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Echinococcus oligarthrus genome

ABSTRACT: Whole genome sequencing of neotrpical species Echinococcus oligarthrus

PROVIDER: PRJEB31222 | ENA |

REPOSITORIES: ENA

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Project description:The cestodes Echinococcus granulosus and Echinococcus multilocularis, as the pathogens of cystic echinococcosis and alveolar echinococcosis respectively, can cause significant health problems to the host and considerable socio-economic losses as a consequence. Based on the genomic data regarding these two species available in public database recently, we carried out high-throughput mRNA and small RNA transcriptomic sequencing of them and generate enormous transcriptomic datasets. A total of 34,717,856 reads (79.79%) mapped to E. granulosus genome, and 38,882,179 reads (87.61%) mapped to E. multiloculari genome. A total of 24,550 (7,925 known and 16,625 novel transcripts) and 23,771 transcripts (8,432 known and 15,339 novel transcripts) were assembled for E. granulosus and E. multilocularis respectively, and the assembly yielded 11,330 genes (6,815 known and 4,515 novel genes) for E. granulosus and 10,101 genes (7,051 known and 3,050 novel genes) for E. multilocularis, compared with the reference genome data. Bioinformatic analysis identified 6,826 AS events from 3,774 E. granulosus genes (33.31%) and 6,644 AS events in 3,611 E. multilocularis genes (35.75%). A total of 76,674 distinct microRNAs of E. granulosus and 115,742 of E. multilocularis were also obtained from small RNA transcriptome sequencing reads. Of these, there were 20 microRNAs of E. granulosus and 22 microRNAs of E. multilocularis that belonged to 19 and 21 microRNA families common to other metazoan lineages separately. 76 and 90 novel microRNAs so far unique to E. granulosus and E. multilocularis were also identified respectively. This study represents an extensive mRNA and small RNA transcriptome dataset obtained from the deep sequencing of these two cestode species. The findings will facilitate a more fundamental understanding of cestode biology, evolution, the host-parasite interplay, and provide new insights into the pathophysiology of echinococcosis, contributing to the development of improved interventions for disease control.

Project description:N6-methyladenosine (m6A) is the methylation of adenosine at position N6 and is notably one of the most abundant modifications found in mRNA of eukaryotes. Although it does not interrupt the coding functions of transcripts, it assists in regulating several RNA functions like splicing, stability, translocation and translation and is associated with disease development, cell proliferation, cell migration, cell invasion, autophagy, cell apoptosis, and drug resistance. In this study, we performed a colorimetric assay, ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), and methylated RNA immunoprecipitation sequencing (MeRIP-seq) to assess the RNA N6-methyladenosine landscape of Echinococcus granulosus; a tapeworm species of the phylum Platyhelminthes that is responsible for a cosmopolitan zoonosis (cystic echinococcosis) of public health importance. While the levels of m6A modification were not significantly different between the life cycle stages, many important genes including notably enriched and expanded protein domains like Dyneins, Hsp70, and Cadherin thought to play important roles in adaptation to parasitism were m6A-modified. These genes were functionally enriched in biological processes like cell division, cell adhesion, microtubule-based movement, important pathways involved in parasitism (e.g. MAPK), and disease processes. Additionally, the m6A alterations were present in the first exon of modified genes, suggesting gene regulatory activities. Conclusively, m6A modification of the mRNA is present in Echinococcus, and is mediated by orthologues of known mammalian methyltransferases but possibly irreversible due to the absence of demethylases. The demonstration of differentially m6A-methylation in the different life cycle stages of Echinococcus suggests a role in the development and survival of the tapeworm. It also provides the groundwork for future studies in understanding the implication of RNA methylation in the treatment of echinococcoses.

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Echinococcus oligarthrus genome

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