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The first mitochondrial genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae), with mitochondrial genome phylogeny of cyclorrhapha.

Li X, Ding S, Cameron SL, Kang Z, Wang Y, Yang D - PLoS ONE (2015)

Bottom Line: In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997.Additionally, we compared automated annotation software MITOS with hand annotation method.Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, China Agricultural University, Beijing, China.

ABSTRACT
Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.

No MeSH data available.


Mitochondrial map of Nemopoda mamaevi Ozerov.Circular maps were drawn with CGView [59]. Arrows indicated the orientation of gene transcription. The tRNAs are denoted by the color blocks and are labelled according to the IUPACIUB single-letter amino acid codes (L1: CUN; L2: UUR; S1: AGN; S2: UCN). The GC content was plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC-skew was plotted as the deviation from the average GC-skew of the entire sequence. The inner cycle indicated the location of genes in the mt genome.
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pone.0123594.g001: Mitochondrial map of Nemopoda mamaevi Ozerov.Circular maps were drawn with CGView [59]. Arrows indicated the orientation of gene transcription. The tRNAs are denoted by the color blocks and are labelled according to the IUPACIUB single-letter amino acid codes (L1: CUN; L2: UUR; S1: AGN; S2: UCN). The GC content was plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC-skew was plotted as the deviation from the average GC-skew of the entire sequence. The inner cycle indicated the location of genes in the mt genome.

Mentions: The complete mt genome of N. mamaevi is a typical circular, double-stranded molecule (GenBank accession number: KM605250; Fig 1) 15,878 bp in length. Mt genome length is medium-sized when compared to the mt genomes of other Diptera, that range from 14,922 bp (Sarcophaga peregrine, Sarcophagidae, NC_023794) to 19,517 bp (Drosophila melanogaster, Drosophilidae [26]). The mt genome of N. mamaevi contains the 37 genes, including 13 PCGs, 22 tRNA genes, two rRNA genes and a large control region, that are usually present in bilaterian animals [3]. The gene order is the same as the inferred ancestral insect mt genome pattern, which is conserved amongst all cyclorrhaphan flies sequenced to date. Twenty three genes are encoded on the majority strand (J-strand), while the minority strand (N-strand) encodes the remaining 14 genes.


The first mitochondrial genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae), with mitochondrial genome phylogeny of cyclorrhapha.

Li X, Ding S, Cameron SL, Kang Z, Wang Y, Yang D - PLoS ONE (2015)

Mitochondrial map of Nemopoda mamaevi Ozerov.Circular maps were drawn with CGView [59]. Arrows indicated the orientation of gene transcription. The tRNAs are denoted by the color blocks and are labelled according to the IUPACIUB single-letter amino acid codes (L1: CUN; L2: UUR; S1: AGN; S2: UCN). The GC content was plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC-skew was plotted as the deviation from the average GC-skew of the entire sequence. The inner cycle indicated the location of genes in the mt genome.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4380458&req=5

pone.0123594.g001: Mitochondrial map of Nemopoda mamaevi Ozerov.Circular maps were drawn with CGView [59]. Arrows indicated the orientation of gene transcription. The tRNAs are denoted by the color blocks and are labelled according to the IUPACIUB single-letter amino acid codes (L1: CUN; L2: UUR; S1: AGN; S2: UCN). The GC content was plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC-skew was plotted as the deviation from the average GC-skew of the entire sequence. The inner cycle indicated the location of genes in the mt genome.
Mentions: The complete mt genome of N. mamaevi is a typical circular, double-stranded molecule (GenBank accession number: KM605250; Fig 1) 15,878 bp in length. Mt genome length is medium-sized when compared to the mt genomes of other Diptera, that range from 14,922 bp (Sarcophaga peregrine, Sarcophagidae, NC_023794) to 19,517 bp (Drosophila melanogaster, Drosophilidae [26]). The mt genome of N. mamaevi contains the 37 genes, including 13 PCGs, 22 tRNA genes, two rRNA genes and a large control region, that are usually present in bilaterian animals [3]. The gene order is the same as the inferred ancestral insect mt genome pattern, which is conserved amongst all cyclorrhaphan flies sequenced to date. Twenty three genes are encoded on the majority strand (J-strand), while the minority strand (N-strand) encodes the remaining 14 genes.

Bottom Line: In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997.Additionally, we compared automated annotation software MITOS with hand annotation method.Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, China Agricultural University, Beijing, China.

ABSTRACT
Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.

No MeSH data available.