Limits...
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.


Predicted secondary structure of the srRNA gene in Nemopoda mamaevi.Roman numerals denote the conserved domain structure. Inferred Watson-Crick bonds are illustrated by lines, GU bonds by dots.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4380458&req=5

pone.0123594.g008: Predicted secondary structure of the srRNA gene in Nemopoda mamaevi.Roman numerals denote the conserved domain structure. Inferred Watson-Crick bonds are illustrated by lines, GU bonds by dots.

Mentions: We inferred secondary structures of lrRNA and srRNA of N. mamaevi using the published rRNA secondary structures of a leafminer Liriomyza sativae (Agromyzidae), the only dipteran so analysed to date, as a model [16]. The lrRNA had 49 helices in five structural domains (I-II, IV-VI, domain III is absent as in other insects), similar to L. sativae [16] and typical of arthropods [69]. The secondary structures of srRNA in N. mamaevi included three domains and 33 helices, again similar to other Diptera [16] (Figs 7 and 8).


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)

Predicted secondary structure of the srRNA gene in Nemopoda mamaevi.Roman numerals denote the conserved domain structure. Inferred Watson-Crick bonds are illustrated by lines, GU bonds by dots.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123594.g008: Predicted secondary structure of the srRNA gene in Nemopoda mamaevi.Roman numerals denote the conserved domain structure. Inferred Watson-Crick bonds are illustrated by lines, GU bonds by dots.
Mentions: We inferred secondary structures of lrRNA and srRNA of N. mamaevi using the published rRNA secondary structures of a leafminer Liriomyza sativae (Agromyzidae), the only dipteran so analysed to date, as a model [16]. The lrRNA had 49 helices in five structural domains (I-II, IV-VI, domain III is absent as in other insects), similar to L. sativae [16] and typical of arthropods [69]. The secondary structures of srRNA in N. mamaevi included three domains and 33 helices, again similar to other Diptera [16] (Figs 7 and 8).

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.