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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

AT% vs AT-Skew and GC% vs GC-Skew in Diptera mitochondrial genomes.Measured in bp percentage (Y-axis) and level of nucleotide skew (X-axis). Values are calculated on full length mitochondrial genomes. Orange circle, Diptera; red circle, Muscomorpha; yellow circle, Tipulomorpha; Green circle, Culicomorpha; blue circle, Tabanomorpha; black circle, Delia antiqua (Anthomyiidae).
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pone.0139736.g002: AT% vs AT-Skew and GC% vs GC-Skew in Diptera mitochondrial genomes.Measured in bp percentage (Y-axis) and level of nucleotide skew (X-axis). Values are calculated on full length mitochondrial genomes. Orange circle, Diptera; red circle, Muscomorpha; yellow circle, Tipulomorpha; Green circle, Culicomorpha; blue circle, Tabanomorpha; black circle, Delia antiqua (Anthomyiidae).

Mentions: This strand bias in nucleotide composition is a universal phenomenon in metazoan mitochondrial genomes. The strand bias can be indicated by a comparative analysis of (A + T)% vs AT-skew and (G + C)% vs GC-skew. The mitochondrial genome analysis of all known families of Diptera is shown in Fig 2. The average AT-skew among the Diptera is 0.032, ranging from -0.034 in Arachnocampa flava to 0.131 in Bactrocera minax, whereas the D. antiqua mitochondrial genome shows a quite weak AT-skew (0.009) (Table 2). The average GC-skew among the Diptera is -0.186, ranging from -0.315 in Bactrocera minax to -0.110 in Mayetiola destructo, and the D. antiqua mitochondrial genome shows a little higher than the average value (-0.172) (Table 3). The AT-skew and GC-skew of most dipteran mitochondrial genomes shows a positive AT-skew and negative GC-skew for the J-strand. AT content and GC content consistently show that the dipteran mitochondrial genomes have higher percentages of A+T. The underlying mechanism of this bias has been generally related to asymmetric mutation and selection pressure during replication and transcription. In the process of DNA replication and transcription, one chain is a single chain longer than the other strand, the deamination rate of A and C is faster in single chain, and therefore, more deamination of A and C occurs, leading to this bias [30]. This nucleotide bias has significance for the study of replication, transcription and rearrangement of the mitochondrial genome.


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)

AT% vs AT-Skew and GC% vs GC-Skew in Diptera mitochondrial genomes.Measured in bp percentage (Y-axis) and level of nucleotide skew (X-axis). Values are calculated on full length mitochondrial genomes. Orange circle, Diptera; red circle, Muscomorpha; yellow circle, Tipulomorpha; Green circle, Culicomorpha; blue circle, Tabanomorpha; black circle, Delia antiqua (Anthomyiidae).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139736.g002: AT% vs AT-Skew and GC% vs GC-Skew in Diptera mitochondrial genomes.Measured in bp percentage (Y-axis) and level of nucleotide skew (X-axis). Values are calculated on full length mitochondrial genomes. Orange circle, Diptera; red circle, Muscomorpha; yellow circle, Tipulomorpha; Green circle, Culicomorpha; blue circle, Tabanomorpha; black circle, Delia antiqua (Anthomyiidae).
Mentions: This strand bias in nucleotide composition is a universal phenomenon in metazoan mitochondrial genomes. The strand bias can be indicated by a comparative analysis of (A + T)% vs AT-skew and (G + C)% vs GC-skew. The mitochondrial genome analysis of all known families of Diptera is shown in Fig 2. The average AT-skew among the Diptera is 0.032, ranging from -0.034 in Arachnocampa flava to 0.131 in Bactrocera minax, whereas the D. antiqua mitochondrial genome shows a quite weak AT-skew (0.009) (Table 2). The average GC-skew among the Diptera is -0.186, ranging from -0.315 in Bactrocera minax to -0.110 in Mayetiola destructo, and the D. antiqua mitochondrial genome shows a little higher than the average value (-0.172) (Table 3). The AT-skew and GC-skew of most dipteran mitochondrial genomes shows a positive AT-skew and negative GC-skew for the J-strand. AT content and GC content consistently show that the dipteran mitochondrial genomes have higher percentages of A+T. The underlying mechanism of this bias has been generally related to asymmetric mutation and selection pressure during replication and transcription. In the process of DNA replication and transcription, one chain is a single chain longer than the other strand, the deamination rate of A and C is faster in single chain, and therefore, more deamination of A and C occurs, leading to this bias [30]. This nucleotide bias has significance for the study of replication, transcription and rearrangement of the mitochondrial genome.

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