Show simple item record Sanders, Sheri Papudeshi, Bhavya Ganote, Carrie Doak, Tom Chafin, Tyler en Reshetnikov, Andrey en Sokolov, Sergey en Pummil, Jeff en Douglas, Marlis en Douglas, Michael en 2019-01-16T20:05:07Z 2019-01-16T20:05:07Z 2019-01-14
dc.identifier.citation T. Chafin, B. Papudeshi, S. Sanders, C. Ganote, A. Reshetnikov, S. Sokolov, T. Doak, J. Pummill, M.R Douglas, M.E. Douglas. 2019. The Genome of Fish Tapeworm Nippotaenia percotti as a Potential Bookmark for Gene Loci that Facilitates Anthropogenic Infection. Plant and Animal Genomes XXVII, San Diego, CA. Retrieved from en
dc.description.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. en
dc.description.sponsorship This research is based upon work supported by the National Science Foundation under grant No. ABI-1759906 to Indiana University. en
dc.language.iso en en
dc.publisher Plant and Animal Genome XXVII en
dc.rights Except where otherwise noted, the contents of this presentation are copyright of the Trustees of Indiana University. This license includes the following terms: You are free to share -to copy, distribute and transmit the work and to remix -to adapt the work under the following conditions: attribution -you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work. en
dc.rights.uri en
dc.subject NCGAS en
dc.subject tapeworm en
dc.subject CAFE en
dc.subject transcriptome assembly en
dc.subject genome assembly en
dc.subject genomic evolution en
dc.title The Genome of Fish Tapeworm Nippotaenia percotti as a Potential Bookmark for Gene Loci that Facilitates Anthropogenic Infection. en
dc.type Presentation en

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