De Novo Transcriptome Assembly and Analysis of the Flat Oyster Pathogenic Protozoa Bonamia Ostreae

Abstract

The flat oyster Ostrea edulis is an oyster species native to Europe. It has declined to functional extinction in many areas of the NE Atlantic for several decades. Factors explaining this decline include over-exploitation of natural populations and diseases like bonamiosis, regulated across both the EU and the wider world and caused by the intracellular protozoan parasite Bonamia ostreae. To date, very limited sequence data are available for this Haplosporidian species. We present here the first transcriptome of B. ostreae. As this protozoan is not yet culturable, it remains extremely challenging to obtain high-quality -omic data. Thanks to a specific parasite isolation protocol and a dedicated bioinformatic pipeline, we were able to obtain a high-quality transcriptome for an intracellular marine micro-eukaryote, which will be very helpful to better understand its biology and to consider the development of new relevant diagnostic tools.

Long amplicons as a tool to identify variable regions of ribosomal RNA for improved taxonomic resolution and diagnostic assay design in microeukaryotes: using ascetosporea as a case study

“…On the contrary, the external transcribed spacer (ETS) appears to be a suitable marker for discriminating between P. canceri and P. orchestiae and M. cochillia and M. cocosarum. The ETS region was identified by mapping transcriptomic reads produced in Chevignon et al (2022) to the full B. ostreae rRNA array produced in this study. Subsequent alignment of the B. ostreae ETS region to Paramarteilia and Marteilia rRNA arrays identified the ETS in these genera.…”

“…For analysis of the structure of the IGS, Bonamia transcriptome reads [accession number PRJNA731671; Chevignon et al (2022)] were mapped as above to the full Bonamia rRNA generated in this study. Coverage at each nucleotide position was determined using SAMtools v1.9 and graphed using R Studio v1.4.1717.…”

“…To determine the location of the non-transcribed spacer (NTS) and external transcribed spacer (ETS) regions of the B. ostreae rRNA array, transcriptome reads from purified B. ostreae parasites [Accession number PRJNA731671; Chevignon et al (2022)] were aligned against the full B. ostreae rRNA array generated in this study and the coverage across the array was determined (Figure 3). A 2,856 bp region, starting at the end of the 28S had no coverage with transcriptome reads, suggesting that this is the NTS region of the IGS.…”

Fifty years of research to counter the decline of the European flat oyster (Ostrea edulis): a review of French achievements and prospects for the restoration of remaining beds and revival of aquaculture production

“…In addition, a few amino acid sequences were characterized for B. ostreae, including two actin genes (López-Flores et al, 2007) and Heat Shock Protein 90 involved in the internalization of the parasite into hemocytes (Prado-Alvarez et al, 2013). More recently, RNA sequencing was carried out from B. ostreae isolated from infected flat oysters (Chevignon et al, 2022). These transcriptomic data were included in a phylogenomic analysis of a set of 229 genes from representative species of all major rhizarian clades, which confirmed the position of B. ostreae within the class Ascetospora (Sierra et al, 2016).…”