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Filtering and characterization of Enteromyxum spp. (Myxozoa) transcriptomes from RNAseq data

AuthorsPicard-Sánchez, Amparo; Cañizares, J.; Ziarsolo, P.; Blanca, J.; Montero-Pau, J.; Sitjà-Bobadilla, Ariadna ; Palenzuela, Oswaldo
Issue Date4-Sep-2017
Citation18th International Conference on Diseases of Fish and Shellfish (2017)
AbstractEnteromyxum spp. are obligate parasites closely related to Cnidarians. They are responsible of serious emaciative diseases in marine aquacultured fish worldwide. Differently to other myxozoans with a 2-host cycle, which develop myxospores and actinospores, Enteromyxum spp. are only known to develop in fish intestines, dwelling in the paracellullar space in an intimate relationship with host cells. Spore production may be quite limited or inexistent, depending on the individual fish-Enteromyxum sp. model. Recent studies have focused on the obtention of transcriptome data from myxozoans, mostly from spore stages that can be easily isolated in large quantities. Although useful for gene hunting and phylogenomic studies, spores presumably contain a limited amount and repertory of expressed genes for functional studies. The goal of this work is to obtain a snapshot of genes expressed by developmental stages of Enteromyxum spp. in the course of their trophic development, invasion and pathogenic action in their hosts. This strategy required specifically designed tools to sort myxozoan RNAseq sequences from those of the hosts. An algorithm based on the transcripts¿ dinucleotide frequencies, and their Blastn score against specific fish/cnidarian datasets, was designed and tutored with curated test data. This resulted in the determination of the algorithm¿s error rate and the assignment of a p value to each filtering decision. As a result, 26,071 out of 281,264 transcripts were assigned to Enteromyxum spp. (p>0.99) while 30,551 were assigned to the hosts (p>0.99) and 57,507 were classified in a ¿greyzone¿ in between. The Enteromyxum filtered dataset was enriched with 4,500 additional transcripts initially classified as ¿fish¿ or ¿greyzone¿ [p(myxo)<0.99] after a repechage round with a curated Myxobolus pendula transcriptome dataset (Foo et al., 2015). The final dataset contains over 30,000 sequences with very low levels of contaminating fish transcripts. Functional annotation and characterization of the dataset, including comparison between E. scophthalmi and E. leei offers a basis for the identification of key molecules related to the development and pathogeny of these parasites. Additional comparative analyses with other myxozoans and free-living cnidarians can enlighten some of the unique adaptions of myxozoans to their parasitic lifestyles.
DescriptionTrabajo presentado en la 18th International Conference on Diseases of Fish and Shellfish, celebrada en Belfast, del 4 al 8 de septiembre de 2017
Appears in Collections:(IATS) Comunicaciones congresos
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