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The Complete Mitochondrial Genome of Delia antiqua and Its Implications in Dipteran Phylogenetics.

Zhang NX, Yu G, Li TJ, He QY, Zhou Y, Si FL, Ren S, Chen B - PLoS ONE (2015)

Bottom Line: All of the tRNAs have the typical clover-leaf structure, except for tRNASer(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects.The location and structure of the two rRNAs are conservative and stable when compared with other insects.Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a paraphyly, and both Oestroidea and Muscoidea are polyphyletic.

View Article: PubMed Central - PubMed

Affiliation: Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China.

ABSTRACT
Delia antiqua is a major underground agricultural pest widely distributed in Asia, Europe and North America. In this study, we sequenced and annotated the complete mitochondrial genome of this species, which is the first report of complete mitochondrial genome in the family Anthomyiidae. This genome is a double-stranded circular molecule with a length of 16,141 bp and an A+T content of 78.5%. It contains 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) and a non-coding A+T rich region or control region. The mitochondrial genome of Delia antiqua presents a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All of the 13 protein-coding genes use ATN as an initiation codon except for the COI gene that starts with ATCA. Most protein-coding genes have complete termination codons but COII and ND5 that have the incomplete termination codon T. This bias is reflected in both codon usage and amino acid composition. The protein-coding genes in the D. antiqua mitochondrial genome prefer to use the codon UUA (Leu). All of the tRNAs have the typical clover-leaf structure, except for tRNASer(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects. There are 7 mismatches with U-U in the tRNAs. The location and structure of the two rRNAs are conservative and stable when compared with other insects. The control region between 12S rRNA and tRNAIle has the highest A+T content of 93.7% in the D. antiqua mitochondrial genome. The control region includes three kinds of special regions, two highly conserved poly-T stretches, a (TA)n stretch and several G(A)nT structures considered important elements related to replication and transcription. The nucleotide sequences of 13 protein-coding genes are used to construct the phylogenetics of 26 representative Dipteran species. Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a paraphyly, and both Oestroidea and Muscoidea are polyphyletic.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree of Diptera mitochondrial genome sequences inferred by Maximum Likelihood analysis.Numbers above branches and with blue color indicate likelihood bootstrap values, and the numbers below branches indicate the branch length. The names of family and superfamily (in bracket) are just after the species names.
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pone.0139736.g004: Phylogenetic tree of Diptera mitochondrial genome sequences inferred by Maximum Likelihood analysis.Numbers above branches and with blue color indicate likelihood bootstrap values, and the numbers below branches indicate the branch length. The names of family and superfamily (in bracket) are just after the species names.

Mentions: We performed phylogenetic analysis using the nucleotide sequences of 13 protein-coding genes of 25 species of complete dipteran mitochondrial genome sequences and the D. antiqua mitochondrial genome using Bombyx mandarina as outgroup. The topological strctures of the 2 phylogenetic trees constructed separately by ML and BI analyses are very similar, with only 1 exception of the location of Culicoides arakawae in the family Ceratopogonidae of the superfamily Chironomoidea (Figs 4 and 5). On the ML tree the species is located at the base of the Culicidae (Culicoidea) clade (Fig 4), whereas on the BI tree it is linked up the Culicidae clade (Fig 5). All but 3 clades are strongly supported with >80 bootstrap values. However, the clade of Ephydroidea + Oestroidea + Muscoidea + Tephritoidea and the clade of Ba. carambolae + Ba. dorsalis in Tephritidae are with bootstrap values equal or less 66 on both trees. On the Ml tree the clade up Culicoides arakawae has only a bootstrap value of 4, and on the BI tree the clade below Culicoides arakawae has a bootstrap value of 88, which indidates that the location of Culicoides arakawae is pending.


The Complete Mitochondrial Genome of Delia antiqua and Its Implications in Dipteran Phylogenetics.

Zhang NX, Yu G, Li TJ, He QY, Zhou Y, Si FL, Ren S, Chen B - PLoS ONE (2015)

Phylogenetic tree of Diptera mitochondrial genome sequences inferred by Maximum Likelihood analysis.Numbers above branches and with blue color indicate likelihood bootstrap values, and the numbers below branches indicate the branch length. The names of family and superfamily (in bracket) are just after the species names.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591329&req=5

pone.0139736.g004: Phylogenetic tree of Diptera mitochondrial genome sequences inferred by Maximum Likelihood analysis.Numbers above branches and with blue color indicate likelihood bootstrap values, and the numbers below branches indicate the branch length. The names of family and superfamily (in bracket) are just after the species names.
Mentions: We performed phylogenetic analysis using the nucleotide sequences of 13 protein-coding genes of 25 species of complete dipteran mitochondrial genome sequences and the D. antiqua mitochondrial genome using Bombyx mandarina as outgroup. The topological strctures of the 2 phylogenetic trees constructed separately by ML and BI analyses are very similar, with only 1 exception of the location of Culicoides arakawae in the family Ceratopogonidae of the superfamily Chironomoidea (Figs 4 and 5). On the ML tree the species is located at the base of the Culicidae (Culicoidea) clade (Fig 4), whereas on the BI tree it is linked up the Culicidae clade (Fig 5). All but 3 clades are strongly supported with >80 bootstrap values. However, the clade of Ephydroidea + Oestroidea + Muscoidea + Tephritoidea and the clade of Ba. carambolae + Ba. dorsalis in Tephritidae are with bootstrap values equal or less 66 on both trees. On the Ml tree the clade up Culicoides arakawae has only a bootstrap value of 4, and on the BI tree the clade below Culicoides arakawae has a bootstrap value of 88, which indidates that the location of Culicoides arakawae is pending.

Bottom Line: All of the tRNAs have the typical clover-leaf structure, except for tRNASer(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects.The location and structure of the two rRNAs are conservative and stable when compared with other insects.Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a paraphyly, and both Oestroidea and Muscoidea are polyphyletic.

View Article: PubMed Central - PubMed

Affiliation: Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China.

ABSTRACT
Delia antiqua is a major underground agricultural pest widely distributed in Asia, Europe and North America. In this study, we sequenced and annotated the complete mitochondrial genome of this species, which is the first report of complete mitochondrial genome in the family Anthomyiidae. This genome is a double-stranded circular molecule with a length of 16,141 bp and an A+T content of 78.5%. It contains 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) and a non-coding A+T rich region or control region. The mitochondrial genome of Delia antiqua presents a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All of the 13 protein-coding genes use ATN as an initiation codon except for the COI gene that starts with ATCA. Most protein-coding genes have complete termination codons but COII and ND5 that have the incomplete termination codon T. This bias is reflected in both codon usage and amino acid composition. The protein-coding genes in the D. antiqua mitochondrial genome prefer to use the codon UUA (Leu). All of the tRNAs have the typical clover-leaf structure, except for tRNASer(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects. There are 7 mismatches with U-U in the tRNAs. The location and structure of the two rRNAs are conservative and stable when compared with other insects. The control region between 12S rRNA and tRNAIle has the highest A+T content of 93.7% in the D. antiqua mitochondrial genome. The control region includes three kinds of special regions, two highly conserved poly-T stretches, a (TA)n stretch and several G(A)nT structures considered important elements related to replication and transcription. The nucleotide sequences of 13 protein-coding genes are used to construct the phylogenetics of 26 representative Dipteran species. Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a paraphyly, and both Oestroidea and Muscoidea are polyphyletic.

No MeSH data available.


Related in: MedlinePlus