DOI: 10.5061/dryad.tx95x69tt
title: Transcriptome-wide comparisons and virulence gene polymorphisms of host-associated genotypes of the cnidarian parasite Ceratonova shasta in salmonids

description: Ceratonova shasta is an important myxozoan pathogen affecting the health
 of salmonid fishes in the Pacific Northwest of North America. C. shasta
 exists as a complex of host-specific genotypes, some with low to moderate
 virulence, and one that causes a profound, lethal infection in susceptible
 hosts. High throughput sequencing methods are powerful tools for
 discovering the genetic basis of these host/virulence differences, but
 deep sequencing of myxozoans has been challenging due to extremely fast
 molecular evolution of this group, yielding strongly divergent sequences
 that are difficult to identify, and unavoidable host contamination. We
 designed and optimized different bioinformatic pipelines to address these
 challenges. We obtained a unique set of comprehensive, host-free myxozoan
 RNA-seq data from C. shasta genotypes of varying virulence from different
 salmonid hosts. Analyses of transcriptome-wide genetic distances and
 maximum likelihood multigene phylogenies elucidated the evolutionary
 relationship between lineages and demonstrated the limited resolution of
 the established Internal Transcribed Spacer marker for C. shasta genotype
 identification, as this marker fails to differentiate between biologically
 distinct genotype II lineages from coho salmon and rainbow trout. We
 further analyzed the datasets based on polymorphisms in two gene groups
 related to virulence: cell migration and proteolytic enzymes including
 their inhibitors. The developed SNP-calling pipeline identified
 polymorphisms between genotypes and demonstrated that variations in both
 motility and protease genes were associated with different levels of
 virulence of C. shasta in its salmonid hosts. The prospective use of
 proteolytic enzymes as promising candidates for targeted interventions
 against myxozoans in aquaculture is discussed. We developed host-free
 transcriptomes of a myxozoan model organism from strains that exhibited
 different degrees of virulence, as a unique source of data that will
 foster functional gene analyses and serve as a base for the development of
 potential therapeutics for efficient control of these parasites.
description: <b>Host filtering at
 read level – <i>Ceratonova shasta</i> and neither reads
 lists</b> Lists of <i>Ceratonova
 shasta</i> mapping reads and reads that did not map neither to host
 (<i>Oncorhynchus mykiss</i>) nor to parasite (<i>C.
 shasta</i>). Reads belong to three different genotypes (I, IIC, IIR)
 and to five different libraries (I, IIC, IIR-RBTJ7, IIR-RBTC16,
 IIR-RBT6). Lists
 of reads, 20 .list files. I_csR1.list I_csR2.list I_neitherR1.list I_neitherR2.list IIC_csR1.list IIC_csR2.list IIC_neitherR1.list
 IIC_neitherR2.list
 IIR_RBTJ7_csR1.list
 IIR_RBTJ7_csR2.list
 IIR_RBTJ7_neitherR1.list IIR_RBTJ7_neitherR2.list IIR_RBTC16_csR1.list IIR_RBTC16_csR2.list IIR_RBTC16_neitherR1.list IIR_RBTC16_neitherR2.list IIR_RBT6_csR1.list IIR_RBT6_csR2.list IIR_RBT6_neitherR1.list IIR_RBT6_neitherR2.list <b>Genotype IIR (RBT6) assembled transcriptomes</b> Two assembled transcriptomes using IIR RBT6 <i>C. shasta</i> only reads or <i>C. shasta</i> only + neither reads. 2 .fasta files IIR_RBT6_cs_only.fasta IIR_RBT6_cs_neither.fasta <b>Host and other contaminants (other microorganisms) IIR RBT6 filtered assemblies</b> Filtered assembled transcriptomes for host (<i>Oncorhynchus mykiss</i>) and other microorganisms (virus, fungi, bacteria) using Taxon ID annotations. 2 .fasta files IIR_RBT6_cs_only_extra_clean.fasta IIR_RBT6_cs_neither_extra_clean.fasta <b>Longest representatives reference IIR RBT6 cs+neither assembly used for SNPs analyses</b> 1 . fasta file IIR_RBT6_cs_neither_extra_clean_woreps.fasta <b>SNPs tables</b> Genotypes called from nucleotide frequencies with a minimum coverage of 5 and 0.25 heterozygosity threshold. 5 .tab files I_genotypes.tab IIC_genotypes.tab IIR_RBTJ7_genotypes.tab IIR_RBTC16_genotypes.tab IIR_RBT6_genotypes.tab Genotypes called from nucleotide frequencies with a minimum coverage of 20 reads and 0.1 heterozygosity threshold. 5 .tab files I_genotypes2000101.tab IIC_genotypes2000101.tab IIR_RBTJ7_genotypes2000101.tab IIR_RBTC16_genotypes2000101.tab IIR_RBT6_genotypes2000101.tab <b>Phylogenomic and SNPs-based phylogenetic alignments </b> 9 .nex and 51 .fasta files cmkb_permissive.nex cmkb_permissive_filtered.nex combined.nex combined_cmkb_curated.nex combined_merops_curated.nex combined_only_available_all.nex merops_permissive.nex merops_permissive_filtered.nex phylogenomic_tree.nex 51 individual genes alignments for phylogenomics in .fasta