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The genome of the hydatid tapeworm Echinococcus granulosus

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TLDR
It is found that genes in bile salt pathways may control the bidirectional development of E. granulosus, and sequence differences in the calcium channel subunit EgCavβ1 may be associated with praziquantel sensitivity.
Abstract
Cystic echinococcosis (hydatid disease), caused by the tapeworm E. granulosus, is responsible for considerable human morbidity and mortality. This cosmopolitan disease is difficult to diagnose, treat and control. We present a draft genomic sequence for the worm comprising 151.6 Mb encoding 11,325 genes. Comparisons with the genome sequences from other taxa show that E. granulosus has acquired a spectrum of genes, including the EgAgB family, whose products are secreted by the parasite to interact and redirect host immune responses. We also find that genes in bile salt pathways may control the bidirectional development of E. granulosus, and sequence differences in the calcium channel subunit EgCavβ1 may be associated with praziquantel sensitivity. Our study offers insights into host interaction, nutrient acquisition, strobilization, reproduction, immune evasion and maturation in the parasite and provides a platform to facilitate the development of new, effective treatments and interventions for echinococcosis control.

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Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Daniel J. Klionsky, +2983 more
- 08 Feb 2021 - 
TL;DR: In this article, the authors present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes.
Journal ArticleDOI

Echinococcosis: Advances in the 21st Century.

TL;DR: Recent acquired genomic and proteomic information can provide a platform for improving diagnosis and for finding new drug and vaccine targets, with direct impact in the future on the control of echinococcosis, which continues to be a global challenge.
Journal ArticleDOI

WormBase ParaSite - a comprehensive resource for helminth genomics.

TL;DR: WormBase ParaSite (http://parasite.wormbase.org) as mentioned in this paper is a portal for the analysis of helminth genomic data, including worms and platy helminths.
Journal ArticleDOI

BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database

TL;DR: The BRAKER2 pipeline as mentioned in this paper generates and integrates external protein support into the iterative process of training and gene prediction by GeneMark-EP+ and AUGUSTUS, and it is favorably compared with other pipelines, e.g. MAKER2, in terms of accuracy and performance.
Posted ContentDOI

BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database

TL;DR: In comparison with BRAKER1 supported by a large volume of transcript data, BRAKER2 could produce a better gene prediction accuracy if the evolutionary distances to the reference species in the protein database were rather small.
References
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Journal ArticleDOI

MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Journal ArticleDOI

Clustal W and Clustal X version 2.0

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Journal ArticleDOI

Mapping and quantifying mammalian transcriptomes by RNA-Seq.

TL;DR: Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3′ untranscribed regions, as well as new candidate microRNA precursors.
Journal ArticleDOI

Tandem repeats finder: a program to analyze DNA sequences

TL;DR: A new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size is presented and its ability to detect tandem repeats that have undergone extensive mutational change is demonstrated.
Journal ArticleDOI

The KEGG resource for deciphering the genome

TL;DR: A knowledge-based approach for network prediction is developed, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes.
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