Phylogenomics of Ascetosporea

University essay from Uppsala universitet/Systematisk biologi; Uppsala universitet/Institutionen för biologisk grundutbildning

Abstract: Ascetosporea is a class of poorly studied unicellular eukaryotes that function as parasites of marine invertebrates. These parasites cause mass mortality events in aquaculture species such as oysters and mussels. The economic importance of these aquaculture species should lead to more attention on the genomics of Ascetosporea and their place on the evolutionary tree of life. With the onset of global warming and rising sea levels and temperatures, many emerging pathogens have been seen and until these are sequenced and analysed, it is difficult to make any conclusions about their relationships and evolution. As there aren’t many genomes and transcriptomes available for Ascetosporea, their position in the larger eukaryotic tree of life remains hypothetical. To attempt to remedy this lack of information, the Burki lab has recently generated sequencing data through sample collection and sequencing for these organisms (genomes and transcriptomes). A curated dataset of the various eukaryotic species was previously created and newly sampled and sequenced Ascetosporean genomes of Paramarteilia sp., Marteilia pararefringens, Paramikrocytos canceri, etc. from multiple sampling locations like Ireland, Norway, Sweden, and the UK were included. These could increase the genomic and transcriptomic data available for Ascetosporea and help to resolve the relationships within Ascetosporea. A few reasons why this group has not yet been placed on the tree of life are that the samples are from host tissue, which makes it difficult to sequence these parasites. These Ascetosporeans have also been seen to be very fast-evolving. After building phylogenetic relationships with single gene trees to allow for the identification of possible contaminants and paralogs, it was seen that there was a lot of contamination in Ascetosporea, due to the sampling being from host tissue material (hosts are open to the environment). After cleaning and filtering the possible contaminated genes, the trees were remade and a possible link between a fungal group called Microsporidia and Ascetosporea was observed in a few genes. This was hypothesized to be lateral gene transfer between the two groups resulting from their similar lifestyles and infection of invertebrates. There were complications like contamination and short blast hits that arose during analysis, and these could be caused by problems by fragmentation in the genome. This fragmentation could have negative effects on genome annotation predictions and consequently phylogenetic and phylogenomic analysis. Due to this and the challenging nature of collecting samples, the read coverage for the genomes is low but it can be used to perform phylogenetic and phylogenomic studies using currently available data and methods. Another expected result was that the sequenced data had contaminants, and a thorough and comprehensive search would have to be conducted on a dataset-wide level to remove any contaminants.

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