茄鐮孢菌複合種感染海龜之致病相關基因體學

Abstract

noneFungi from the genus Fusarium is a common pathogen that infects plants, human, and animals. In particular, some members from the Fusarium solani species complex (FSSC) were comparatively well-studied because the most impacted hosts were agriculturally important plants. In animals, fusariosis caused by FSSC was increasingly reported in domestic, captive and wild animals in recent decades. Whilst it is commonly reported as an opportunistic pathogen towards animals, most reports were only able to identify the disease causative FSSC members and describe its pathologic changes on the infected host. Sea turtle egg fusariosis (STEF) has been reported around the globe and has caused huge mortality in this endangered animal. However, little is known regarding the ecology and pathology of STEF. The establishment of hatchery is part of the conservation works to protect sea turtle eggs. Nonetheless, a particular hatchery practice – reusing sand for egg incubation for several nesting seasons – is to be suspected for inducing higher FSSC infection risk in incubating eggs. This study determined the microbial diversity and pathogen abundance of nest sand (Chapter 1) to find the association between used-nest sand and FSSC infection on eggs. Distinct microbiota and a higher relative abundance of FSSC were found in nest sand of sea turtle hatcheries that reuse the sand compared to the nesting beach and hatchery which did not reuse sand. This work emphasizes that stringency in hatchery management must be maintained for the efforts of conservation to not be in vain. Besides the field survey, this study further determines the genomic basis of pathogenicity in FSSC pathogens isolated from dead sea turtle eggs and various host types (Chapter 2). Highly contiguated assemblies of six FSSC strains were produced and compared, revealing a spectrum of conservation patterns in the FSSC chromosome which canbe categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). Each chromosome type varied in structural architectures, with FC and LS chromosomes containing a significantly higher proportion of repetitive elements than core chromosomes and enriched in functions related to pathogenicity and niche expansion. These findings provide evidence that genome compartmentalisation was the outcome of multi-speed evolution amongst FSSC chromosomes, which is in contrast to the commonly recognized “two-speed” genome concept in fungal pathogens. In addition to the classification of FSSC’s genomic characteristics, several experiments were conducted to observe the infection scenarios and described the transcriptome responses of FSSC pathogens and Chinese soft-shelled turtle Pelodiscus sinensis eggs post-inoculation (Chapter 3). The experiments demonstrated that F. falciforme and F. keratoplasticum can penetrate eggshells and colonise egg inclusions, indicating FSSC are opportunistic pathogens toward eggs and identified differentially genes also associated with plant pathogenicity including the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. The outcome of this dissertation should allow the gain of fundamental knowledge regarding the pathology behind FSSC on eggs, which represents the beginning of critical steps towards the management of epidemics to reduce disease occurrences in the wild and man-managed settings. Moreover, this study establishes genomic resources and an animal model for fungal pathogens of the trans-kingdom hosts.