Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms.

Alternative Splicing Animals Gene Regulatory Networks Genome, Protozoan Glycosylation Livestock / parasitology Molecular Sequence Annotation / methods Protozoan Proteins / genetics Sequence Analysis, RNA Theileria parva / genetics
East coast fever Genome N-glycosylation Re-annotation Theileria

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
03 Apr 2020
Historique:
received: 27 08 2019
accepted: 18 03 2020
entrez: 5 4 2020
pubmed: 5 4 2020
medline: 20 11 2020
Statut: epublish

Résumé

The apicomplexan parasite Theileria parva causes a livestock disease called East coast fever (ECF), with millions of animals at risk in sub-Saharan East and Southern Africa, the geographic distribution of T. parva. Over a million bovines die each year of ECF, with a tremendous economic burden to pastoralists in endemic countries. Comprehensive, accurate parasite genome annotation can facilitate the discovery of novel chemotherapeutic targets for disease treatment, as well as elucidate the biology of the parasite. However, genome annotation remains a significant challenge because of limitations in the quality and quantity of the data being used to inform the location and function of protein-coding genes and, when RNA data are used, the underlying biological complexity of the processes involved in gene expression. Here, we apply our recently published RNAseq dataset derived from the schizont life-cycle stage of T. parva to update structural and functional gene annotations across the entire nuclear genome. The re-annotation effort lead to evidence-supported updates in over half of all protein-coding sequence (CDS) predictions, including exon changes, gene merges and gene splitting, an increase in average CDS length of approximately 50 base pairs, and the identification of 128 new genes. Among the new genes identified were those involved in N-glycosylation, a process previously thought not to exist in this organism and a potentially new chemotherapeutic target pathway for treating ECF. Alternatively-spliced genes were identified, and antisense and multi-gene family transcription were extensively characterized. The process of re-annotation led to novel insights into the organization and expression profiles of protein-coding sequences in this parasite, and uncovered a minimal N-glycosylation pathway that changes our current understanding of the evolution of this post-translational modification in apicomplexan parasites.

Sections du résumé

BACKGROUND BACKGROUND
The apicomplexan parasite Theileria parva causes a livestock disease called East coast fever (ECF), with millions of animals at risk in sub-Saharan East and Southern Africa, the geographic distribution of T. parva. Over a million bovines die each year of ECF, with a tremendous economic burden to pastoralists in endemic countries. Comprehensive, accurate parasite genome annotation can facilitate the discovery of novel chemotherapeutic targets for disease treatment, as well as elucidate the biology of the parasite. However, genome annotation remains a significant challenge because of limitations in the quality and quantity of the data being used to inform the location and function of protein-coding genes and, when RNA data are used, the underlying biological complexity of the processes involved in gene expression. Here, we apply our recently published RNAseq dataset derived from the schizont life-cycle stage of T. parva to update structural and functional gene annotations across the entire nuclear genome.
RESULTS RESULTS
The re-annotation effort lead to evidence-supported updates in over half of all protein-coding sequence (CDS) predictions, including exon changes, gene merges and gene splitting, an increase in average CDS length of approximately 50 base pairs, and the identification of 128 new genes. Among the new genes identified were those involved in N-glycosylation, a process previously thought not to exist in this organism and a potentially new chemotherapeutic target pathway for treating ECF. Alternatively-spliced genes were identified, and antisense and multi-gene family transcription were extensively characterized.
CONCLUSIONS CONCLUSIONS
The process of re-annotation led to novel insights into the organization and expression profiles of protein-coding sequences in this parasite, and uncovered a minimal N-glycosylation pathway that changes our current understanding of the evolution of this post-translational modification in apicomplexan parasites.

Identifiants

DOI: 10.1186/s12864-020-6683-0 PMID: 32245418 PMC: PMC7126163
pubmed: 32245418
doi: 10.1186/s12864-020-6683-0
pii: 10.1186/s12864-020-6683-0
pmc: PMC7126163
doi:

Substances chimiques

Protozoan Proteins 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

279

Subventions

Organisme : National Institute of Allergy and Infectious Diseases
ID : AI007540-14
Organisme : Bill and Melinda Gates Foundation
ID : OPP1078791
Organisme : Agricultural Research Service
ID : 59-5348-4-001

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Auteurs

Kyle Tretina (K)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

Roger Pelle (R)

Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya.

Joshua Orvis (J)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

Hanzel T Gotia (HT)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

Olukemi O Ifeonu (OO)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

Priti Kumari (P)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

Nicholas C Palmateer (NC)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

Shaikh B A Iqbal (SBA)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

Lindsay M Fry (LM)

Animal Disease Research Unit, Agricultural Research Service, USDA, Pullman, WA, 99164, USA.
Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, 99164, USA.

Vishvanath M Nene (VM)

International Livestock Research Institute, Nairobi, Kenya.

Claudia A Daubenberger (CA)

Swiss Tropical and Public Health Institute, Basel, Switzerland.
University of Basel, Basel, Switzerland.

Richard P Bishop (RP)

Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, 99164, USA.

Joana C Silva (JC)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. jcsilva@som.umaryland.edu.
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. jcsilva@som.umaryland.edu.
ORCID: 0000-0001-6502-7026

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Classifications MeSH

Recherchemedicale.com › Phénomènes génétiques › Régulation de l'expression des gènes › Maturation post-transcriptionnelle des ARN › Épissage des ARN › Épissage alternatif › Re-annotation of the Theileria parva genome...
Recherchemedicale.com › Eucaryotes › Animaux › Re-annotation of the Theileria parva genome...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Séquences d'acides nucléiques régulatrices › Réseaux de régulation génique › Re-annotation of the Theileria parva genome...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Génome › Génome de protozoaire › Re-annotation of the Theileria parva genome...
Recherchemedicale.com › Métabolisme › Métabolisme glucidique › Glycosylation › Re-annotation of the Theileria parva genome...
Recherchemedicale.com › Eucaryotes › Animaux › Groupes animaux › Animaux domestiques › Bétail › Re-annotation of the Theileria parva genome...
Recherchemedicale.com › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › Re-annotation of the Theileria parva genome...
Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines de protozoaire › Re-annotation of the Theileria parva genome...
Recherchemedicale.com › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › Re-annotation of the Theileria parva genome...
Recherchemedicale.com › Eucaryotes › Alveolata › Apicomplexa › Piroplasmia › Piroplasmida › Theileria › Theileria parva › Re-annotation of the Theileria parva genome...