Complete mitochondrial genome sequences from five Eimeria species (Apicomplexa; Coccidia; Eimeriidae) infecting domestic turkeys

Abstract

BackgroundClinical and subclinical coccidiosis is cosmopolitan and inflicts significant losses to the poultry industry globally. Seven named Eimeria species are responsible for coccidiosis in turkeys: Eimeria dispersa; Eimeria meleagrimitis; Eimeria gallopavonis; Eimeria meleagridis; Eimeria adenoeides; Eimeria innocua; and, Eimeria subrotunda. Although attempts have been made to characterize these parasites molecularly at the nuclear 18S rDNA and ITS loci, the maternally-derived and mitotically replicating mitochondrial genome may be more suited for species level molecular work; however, only limited sequence data are available for Eimeria spp. infecting turkeys. The purpose of this study was to sequence and annotate the complete mitochondrial genomes from 5 Eimeria species that commonly infect the domestic turkey (Meleagris gallopavo).MethodsSix single-oocyst derived cultures of five Eimeria species infecting turkeys were PCR-amplified and sequenced completely prior to detailed annotation. Resulting sequences were aligned and used in phylogenetic analyses (BI, ML, and MP) that included complete mitochondrial genomes from 16 Eimeria species or concatenated CDS sequences from each genome.ResultsComplete mitochondrial genome sequences were obtained for Eimeria adenoeides Guelph, 6211 bp; Eimeria dispersa Briston, 6238 bp; Eimeria meleagridis USAR97-01, 6212 bp; Eimeria meleagrimitis USMN08-01, 6165 bp; Eimeria gallopavonis Weybridge, 6215 bp; and Eimeria gallopavonis USKS06-01, 6215 bp). The order, orientation and CDS lengths of the three protein coding genes (COI, COIII and CytB) as well as rDNA fragments encoding ribosomal large and small subunit rRNA were conserved among all sequences. Pairwise sequence identities between species ranged from 88.1% to 98.2%; sequence variability was concentrated within CDS or between rDNA fragments (where indels were common). No phylogenetic reconstruction supported monophyly of Eimeria species infecting turkeys; Eimeria dispersa may have arisen via host switching from another avian host. Phylogenetic analyses suggest E. necatrix and E. tenella are related distantly to other Eimeria of chickens.ConclusionsMitochondrial genomes of Eimeria species sequenced to date are highly conserved with regard to gene content and structure. Nonetheless, complete mitochondrial genome sequences and, particularly the three CDS, possess sufficient sequence variability for differentiating Eimeria species of poultry. The mitochondrial genome sequences are highly suited for molecular diagnostics and phylogenetics of coccidia and, potentially, genetic markers for molecular epidemiology.

Characterization of two complete Isospora mitochondrial genomes from passerine birds: Isospora serinuse in a domestic canary and Isospora manorinae in a yellow-throated miner

“…(8 from chickens, 6 from the domestic turkeys (Ogedengbe et al, 2014), 6 from rabbits (Liu et al, 2015;Tian et al, 2015) and one from a striped skunk (Mephitis mephitis).…”

“…Among the apicomplexan organisms, Eimeria is phylogenetically closest genus to Isospora based on 18S gene sequences (Yang et al, 2015a). The complete mt genome sequences for 19 Eimeria species have been reported (Hikosaka et al, 2010;Lin et al, 2011;Liu et al, 2012 and2015;Heitlinger et al, 2014;Ogedengbe et al, 2014;Hafeez et al, 2016;Tian et al, 2015), all of which range from 6.1 to 6.4 kb in size with highly conserved content and structure (Liu et al, 2015). Currently only one Isospora mt genome sequence has been reported .…”

Molecular detection of field isolates of Turkey Eimeria by polymerase chain reaction amplification of the cytochrome c oxidase I gene

“…Amplification was performed using a Veriti® 96-well Thermal Cycler (Applied Biosystems, Foster City, CA). The primers used were kindly provided by Dr. John R. Barta (University of Guelph, ON, Canada) and their sequences (Ogedengbe et al 2014) are shown in Table 1. The reaction mixture for each sample comprised 5 μL (20 ng) of gDNA, 12.5 μL of PCR master mix (Promega Corporation, Madison, WI), 400 nM forward primer, 400 nM reverse primer, and nuclease-free water to make up a final volume of 25 μL.…”

A linear mitochondrial genome of Cyclospora cayetanensis (Eimeriidae, Eucoccidiorida, Coccidiasina, Apicomplexa) suggests the ancestral start position within mitochondrial genomes of eimeriid coccidia

“…(see Ogedengbe et al, 2013, 2014) failed repeatedly with C. cayetanensis . Thereafter, shorter regions of the mt genome were amplified with primers targeting conserved regions of other apicomplexan mitochondrial genomes.…”

“…These efforts failed repeatedly with C. cayetanensis but succeeded in the case of coccidia in the genera Eimeria, Caryospora and Isospora (e.g. Lin et al, 2011; Ogedengbe et al, 2013, 2014; 2015; Ogedengbe and Barta, 2015), all of which possess circular-mapping mt genomes; Eimeria tenella was used as positive control for all such PCRs due to its linear concatenated genome.…”