Genome and transcriptome analysis of fish tapeworm Nippotaenia percotti through scientific collaboration between research labs and national cyberinfrastructure.

Abstract

Tapeworms (Cestoda) are endoparasites infecting all vertebrates. Most (>50%) of their described diversity is within the clade Cyclophyllidea, a common, chronic source of anthropogenic infection. We report the first sequenced genome for the tapeworm Nippotaenia percotti (Nippotaeniidea - the putative sister group to Cyclophyllidea), which is host-specific to a fish in the Amur River. The genome was derived for comparative purposes, to explore evolutionary change in functional gene loci of immunological import. Pooled individuals were sequenced on Illumina (HiSeq 2000) and PacBio (RSII), with additional RNAseq on the HiSeq 2500. Hybrid assemblies were completed in SPAdes with long-read scaffolding in LINKS. The assembly was further improved using Redundans and Pilon, generating 3,410 contigs at an N50 of 209,561bp. Transcriptomes were assembled using a combined de novo approach (CDTA) with multiple assemblers and k-mers. Assembled transcripts were combined using EvidentialGene, producing 28,226 assembled transcripts at an N50 of 2,290bp, then annotated using Trinotate. The assembled genome was annotated using MAKER, identifying 30,671 genes, using our assembled transcriptome and genomes of closely-related cestodes. Gene evolution was examined using 15 cestode genomes from the WormBase Parasite database, with the MCL algorithm identifying 16,099 orthologous genes clusters. Gene loss/gain was assessed by contrasting gene clusters with the cestode phylogenetic tree constructed with core genes identified by BUSCO, using IQ-Tree. Nippotaenia percotti’s genome provides a baseline for future investigations into candidate-gene families potentially involved with anthropogenic infection and would also sponsor improvements in tapeworm treatment and control.