Eimeria genomics: Where are we now and where are we going?

https://doi.org/10.1016/j.vetpar.2015.05.007Get rights and content

Highlights

  • Review of genomics progress for Eimeria species parasites.

  • Overview of available sequencing technologies.

  • Future applications for Eimeria genomics.

Abstract

The evolution of sequencing technologies, from Sanger to next generation (NGS) and now the emerging third generation, has prompted a radical frameshift moving genomics from the specialist to the mainstream. For parasitology, genomics has moved fastest for the protozoa with sequence assemblies becoming available for multiple genera including Babesia, Cryptosporidium, Eimeria, Giardia, Leishmania, Neospora, Plasmodium, Theileria, Toxoplasma and Trypanosoma. Progress has commonly been slower for parasites of animals which lack zoonotic potential, but the deficit is now being redressed with impact likely in the areas of drug and vaccine development, molecular diagnostics and population biology. Genomics studies with the apicomplexan Eimeria species clearly illustrate the approaches and opportunities available. Specifically, more than ten years after initiation of a genome sequencing project a sequence assembly was published for Eimeria tenella in 2014, complemented by assemblies for all other Eimeria species which infect the chicken and Eimeria falciformis, a parasite of the mouse. Public access to these and other coccidian genome assemblies through resources such as GeneDB and ToxoDB now promotes comparative analysis, encouraging better use of shared resources and enhancing opportunities for development of novel diagnostic and control strategies. In the short term genomics resources support development of targeted and genome-wide genetic markers such as single nucleotide polymorphisms (SNPs), with whole genome re-sequencing becoming viable in the near future. Experimental power will develop rapidly as additional species, strains and isolates are sampled with particular emphasis on population structure and allelic diversity.

Introduction

The word ‘genomics’ is widely considered to have appeared in 1986 (Kuska, 1998), with the first appearance of the term in the National Center for Biotechnology Information literature database appearing in 1987. By the year 2000 more than 1500 publications had appeared including the word ‘genomics’ as a searchable term, with 15,991 publications last year (2014). Many definitions of the term have been proposed, with a common theme being studies of the genome of an organism and genome-wide analysis of the genes it contains using DNA sequencing and bioinformatics methods. Progress in genomics led to publication of the first eukaryotic chromosome sequence in 1992, followed by the first full eukaryotic genome in 1996 (Oliver et al., 1992, Goffeau et al., 1996), but the roll out of genomics technologies has largely been constrained by the cost and availability of Sanger (or first generation) sequencing and the expertise required for analysis. As a consequence, genomics approaches were initially only accessible for the human genome and other model or medically relevant organisms. The advent of second or next generation sequencing technologies (NGS), providing faster, cheaper and higher throughput approaches, has unlocked genomics for use with veterinary and diagnostic purposes. While the rate of exploitation is not yet comparable with human and medical pathogen genomics, illustrated by greater fragmentation for most livestock and veterinary pathogen genomes (Table 1), sequence resources and associated opportunities are developing fast. Progress in genome sequencing and genome-wide analyses for the Eimeria species illustrates the impact of these advances and the opportunities which are only now becoming readily available.

Section snippets

Eimeria and the disease coccidiosis

Eimeria are obligate protozoan parasites which have evolved to exhibit immense diversity in host range including mammals, birds, reptiles, fish and amphibians, with each parasite species commonly defined by absolute host specificity (Jirku et al., 2009, Gibson-Kueh et al., 2011, Yang et al., 2012, Chapman et al., 2013, Jirku et al., 2013, Kvicerova and Hypsa, 2013). As a consequence there are likely to be many thousands of Eimeria species. Eimeria that infect wild vertebrates can become

Sequencing technologies

DNA sequencing by fragmentation or chain termination first appeared in the late 1970s with the latter, commonly referred to as Sanger sequencing, becoming dominant due to methodological advantage (Maxam and Gilbert, 1977, Sanger et al., 1977). The following 25 years saw considerable innovation and improvement to the Sanger sequencing technique and associated data analysis but limitations including requirements for minimum template quality and quantity, restricted throughput capacity and high

Application to eimerian genomes

Genome sequencing started for Eimeria in 2002, beginning with the reference Eimeria tenella Houghton strain (Chapman and Shirley, 2003). Prior to 2002 genomic resources were scarce, largely limited to Sanger sequencing reads covering the ribosomal DNA clusters, sporozoite and second generation merozoite expressed sequence tag (EST) cDNA reads, sequenced random amplified polymorphic DNA (RAPD) markers, and a panel of specific protein-coding genes including several kinases and microneme proteins (

