Dataset Information

Echinococcus granulosus

ABSTRACT: Echinococcus granulosus (sensu stricto) genome sequencing, assembly and annotation

PROVIDER: PRJNA754835 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
		Other
	SRR15522570_subreads.fastq.gz	Fastqsanger.gz
	SRR15522571_subreads.fastq.gz	Fastqsanger.gz
	SRR15522572.fastq.gz	Fastqsanger.gz
	SRR15522573.fastq.gz	Fastqsanger.gz

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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:TGF-Î² is a crucial cytokine participate in the interplay between the intermediate host and helminthes. TGF-Î² receptors were discovered in many cestode, and could bind the human TGF-Î². However, the function of host TGF-Î² on the Echinococcus is still not elucidated, and this paper aim to explore the question at transcription level. Microarray analysis was used to investigate differential expression genes in protoscolices of Echinococcus granulosus cultured in the presence or absence of human TGF-Î² at different time points (4h, 8h and 24h) in vitro. A total of 523 genes were up- or down-regulated in response to TGF-Î², compared with control group, 390 genes were up-regulated and 47 genes were down-regulated at 8h, and 376 genes were up-regulated and 19 genes were down-regulated at 12h, including 310 differential genes were regulated at both time point. Only 1 gene down-regulated at 4 h. Gene ontology (GO) analysis showed that the biological process of the up-regulated genes in protoscolex were predominantly involved in DNA packaging, nucleosome assembly, chromatin assembly, etc. And the cellular component gene were located in cell nucleus. TGF-Î² appeared to promote growth or development of the protoscolex by up-regulated the gene related with mitosis. In addition, the study also indicated that TGF-Î² has a multiple influence on the protoscolex, as reflected in the increased stimulation of gene expression of the ErbB signaling pathway, MAPK signaling pathway, Notch signaling pathway and VEGF signaling pathway. Isolated E. granulosus protoscoleces were treated with human TGF-Î² at different time points (4h, 8h and 24h) in vitro, and replicated 3 times. Each samples independently grown and harvested. And was extracted of total RNA using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each RNA sample separately on the GeneChip of Echinococcus granulosus Genome Array (Capitalbio) at CapitalBio Corporation (Beijing, China). The reference samples are protoscoleces treated by human TGF-Î²(0 h)

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Echinococcus granulosus

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