Limits...
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

The structure of the mitochondrial genome of Delia antiqua.The color-filled blocks indicate tRNAs, while the un-filled white blocks denote protein-coding genes, rRNA and control regions. The protein-coding genes, rRNA and control regions with black name are located on majority strand, whereas those with red names are on minority strand.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4591329&req=5

pone.0139736.g001: The structure of the mitochondrial genome of Delia antiqua.The color-filled blocks indicate tRNAs, while the un-filled white blocks denote protein-coding genes, rRNA and control regions. The protein-coding genes, rRNA and control regions with black name are located on majority strand, whereas those with red names are on minority strand.

Mentions: The complete mitochondrial genome of D. antiqua is a double stranded circular molecule with a length of 16,141 bp (Fig 1, GenBank accession number KT026595). The genome is medium-sized in compared with other Diptera mitochondrial genomes that range from 14,503 bp (Rhopalomyia pomum) to 19,517 bp (Drosophila melanogaster) in length. It includes 37 genes (13 protein coding genes, 22 tRNAs and 2 rRNAs) and a non-coding region (A+T rich region, also called as the control region) (Table 1). There are 23 genes located on the J-strand (9 protein coding genes and 14 tRNAs) with the other 14 genes on the N-strand (4 protein coding genes, 8 tRNAs and 2 rRNAs). Fourteen intergenic spacers were found to have a total length of 127 bp, ranging in size from 2–26 bp and with the longest intergenic spacer located between tRNAArg and tRNAAsn. On the other hand, there were 12 gene overlaps in the mitochondrial genome of D. antiqua and they involve in a total of 43 bp; the longest overlap was 8 bp and appears between tRNATrp and tRNACys.


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)

The structure of the mitochondrial genome of Delia antiqua.The color-filled blocks indicate tRNAs, while the un-filled white blocks denote protein-coding genes, rRNA and control regions. The protein-coding genes, rRNA and control regions with black name are located on majority strand, whereas those with red names are on minority strand.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139736.g001: The structure of the mitochondrial genome of Delia antiqua.The color-filled blocks indicate tRNAs, while the un-filled white blocks denote protein-coding genes, rRNA and control regions. The protein-coding genes, rRNA and control regions with black name are located on majority strand, whereas those with red names are on minority strand.
Mentions: The complete mitochondrial genome of D. antiqua is a double stranded circular molecule with a length of 16,141 bp (Fig 1, GenBank accession number KT026595). The genome is medium-sized in compared with other Diptera mitochondrial genomes that range from 14,503 bp (Rhopalomyia pomum) to 19,517 bp (Drosophila melanogaster) in length. It includes 37 genes (13 protein coding genes, 22 tRNAs and 2 rRNAs) and a non-coding region (A+T rich region, also called as the control region) (Table 1). There are 23 genes located on the J-strand (9 protein coding genes and 14 tRNAs) with the other 14 genes on the N-strand (4 protein coding genes, 8 tRNAs and 2 rRNAs). Fourteen intergenic spacers were found to have a total length of 127 bp, ranging in size from 2–26 bp and with the longest intergenic spacer located between tRNAArg and tRNAAsn. On the other hand, there were 12 gene overlaps in the mitochondrial genome of D. antiqua and they involve in a total of 43 bp; the longest overlap was 8 bp and appears between tRNATrp and tRNACys.

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