Transcriptomic analyses

Eimerian parasites follow a strict faecal-oral life cycle which features three distinct phases and no intermediate host. The first phase, termed sporogony or sporulation, occurs outside of the host and includes asexual replication as the parasite develops from a single non-infectious unsporulated oocyst into an infective sporulated oocyst, containing eight sporozoites accommodated in pairs within four sporocysts. The second phase, known as schizogony or merogony, occurs within the host and

What next for Eimeria genomics?

The publication of genome sequences for all seven Eimeria species which infect chickens represented the culmination of more than a decade of work from a consortium of 20 institutions across ten countries (Reid et al., 2014). The provision of reference genome assemblies, combined with the reduced cost and greater power of NGS technologies, now provides enormous opportunity for genomics-led studies and diagnostics with these parasites. Access to a first mammalian-infecting Eimeria genome assembly

Applications for Eimeria genomics?

Addition of Eimeria to the ever-expanding club of sequenced genomes has dramatically expanded the scope for studies of biology, prophylaxis, therapy and vaccination. Comparison between genome assemblies representing related coccidians is straightforward and accessible using GeneDB, or ToxoDB within the EuPathDB resource (http://toxodb.org/toxo/http://toxodb.org/toxo/); (Gajria et al., 2008, Logan-Klumpler et al., 2012, Aurrecoechea et al., 2013). ToxoDB currently facilitates access to eight

Conclusions

The landmark publication of eight eimerian genome sequences in 2014 has provided a massive boost for studies with Eimeria, related apicomplexans and many protozoa. Given greater access to sequence data and the rapidly developing availability of NGS technologies with reduced cost, experimental limitations have now moved on to our capacity for data analysis and interpretation (Padmanabhan et al., 2013). Looking to the future improved bioinformatics pipelines will be required to improve

References (83)

  • L.J. Knoll et al.

    Adaptation of signature-tagged mutagenesis for Toxoplasma gondii: a negative screening strategy to isolate genes that are essential in restrictive growth conditions

    Mol. Biochem. Parasitol.

    (2001)
  • B. Lassen et al.

    Estimation of the economical effects of Eimeria infections in Estonian dairy herds using a stochastic model

    Prev. Vet. Med.

    (2012)
  • J. Novaes et al.

    A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages

    Int J. Parasitol.

    (2012)
  • R.D. Oakes et al.

    The rhoptry proteome of Eimeria tenella sporozoites

    Int. J. Parasitol.

    (2013)
  • R. Padmanabhan et al.

    Genomics and metagenomics in medical microbiology

    J. Microbiol. Methods

    (2013)
  • H. Revets et al.

    Identification of virus-like particles in Eimeria stiedae

    Mol. Biochem. Parasitol.

    (1989)
  • M.W. Shirley et al.

    The Eimeria genome projects: a sequence of events

    Trends Parasitol.

    (2004)
  • F.M. Tomley et al.

    EtMIC4: a microneme protein from Eimeria tenella that contains tandem arrays of epidermal growth factor-like repeats and thrombospondin type-I repeats

    Int. J. Parasitol.

    (2001)
  • E.L. van Dijk et al.

    Ten years of next-generation sequencing technology

    Trends Genet.

    (2014)
  • K.L. Wan et al.

    A survey of genes in Eimeria tenella merozoites by EST sequencing

    Int. J. Parasitol.

    (1999)
  • W. Yan et al.

    Stable transfection of Eimeria tenella: constitutive expression of the YFP-YFP molecule throughout the life cycle

    Int. J. Parasitol.

    (2009)
  • S. Aarthi et al.

    Expressed sequence tags from Eimeria brunetti-preliminary analysis and functional annotation

    Parasitol. Res.

    (2011)
  • N. Amiruddin et al.

    Characterisation of full-length cDNA sequences provides insights into the Eimeria tenella transcriptome

    BMC Genomics

    (2012)
  • C. Aurrecoechea et al.

    EuPathDB: the eukaryotic pathogen database

    Nucleic Acids Res.

    (2013)
  • N. Bacciu et al.

    QTL detection for coccidiosis (Eimeria tenella) resistance in a Fayoumi × Leghorn F(2) cross, using a medium-density SNP panel

    Genet. Sel. Evol.

