Mitochondrial genomes advance phylogenetic hypotheses for Tylenchina (Nematoda: Chromadorea)

Abstract

K. (2015). Mitochondrial genomes advance phylogenetic hypotheses for Tylenchina (Nematoda: Chromadorea). -Zoologica Scripta, 44, 446-462. Within the nematode class Chromadorea, the suborder Tylenchina is an ecologically and morphologically diverse assemblage of nematodes that includes free-living microbivores, fungivores and various types of plant parasites. A recent nematode classification system based largely on SSU rDNA phylogenetic trees classified suborder Tylenchina to include four infraorders: Panagrolaimomorpha, Cephalobomorpha, Tylenchomorpha and Drilonematomorpha, and phylogenetic relationships among species of these infraorders have not always been robustly supported. In this study, we determined the complete mitochondrial genome sequences of three Tylenchina species (Aphelenchus avenae [Aphelenchidae, Tylenchomorpha], Halicephalobus gingivalis, Panagrellus redivivus [Panagrolaimomorpha]) and the partial genome sequence of Acrobeles complexus (Cephalobomorpha) and used these sequences to infer phylogenetic relationships among representatives of the Tylenchina and other nematodes. Phylogenetic analysis of amino acid sequences for 12 protein-coding genes of 100 nematode species supports monophyly of: Chromadorea, Spiruromorpha, Oxyuridomorpha, Ascarididae + Toxocaridae + Anisakidae, Meloidogynidae + Pratylenchidae + Heteroderidae and Aphelenchoidea. Bayesian and maximum-likelihood analyses also show the nested position of Diplogasteromorpha within Rhabditomorpha, and Rhigonematomorpha within Ascaridomorpha. These analyses also show non-monophyly of: clade III, Ancylostomatidae, Panagrolaimomorpha, Tylenchina and Tylenchomorpha. Reconstructed mitochondrial genome phylogeny also revealed that among two main Tylenchomorpha groups, the monophyletic group representing Aphelenchoidea species was sister to the large clade consisting of Ascaridomorpha, Diplogasteromorpha, Rhabditomorpha and Rhigonematomorpha and some Panagrolaimomorpha species, whereas Tylenchoidea species were sister to the most inclusive assemblage containing all infraordinal groups of Chromadorea, except for P. redivivus (Panagrolaimomorpha) and Acrobeles complexus (Cephalobomorpha). The monophyly of Aphelenchoidea (i.e. sister relationship between Aphelenchidae and Aphelenchoididae) recovered in this study indicates that similarity in certain aspects of pharyngeal structure between these two families appears best explained by common ancestry, rather than convergent evolution.

The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class

“…Statistical support values were very high, particularly in the BI analysis, where all posterior probability values were 1.0. In (partial) agreement with previous studies using both nSSU rRNA and mitochondrial phylogenomics approaches [ 1 , 5 , 27 , 32 ]. Our results indicate that Spirurida order is divided into both morphologically [ 1 ] and genetically clearly defined Spirurina suborder, here comprised of (Physalopteridae + (Thelaziidae + (Gongylonematidae + (Setariidae [paraphyletic] + Onchocercidae)))), and a monophyletic clade comprising (Gnathostomatidae + (Camallanidae + (Dracunculidae + Philometridae))), henceforth referred to as Camallanina suborder (Fig.…”

“…Sister group relationship between the Camallanoidea superfamily (Camallanidae family) and Dracunculoidea superfamily (Philometridae and Dracunculidae in this study) is well-established [ 1 , 5 , 33 , 34 ]. Paraphyly of Thelaziidae family, and particularly the problematic taxonomy of Spirocerca and Thelazia genera was also observed before [ 1 , 5 , 27 , 35 ]. A very similar topology of Spirurina clade, including the sister group relationship between Spirocerca and Gongylonema genera, was produced before using a smaller number of mitogenomes [ 32 , 36 ].…”

“…Duplicated tRNAs are also not particularly rare [ 10 ], but usually it is merely one tRNA that is duplicated, e.g. [ 27 ], whereas C. cotti mitogenome possesses seven pairs of duplicated tRNAs: Trp, Tyr, Ala, Asp, Gln, Ile, and Thr. On the other hand, nematodes usually possess all 22 standard tRNAs [ 9 , 10 ], whereas we could identify only 19, with tRNA-Leu1 (CUN) , Ser2 (AGN) and tRNA-Phe missing.…”

“…None of the C. cotti PCGs were major outliers regarding the size. Most of the genes used the two start (8 TTG + 3 ATT) and three stop (4 TAG, 3 TAA, 7 T--) codons common for nematodes [ 9 , 13 , 20 , 27 ]. The third observed start codon, GTT for cytb (and cytb-2 ) and nad4 , was also observed in a number of closely related nematodes [ 38 , 62 , 63 ].…”

“…Sequencing of the complete mitochondrial genome of C. cotti , and the associated phylogenomic analysis using all available mitogenomes belonging to Spirurida order, are meant to address this problem. More importantly, as both mitochondrial genomes that are currently available for the entire Camallanina suborder, Philometroides sanguineus [ 26 ] and Dracunculus medinensis (unpublished), exhibit unique gene orders [ 26 , 27 ], we hypothesised that this mitogenomic architecture might be idiosyncratic to the entire Camallanina suborder. To establish whether the unique Dracunculoidea architecture is shared with the sister superfamily Camallanoidea, and thus contribute to the understanding of the evolution of mitochondrial genomic architecture of nematodes, we have sequenced and characterised the mitogenome of C. cotti and compared it structurally to the available Spirurida mitogenomes.…”