hallmarks of two-speed
genome evolution which has previously only been described in plant pathogens.
The main findings of my thesis have been recently published in PNAS
(Wacker et al. 2023a) in a comprehensive report of the first two-speed genome architecture described for a pathogen of vertebrates, shedding new
light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions. | en_GB |