    (2014)
  • P. Bedrnik

    Comment on the review anticoccidial vaccines for broiler chickens: pathways to success by R.B. Williams (2002). Avian Pathology, 31, 317–353

    Avian Pathol.

    (2003)
  • S.T. Bennett et al.

    Toward the 1000 dollars human genome

    Pharmacogenomics

    (2005)
  • D.P. Blake et al.

    Genetic mapping identifies novel highly protective antigens for an apicomplexan parasite

    PLoS Pathog.

    (2011)
  • D.P. Blake et al.

    The influence of immunizing dose size and schedule on immunity to subsequent challenge with antigenically distinct strains of Eimeria maxima

    Avian Pathol.

    (2005)
  • T. Blazejewski et al.

    Systems-based analysis of the Sarcocystis neurona genome identifies pathways that contribute to a heteroxenous life cycle

    MBio

    (2015)
  • H.D. Chapman et al.

    Vaccination of chickens against coccidiosis ameliorates drug resistance in commercial poultry production

    Int. J. Parasitol. Drugs Drug Resist.

    (2014)
  • H.D. Chapman et al.

    The Houghton strain of Eimeria tenella: a review of the type strain selected for genome sequencing

    Avian Pathol.

    (2003)
  • R.A. Dalloul et al.

    Poultry coccidiosis: recent advancements in control measures and vaccine development

    Expert Rev. Vaccines

    (2006)
  • H. Dong et al.

    Analysis of differentially expressed genes in the precocious line of Eimeria maxima and its parent strain using suppression subtractive hybridization and cDNA microarrays

    Parasitol. Res.

    (2011)
  • P.P. Dunn et al.

    Sequence, expression and localization of calmodulin-domain protein kinases in Eimeria tenella and Eimeria maxima

    Parasitology

    (1996)
  • S. Fernandez et al.

    A survey of the inter- and intraspecific RAPD markers of Eimeria spp. of the domestic fowl and the development of reliable diagnostic tools

    Parasitol. Res.

    (2003)
  • B. Gajria et al.

    ToxoDB: an integrated Toxoplasma gondii database resource

    Nucleic Acids Res.

    (2008)
  • K. Gandhi et al.

    Next generation sequencing to detect variation in the Plasmodium falciparum circumsporozoite protein

    Am. J. Trop. Med. Hyg.

    (2012)
  • J. Gertz et al.

    Transposase mediated construction of RNA-seq libraries

    Genome Res.

    (2012)
  • A. Goffeau et al.

    Life with 6000 genes

    Science

    (1996)
  • E. Heitlinger et al.

    The genome of Eimeria falciformis – reduction and specialization in a single host apicomplexan parasite

    BMC Genomics

    (2014)
  • Cited by (41)

    • Exploiting digital droplet PCR and Next Generation Sequencing technologies to determine the relative abundance of individual Eimeria species in a DNA sample

      2021, Veterinary Parasitology
      Citation Excerpt :

      However, the variation within and between the oocyst morphometrics of at least some Eimeria species infecting chickens makes identification based solely on oocyst features challenging and problematic (Long and Joyner, 1984). The first DNA-based molecular assay for the identification of Eimeria species was developed in 1990 (Williams et al., 1990), although these early tests were replaced following technology advancements and as the knowledge base increased (Blake, 2015). A variety of assays have been developed since that require the characterization of species-specific sequences in a range of genetic targets to permit the development of unique primer sets for each Eimeria species.

    • Anticoccidial effect of toltrazuril and Radix Sophorae Flavescentis combination: Reduced inflammation and promoted mucosal immunity

      2021, Veterinary Parasitology
      Citation Excerpt :

      Coccidiosis poses a serious threat to the poultry industry because of its high morbidity and mortality, resulting in substantial economic losses worldwide (Huang et al., 2018). The Eimeria of the phylum Apicomplexan is responsible for coccidiosis in birds (van Dooren and Striepen, 2013; Blake, 2015; Liu et al., 2016). As an obligate intracellular parasite (Lv et al., 2018), the Eimeria tenella dwelling within cecal epithelial cells (del Cacho et al., 2004b; Zhou et al., 2019) is highly pathogenic, and can seriously destroy intestinal tissues (Morris et al., 2007; Liu et al., 2016; Zhou et al., 2020).

    View all citing articles on Scopus
    View full text