Gene rearrangements in the mitochondrial genome of ten ascaris species and phylogenetic implications for Ascaridoidea and Heterakoidea families

Han, Lei; Yang, Yunxia; Li, Haimeng; Zhou, Xiaoyu; Zhou, Mengchao; Liu, Tianlu; Lu, Yaxian; Wang, Qing; Yang, Shangcheng; Shi, Minhui; Liu, Xiuyun; Du, Shan; Guan, Chunyu; Zhang, Yong; Guo, Wei; Wang, Jiangang; Chai, Hongliang; Liu, Huan; Liu, Quan; Sun, Hui; Hou, Zhijun

doi:10.1016/j.ijbiomac.2022.08.021

Cited by 6 publications

(4 citation statements)

References 47 publications

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“…Perhaps, studies using mitogenome data from more large-scale species or isolates of Toxocara as well as taxa within the families Toxocaridae and Ascarididae worldwide are required to ascertain the phylogenetic relationships of T. vitulorum in the whole Toxocara and of the genera Porrocaecum and Toxocara in the superfamily Ascaridoidea of the order Ascaridida. Furthermore, the species of the family Toxocaridae were determined to be more closely related to species of the family Ascarididae than to species of the families Anisakidae, Ascaridiidae, and Cucullanidae, which was consistent with results of previous morphological and molecular studies [ 33 , 42 , 45 , 46 , 48 , 50 , 51 , 54 , 67 , 70 , 75 , 81 , 82 , 83 , 84 ] and also demonstrated the phylogenetic stability of the paraphyletic relationships characterized in the present study.…”

Section: Resultssupporting

confidence: 89%

“…Further, compared to other 11 PCGs, the nad4 and nad6 genes shared the same topology as the genome-level phylogenetic analysis, suggesting that nad4 and nad6 among PCGs might be the best genetic markers and therefore could be instead of the mitogenome for molecular diagnostic, systematic, and evolutionary biological studies of this parasite and other related species in Ascaridida. Of course, the marker effectiveness of the nad4 and nad6 genes remains further validated when more additional Ascaridida mitogenomes become available, especially from the genus Toxocara , although concatenated mtDNA datasets are still the best molecular marker choice for evolutionary and phylogenetic studies of Ascaridida nematodes [ 33 , 42 , 45 , 46 , 48 , 50 , 51 , 54 , 67 , 70 , 75 , 81 , 82 ].…”

Section: Resultsmentioning

confidence: 99%

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The Complete Mitogenome of Toxocara vitulorum: Novel In-Sights into the Phylogenetics in Toxocaridae

Xie

Wang

Chen

et al. 2022

Animals

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Toxocara vitulorum (Ascaridida: Nematoda) is one of the most common intestinal nematodes of cattle and buffalos and, therefore, represents a serious threat to their populations worldwide. Despite its significance in veterinary health the epidemiology, population genetics, and molecular ecology of this nematode remain poorly understood. The mitogenome can yield a foundation for studying these areas and assist in the surveillance and control of T. vitulorum. Herein, the first whole mitogenome of T. vitulorum was sequenced utilizing Illumina technology and characterized with bioinformatic pipeline analyses. The entire genome of T. vitulorum was 15,045 bp in length and contained 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The gene arrangement (GA) of T. vitulorum was similar to those of other Toxocara species under GA3. The whole genome showed significant levels of AT and GC skew. Comparative mitogenomics including sequence identities, Ka/Ks, and sliding window analysis, indicated a purifying selection of 12 PCGs with cox1 and nad6 having the lowest and highest evolutionary rate, respectively. Whole amino acid sequence-based phylogenetic analysis supported a novel sister-species relationship of T. vitulorum with the congeneric species Toxocara canis, Toxocara cati, and Toxocara malaysiensis in the family Toxocaridae. Further, 12 (PCGs) single gene-based phylogenies suggested that nad4 and nad6 genes shared same topological trees with that of the whole genome, suggesting that these genes were suitable as novel genetic markers for phylogenetic and evolutionary studies of Ascaridida species. This complete mitogenome of T. vitulorum refined phylogenetic relationships in Toxocaridae and provided the resource of markers for population genetics, systematics, and epidemiology of this bovine nematode.

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Section: Resultssupporting

confidence: 89%

Section: Resultsmentioning

confidence: 99%

The Complete Mitogenome of Toxocara vitulorum: Novel In-Sights into the Phylogenetics in Toxocaridae

Xie

Wang

Chen

et al. 2022

Animals

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“…The complete mt genome of T. apodemi contained 12 PCGs ( cox 1- cox 3, cyt b, atp 6, nad 1- nad 6, and nad 4L), 22 tRNAs, 2 ribosomal RNAs (rRNAs), and 2 non-coding regions (NCRs) (Table 1, Figure 1). All mt genes of T. apodemi were transcribed in the same direction, which was the same as for the other species in Toxocara available in GenBank, but different from those of Ascaridia columbae and Ascaridia galli in superfamily Heterakoidea (Liu et al 2013a; Han et al 2022). A total of 3,423 amino acids were encoded by 12 PCGs in the complete T. apodemi mt genome.…”

Section: Resultsmentioning

confidence: 99%

“…It is a metric commonly used to measure codon usage bias. In Ascaridomorpha, the most commonly used codons are UUG, ACU, CCU, GCU, AGA, and AGU (Han et al 2022). In the complete mt genome of T. apodemi , UUG (RSCU = 3.82), ACU (RSCU = 3.18), CCU (RSCU = 3.18), CGU (RSCU = 3.15), and UCU (RSCU = 3.07) were the most frequently used, and CUC (RSCU = 0), CGA (RSCU = 0), CCA (RSCU = 0.05), and UUC (RSCU = 0.07) were the least used (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

Characterisation of the mitochondrial genome and phylogenetic analysis of Toxocara apodemi (Nematoda: Ascarididae)

Gao,

Hu,

et al. 2024

J. Helminthol.

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We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad4 had the highest sequence divergence, and cox1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad2, and the smallest was found in cox2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi, which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.

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Evaluation of the efficacy of disinfectants and disinfection methods against Ascaris suum eggs

Zhang,

Lu,

et al. 2024

Veterinary Parasitology

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Gene rearrangements in the mitochondrial genome of ten ascaris species and phylogenetic implications for Ascaridoidea and Heterakoidea families

Cited by 6 publications

References 47 publications

The Complete Mitogenome of Toxocara vitulorum: Novel In-Sights into the Phylogenetics in Toxocaridae

The Complete Mitogenome of Toxocara vitulorum: Novel In-Sights into the Phylogenetics in Toxocaridae

Characterisation of the mitochondrial genome and phylogenetic analysis of Toxocara apodemi (Nematoda: Ascarididae)

Evaluation of the efficacy of disinfectants and disinfection methods against Ascaris suum eggs

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