Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa)

Ogedengbe, Mosun E.; El-Sherry, Shiem; Ogedengbe, Joseph D.; Chapman, H. D.; Barta, John R.

doi:10.1016/j.ijpara.2017.07.008

Cited by 46 publications

(31 citation statements)

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“…At the tips of the phylogeny, 18S sequences of E. falciformis and E. vermiformis isolates clustered with isolates from hosts of different genera or even families (Figure 2). This result was expected to some extent, as phylogenetic analyses with 18S sequences usually fail to separate closely related parasites isolated from closely related hosts (Ogedengbe et al, 2018). (Ogedengbe et al, 2011(Ogedengbe et al, , 2018.…”

Section: Discussionmentioning

confidence: 92%

“…Previous studies described COI as a universal barcode variable enough to resolve relationships between coccidians, including Eimeria (Ogedengbe et al, , ). We therefore expected to differentiate our house mouse isolates from species found in other hosts using COI.…”

Section: Discussionmentioning

confidence: 99%

“…Genetic markers from nuclear (nu) and mitochondrial (mt) genomes, and less frequently of the apicoplast (ap) genome, have been used to complement morphological taxonomy with phylogenetic analyses (Hnida & Duszynski, , ; Kvičerová, Mikeš, & Hypša, ; Ogedengbe, Ogedengbe, Hafeez, & Barta, ; Zhao & Duszynski, ). Based on the assumption of host specificity of individual Eimeria species, phylogenetic analysis of nuclear small subunit ribosomal (18S) rDNA and cytochrome c oxidase I (COI) fragments supports predominant host–parasite cospeciation (Ogedengbe, El‐Sherry, Ogedengbe, Chapman, & Barta, ). Species infecting rodents, however, are found in two separate clades, generating marked discrepancy between parasite and host phylogeny at deeper nodes (Kvičerová & Hypša, ).…”

Section: Introductionmentioning

confidence: 99%

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Generalist Eimeria species in rodents: Multilocus analyses indicate inadequate resolution of established markers

Jarquín‐Díaz

Balard

Mácová

et al. 2020

Ecology and Evolution

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Intracellular parasites of the genus Eimeria are described as tissue/host‐specific. Phylogenetic classification of rodent Eimeria suggested that some species have a broader host range than previously assumed. We explore whether Eimeria spp. infecting house mice are misclassified by the most widely used molecular markers due to a lack of resolution, or whether, instead, these parasite species are indeed infecting multiple host species. With the commonly used markers (18S/COI), we recovered monophyletic clades of E. falciformis and E. vermiformis from Mus that included E. apionodes identified in other rodent host species (Apodemus spp., Myodes glareolus, and Microtus arvalis). A lack of internal resolution in these clades could suggest the existence of a species complex with a wide host range infecting murid and cricetid rodents. We question, however, the power of COI and 18S markers to provide adequate resolution for assessing host specificity. In addition to the rarely used marker ORF470 from the apicoplast genome, we present multilocus genotyping as an alternative approach. Phylogenetic analysis of 35 nuclear markers differentiated E. falciformis from house mice from isolates from Apodemus hosts. Isolates of E. vermiformis from Mus are still found in clusters interspersed with non‐Mus isolates, even with this high‐resolution data. In conclusion, we show that species‐level resolution should not be assumed for COI and 18S markers in coccidia. Host–parasite cospeciation at shallow phylogenetic nodes, as well as contemporary coccidian host ranges more generally, is still open questions that need to be addressed using novel genetic markers with higher resolution.

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Section: Discussionmentioning

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Generalist Eimeria species in rodents: Multilocus analyses indicate inadequate resolution of established markers

Jarquín‐Díaz

Balard

Mácová

et al. 2020

Ecology and Evolution

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“…This suggests invasion of two different species of coccidia in both grouse species. The newest data presented by Ogedengbe et al (2018) suggests that the morphology-based classification could be insufficient for proper Eimeria classification, and that molecular analysis is more reliable in this respect. Sequencing of small genome regions, such as mitochondrial cytochrome oxidase subunit 1 (cox-1) locus and 18S rRNA gene, has been commonly used to infer the relatedness of field Eimeria isolates (Clark et al 2017).…”

Section: Discussionmentioning

confidence: 99%

“…2b and 3b). Compared to the 18S rRNA gene, the cox-1 gene is quickly evolving (sequence divergence rate of 1–2% per million years) and for this reason, the cox-1 gene sequences are a better base for the identification and phylogenetic analysis than the 18S rRNA gene sequences (El-Sherry et al 2013; Ogedengbe et al 2018). Summarizing, the phylogenetic tree based on mitochondrial gene sequences is in this case more reliable.…”

Section: Discussionmentioning

confidence: 99%

Molecular analysis of cox-1 and 18S rRNA gene fragments of Eimeria species isolated from endangered grouse: capercaillie (Tetrao urogallus) and black grouse (Tetrao tetrix)

et al. 2018

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This paper is the first record describing the molecular analysis of Eimeria species occurring in capercaillie (Tetrao urogallus) and black grouse (Tetrao tetrix) which inhabit northern Eurasia and are species critically endangered of extinction. Actions undertaken to protect endangered species, such as breeding individuals in closed aviaries, could allow saving those birds, but they also pose risk of accidental healing of invasive diseases, like coccidiosis. Therefore, an investigation was conducted on fecal samples collected from the capercaillies and black grouse originating from the Kirov region (Russia) and breeding centers located in Poland. Results indicate that the average prevalence of Eimeria revealed 72% (average OPG = 3548) and 80% (average OPG = 5220) in capercaillies and black grouse respectively. Most of the Eimeria spp. oocysts were non-sporulated; however, two different morphological types were observed. The phylogenetic analysis of cox-1 and 18S rRNA genes revealed the analyzed Eimeria sequences to belong to two species. In addition, it showed some similarities between both analyzed genes. Most of the sequences obtained from both grouse species coccidia belonged to one species partially homologous to the Eimeria spp. isolated from ring-necked pheasant (approx. 94 and 96% for cox-1 and 18S rRNA genes, respectively). Two strains isolated from capercaillies imported from Russia were related to turkey coccidia: E. innocua and E. dispersa (97–99% homology) in the cox-1 gene analysis and only one of them was related to those Eimeria species in the 18S rRNA gene analysis (98–99% homology).

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Phylogenetic analysis of Eimeria tenella isolated from the litter of different chicken farms in Mymensingh, Bangladesh

Alam

Dey

Rony

et al. 2022

Veterinary Medicine & Sci

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Background Eimeria tenella is the most pathogenic intracellular protozoan parasite of seven Eimeria species causing chicken coccidiosis around the world. This species is particularly responsible for caecal coccidiosis leading to serious morbidity–mortality and financial loss in poultry production. Methods The present study explored the genetic diversity of E. tenella. Litter slurry was collected from 18 broiler farms located in Mymensingh district, Bangladesh. Litter samples were processed for oocyst isolation–identification using parasitological techniques followed by genomic DNA extraction from sporulated oocysts. For molecular analysis, the internal transcribed spacer 1 gene of E. tenella was amplified using species‐specific primers and sequenced. After editing and alignment, 263 bp sequences were used for analysis. Results Genetic analysis showed seven distinct genotypes and detected six single nucleotide polymorphisms among the 18 E. tenella isolates. The nucleotide and genotype diversity were 0.00507 and 0.8235, respectively. A phylogenetic tree was constructed with 66 sequences (seven studied genotypes and 59 reference sequences from GenBank database). The neighbour‐joining tree represented that the studied E. tenella isolates were grouped with reference E. tenella isolates with strong nodal support (100%) and the nucleotide sequences of E. tenella, E. necatrix, E. acervulina, E. brunetti, E. maxima, E. mitis and E. praecox formed separate clusters without any geographical boundaries. Conclusions This is the first study on the genetic analysis of E. tenella from Mymensingh district, Bangladesh. These findings will provide baseline data on the species conformation and genetic variations of E. tenella. Further extensive investigation will be needed to reveal the population genetic structure of this parasite and thus will facilitate the planning of effective control strategies.

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Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa)

Cited by 46 publications

References 58 publications

Generalist Eimeria species in rodents: Multilocus analyses indicate inadequate resolution of established markers

Generalist Eimeria species in rodents: Multilocus analyses indicate inadequate resolution of established markers

Molecular analysis of cox-1 and 18S rRNA gene fragments of Eimeria species isolated from endangered grouse: capercaillie (Tetrao urogallus) and black grouse (Tetrao tetrix)

Phylogenetic analysis of Eimeria tenella isolated from the litter of different chicken farms in Mymensingh, Bangladesh

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