Molecular phylogenetic analyses of tissue coccidia (sarcocystidae; apicomplexa) based on nuclear 18s RDNA and mitochondrial COI sequences confirms the paraphyly of the genus Hammondia

Abstract

Partial mitochondrial cytochrome c oxidase subunit I (mt COI) sequences were generated from: Toxoplasma gondii (strains 18S rDNA and COI sequences were Bayesian analysed using partitioned nucleotide substitution models [HKY + I + G for 18S; GTR + I + G codon (code = metmt) for COI]. Phylogenetic hypotheses supported a monophyletic Sarcocystidae and its subfamilie with two major clades within the Toxoplasmatinae: (1) a monophyletic clade of Cystoisospora spp. with Nephroisospora eptesici; and (2) a clade of Toxoplasma, Neospora and Hammondia. Within the latter, Hammondia was shown to be paraphyletic; H. heydorni and H. triffittae were monophyletic with N. caninum [canine definitive hosts (DHs)], whereas H. hammondi was monophyletic with T. gondii (feline DHs). A new genus is erected to resolve the paraphyly of the genus Hammondia confirmed using mt COI and combined 18S/COI sequence datasets.

Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

“…5 ); bootstrap support for this scenario was relatively weak (62–74%). Such a tree topology has been observed previously for the tissue coccidia and was attributed to potential lack of key species ( Ogedengbe et al, 2016 ). We were able to remedy this situation by excluding the 3rd codon position from phylogenetic analysis, which resulted in almost the same tree, but rendered the Toxoplasmatinae and Sarcocystinae as separate, monophyletic subclades of the Sarcocystidae.…”

Morphological and molecular characterization of Cystoisospora sp. from Asian small-clawed otters Aonyx cinereus

“…Numerous phylogenetic studies have focused on the analysis of 18S, 28S, ITS, and cox1 genes, and 18S and cox1 genes have been commonly used for coccidians belonging to the families Sarcocystidae and Eimeriidae ( Carreno et al, 1998 ; Morrison et al, 2004 ; Ogedengbe et al, 2011 , 2016 ). The coccidian 18S sequence is phylogenetically useful for distant taxa, but seems to be much less variable than that in other protozoan parasites and to be insufficient for resolving the relationships among closely related coccidian species ( Morrison et al, 2004 ).…”

“…In contrast, the cox1 sequence provides sufficient sequence divergence for studying phylogenetic relationships among closely related coccidian species. Ogedengbe et al (2016) made specific cox1 primers for Sarcocystidae groups and suggested that cox1 sequences from sarcocystids (i.e., Toxoplasma , Neospora , and Hammondia ) appeared well suited for species delimitation; however, sequences from Cystoisospora spp. showed remarkably limited sequence variation.…”

“…The partial fragment of the 18S rRNA gene (18S) and the mitochondrial gene encoding cytochrome c oxidase subunit 1 ( cox1 ) were amplified using the primer sets EF (5′-GAACTGCGAATGGCTCATT-3′)/ER (5′-CTTGCGCCTACTAGGCATTC-3′) ( Kvicerová et al, 2008 ) and Sdae-Cox1_260F (5′-GATCTTTATGTTYTTRATGCC-3′)/Sdae-Cox1_1147R (5′-CATTACCCATAACYACACC-3′) ( Ogedengbe et al, 2016 ), respectively. The PCR mixture contained 2.5 μL of 10× Ex Taq buffer (Takara Bio Inc., Japan), 0.2 mM dNTPs (Takara Bio, Inc.), 0.2 μM each primer, 1 U Ex Taq polymerase (Takara Bio, Inc.), and 1 μL DNA extract in a total volume of 20 μL.…”

“…Phylogenetic trees of concatenated 18S and cox1 sequence data were generated using MEGA. Each sequence was derived from the same isolate/strain available in the GenBank/DDBJ/EMBL databases, as described by Ogedengbe et al (2016) . In total, 14 concatenated sequences, including two new sequences derived from Cystoisospora sp.…”