Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-Seq of E.tenella Houghton life cycle stages

ABSTRACT: Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including E. tenella. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. sporozoites, merozoites, unsporulated oocysts, sporulated oocysts) of E. tenella Houghton. The aim is to make transcriptional landscape maps of different life cycle stages of E. tenella at single base pairs resolution and utilise this information to identify the genes and define the precise gene boundaries. Gene finding has been a rather difficult task in Eimeria. Obtaining the precise transcript boundaries by Illumina RNA-Seq protocol is expected to expedite gene finding in Eimeria tenella. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

ORGANISM(S): Eimeria tenella

SUBMITTER:

PROVIDER: E-ERAD-109 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Genomic analysis of the causative agents of coccidiosis in domestic chickens.

Reid Adam J AJ Blake Damer P DP Ansari Hifzur R HR Billington Karen K Browne Hilary P HP Bryant Josephine J Dunn Matt M Hung Stacy S SS Kawahara Fumiya F Miranda-Saavedra Diego D Malas Tareq B TB Mourier Tobias T Naghra Hardeep H Nair Mridul M Otto Thomas D TD Rawlings Neil D ND Rivailler Pierre P Sanchez-Flores Alejandro A Sanders Mandy M Subramaniam Chandra C Tay Yea-Ling YL Woo Yong Y Wu Xikun X Barrell Bart B Dear Paul H PH Doerig Christian C Gruber Arthur A Ivens Alasdair C AC Parkinson John J Rajandream Marie-Adèle MA Shirley Martin W MW Wan Kiew-Lian KL Berriman Matthew M Tomley Fiona M FM Pain Arnab A

Genome research 20140711 10

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have ...[more]

PMID: 25015382

Similar Datasets

Project description:Purpose: Parasites of the genus Eimeria, and the closely related human pathogen Cyclospora cayetanensis, cause enteric disease in livestock and people worldwide. These coccidian parasites must undergo maturation (sporulation) before becoming infectious. Understanding oocyst maturation would benefit attempts to reduce the harm they cause to veterinary and human health. No animal model exists to study C. cayetanensis and the parasite cannot be grown in culture. We assessed transcription in maturing oocysts of Eimeria acervulina, a widespread chicken parasite, in order to identify markers of viability and those that may differentiate immature and mature oocysts. We also investigated predicted gene function and determined which of this parasite’s genes also occur in C. cayetanensis. Methods: E. acervulina oocysts were collected from chickens (3 biological replicates) and allowed to sporulate for 24 hours. RNA was extracted from oocysts that were collected every four hours and subjected to RNA-Sequencing. Data were screened for constitutively expressed genes throughout the time course. We also identified differentially expressed genes between immature and mature oocysts. We performed functional characterization of constitutively -expressed and significantly differentially-expressed genes and also biochemical pathway analysis. RT–qPCR validation on selected constitutively and differentially-expressed genes was performed using SYBR Green assays. Results: RNA-Seq yielded ~2 billion paired-end reads, 92% of which mapped to the E. acervulina genome. The ~6,900 annotated genes underwent temporally-coordinated patterns of gene expression. Fifty-three constitutively expressed genes each contributed >1,000 TPM throughout, including those encoding cation-transporting ATPases, an oocyst wall protein, a palmitoyltransferase, membrane proteins, and hypothetical proteins. These genes were enriched for 285 gene ontology (GO) terms and 13 genes were associated with a total of 17 KEGG pathways, defining housekeeping processes and functions important throughout sporulation. Expression of more than 40% of these genes (2,928) differed in sporulated vs. unsporulated oocysts; of these, nearly two-thirds (1,843) increased their expression over time. Eight genes expressed most in unsporulated oocysts, and encoding proteins promoting oocyst maturation and development, could be assigned to 37 GO terms and 5 KEGG pathways. Fifty-six genes underwent significant upregulation in sporulated oocysts, each contributing at least 1,000 TPM. Of these, 40 were annotated by 215 GO assignments and 9 were associated with 18 KEGG pathways, encoding products involved in respiration, carbon fixation, energy utilization, invasion, motility, and stress and detoxification responses. Several RT-qPCR assays confirmed RNA-Seq as a valid means to estimate gene expression. Conclusions: Sporulation orchestrates coordinated changes in the expression of many coccidian genes, most especially those important to metabolic activity. These data elucidate the biology of coccidian development, provide means to evaluate the maturity of parasite cohorts, and may prove useful in predicting infectiousness. Moreover, because many of these genes have homologues in C. cayetanensis, they may prove useful as biomarkers for infectiousness.

Dataset Information

RNA-Seq of E.tenella Houghton life cycle stages

Publications

Genomic analysis of the causative agents of coccidiosis in domestic chickens.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets