First Description of the Mitogenome and Phylogeny of Culicinae Species from the Amazon Region

Nascimento, Bruna Laís Sena do; Silva, Fábio Silva da; Neto, Joaquim Pinto Nunes; Medeiros, Daniele Barbosa de Almeida; Cruz, Ana Cecília Ribeiro; Silva, Sandro Patroca da; Silva, Lucas Henrique da Silva e; Monteiro, Hamilton Antônio de Oliveira; Dias, Daniel Damous; Vieira, Durval Bertram Rodrigues; Rosa, José Wilson; Brandão, Roberto Carlos Feitosa; Chiang, Jannifer Oliveira; Martins, Lívia Carício; Vasconcelos, Pedro Fernando da Costa

doi:10.3390/genes12121983

Cited by 12 publications

(9 citation statements)

References 69 publications

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“…Only the predicted secondary structure of the tRNA ser1 gene was atypical, lacking a DHU arm and instead forming a DHU loop (Figure S2). This pattern has been reported in other insects [36,37].…”

Section: Trna Structure Analysissupporting

confidence: 89%

“…The average (A + T) contents of PCGs, tRNA, and rRNA coding regions were 76.78%, 78.25%, and 81.43%, respectively. The mitochondrial genomes of the ten species in Hyrcanus group had positive A-T skew values, with a mean value of 0.028, and G-C skew values were all negative, with a mean value of −0.156 (Figure 2a-c, Table S2), close to values for other mosquitoes [35][36][37].…”

Section: Overall Composition and Structure Of The Mitochondrial Genomementioning

confidence: 70%

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Phylogenetic Analysis of Some Species of the Anopheles hyrcanus Group (Diptera: Culicidae) in China Based on Complete Mitochondrial Genomes

Dong¹,

Yuan

Yang³

et al. 2023

Genes

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Some species of the Hyrcanus group are vectors of malaria in China. However, the member species are difficult to identify accurately by morphology. The development of sequencing technologies offers the possibility of further studies based on the complete mitochondrial genome. In this study, samples of mosquitoes of the Hyrcanus group were collected in China between 1997 and 2015. The mitochondrial genomes of ten species of the Hyrcanus group were analyzed, including the structure and base composition, codon usage, secondary structure of tRNA, and base difference sites in protein coding regions. Phylogenetic analyses using maximum-likelihood and Bayesian inference were performed based on mitochondrial genes and complete mitochondrial genomes The mitochondrial genome of 10 Hyrcanus group members ranged from 15,403 bp to 15,475 bp, with an average 78.23% (A + T) content, comprising of 13 PCGs (protein coding genes), 22 tRNAs, and 2 rRNAs. Site differences between some closely related species in the PCGs were small. There were only 36 variable sites between Anopheles sinensis and Anopheles belenrae for a variation ratio of 0.32% in all PCGs. The pairwise interspecies distance based on 13 PCGs was low, with an average of 0.04. A phylogenetic tree constructed with the 13 PCGs was consistent with the known evolutionary relationships. Some phylogenetic trees constructed by single coding regions (such as COI or ND4) or combined coding regions (COI + ND2 + ND4 + ND5 or ND2 + ND4) were consistent with the phylogenetic tree constructed using the 13 PCGs. The phylogenetic trees constructed using some coding genes (COII, ND5, tRNAs, 12S rRNA, and 16S rRNA) differed from the phylogenetic tree constructed using PCGs. The difference in mitochondrial genome sequences between An. sinensis and An. belenrae was very small, corresponding to intraspecies difference. The combination of all 13 PCG sequences was demonstrated to be optimal for phylogenetic analysis in closely related species.

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Section: Trna Structure Analysissupporting

confidence: 89%

Section: Overall Composition and Structure Of The Mitochondrial Genomementioning

confidence: 70%

Phylogenetic Analysis of Some Species of the Anopheles hyrcanus Group (Diptera: Culicidae) in China Based on Complete Mitochondrial Genomes

Dong¹,

Yuan

Yang³

et al. 2023

Genes

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“…The relative synonymous codon usage bias (RSCU) for PCGs was determined with the trematode mt genetic code in CodonW. ( do Nascimento et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

Qiu

Lou

et al. 2022

International Journal for Parasitology: Parasites and Wildlife

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“…DNAStar (v. 5.0) was used to calculate the A+T and G+C contents of each gene, and the AT skew and GC skew values were calculated using the formulas AT skew = (A − T)/(A + T) and GC skew = (G − C)/(G + C) for the coding genes [ 19 ]. Synonymous codon usage bias in PCGs was analyzed using CodonW [ 20 ], and relative synonymous codon usage (RSCU) values were determined. Sliding window analysis and pairwise comparisons of the proportions of non-synonymous ( dN ) and synonymous ( dS ) substitutions ( dN/dS ) among the obtained sequences were performed using DnaSP (v. 6) [ 21 ].…”

Section: Methodsmentioning

confidence: 99%

First Description of the Mitogenome Features of Neofoleyellides Genus (Nematoda: Onchocercidae) Isolated from a Wild Bird (Pyrrhocorax pyrrhocorax)

Wang

et al. 2022

Animals

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The Onchocercidae family is composed of more than 30 valid nematode species with notable zoonotic potential. Current limitations in molecular characterization methods and species identification are the main obstacles to a better understanding of the biology of Onchocercidae species, particularly in wildlife. This study describes for the first time the complete mitochondrial (mt) genome sequence of Neofoleyellides sp. isolated from a wild bird (Pyrrhocorax pyrrhocorax) and belonging to the Neofoleyellides genus (Nematoda: Onchocercidae). The mt genome of Neofoleyellides sp. (GenBank accession number: ON641583) was a typical circular DNA molecule of 13,628 bp in size with an AT content of 76.69%. The complete mt genome comprised 36 functional subunits, including 12 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. The most common start codon was ATT/ATG except for nad2 with TTG, and TAA was the termination codon for all protein-coding genes (PCGs). Phylogenetic analysis of the concatenated and aligned amino acid sequences of the 12 PCGs showed that the trees generated using different methods (Bayesian inference and maximum likelihood) with different partition schemes shared similar topologies. The isolated Neofoleyellides sp. was placed in the Onchocercidae family and formed a sister branch with the genera Onchocerca and Dirofilaria. The entire mt genome of Neofoleyellides sp. presented in this study could provide useful data for studying the population genetics and phylogenetic relationships of Onchocercidae species.

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First Description of the Mitogenome and Phylogeny of Culicinae Species from the Amazon Region

Cited by 12 publications

References 69 publications

Phylogenetic Analysis of Some Species of the Anopheles hyrcanus Group (Diptera: Culicidae) in China Based on Complete Mitochondrial Genomes

Phylogenetic Analysis of Some Species of the Anopheles hyrcanus Group (Diptera: Culicidae) in China Based on Complete Mitochondrial Genomes

Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

First Description of the Mitogenome Features of Neofoleyellides Genus (Nematoda: Onchocercidae) Isolated from a Wild Bird (Pyrrhocorax pyrrhocorax)

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