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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.


Phylogenetic tree of Brachycera families based on mt genome data.Cladogram of relationships resulting from Bayesian analyses with datasets PCG12 and PCG12RNA, with Cydistomyia duplonotata (Nemestrinidae) and Trichophthalma punctata (Tabanidae) as outgroups. Squares at the nodes are Bayesian posterior probabilities for 1, 2, 5 and 6, ML bootstrap values for 3, 4, 7 and 8. Dataset of PCG123, 1 and 3, PCG123RNA, 2 and 4, PCG12, 5 and 7, PCG12RNA, 6 and 8. Black indicates posterior probabilities = 1.00 or ML bootstrap = 100, gray indicates posterior probabilities ≥ 0.90 or ML bootstrap ≥ 70, white indicates posterior probabilities < 0.90 or ML bootstrap < 70, ‘ns’ indicates not support, * indicates posterior probabilities = 1.00 or ML bootstrap = 100 in eight trees. A. Part of the Bayesian tree of datasets PCG123 and PCG123RNA as well as ML tree of datasets PCG123, PCG12 and PCG12RNA. B. Part of the ML tree of dataset PCG123RNA.
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pone.0123594.g010: Phylogenetic tree of Brachycera families based on mt genome data.Cladogram of relationships resulting from Bayesian analyses with datasets PCG12 and PCG12RNA, with Cydistomyia duplonotata (Nemestrinidae) and Trichophthalma punctata (Tabanidae) as outgroups. Squares at the nodes are Bayesian posterior probabilities for 1, 2, 5 and 6, ML bootstrap values for 3, 4, 7 and 8. Dataset of PCG123, 1 and 3, PCG123RNA, 2 and 4, PCG12, 5 and 7, PCG12RNA, 6 and 8. Black indicates posterior probabilities = 1.00 or ML bootstrap = 100, gray indicates posterior probabilities ≥ 0.90 or ML bootstrap ≥ 70, white indicates posterior probabilities < 0.90 or ML bootstrap < 70, ‘ns’ indicates not support, * indicates posterior probabilities = 1.00 or ML bootstrap = 100 in eight trees. A. Part of the Bayesian tree of datasets PCG123 and PCG123RNA as well as ML tree of datasets PCG123, PCG12 and PCG12RNA. B. Part of the ML tree of dataset PCG123RNA.

Mentions: The phylogenetic trees conducted from both Bayesian and ML analyses have very similar topologies across four datasets (Fig 10). The monophyly of Cyclorrhapha, Opomyzoidea, Tephritoidea and Ephydroidea were consistently supported (posterior probability = 1.00, ML bootstrap = 100), as was the monophyly of Schizophora (posterior probability = 1.00, ML bootstrap = 85/100/100/100) and Calyptratae (posterior probability = 1.00, ML bootstrap = 41/73/87/84). Several recent researchers have concluded that ‘Aschiza’ is not monophyletic [71–76], here we add support for this conclusion from mt genome data. Phoridae was sister group of other Cyclorrhapha (posterior probability = 1.00, ML bootstrap = 100), and Syrphoidea was sister group of the Schizophora (posterior probability = 1.00, ML bootstrap = 85/100/100/100). This supports Wiegmann et. al’s findings regarding basal branching events within the Cyclorrhapha [77], however their nodal support for the relationship Phoridae + (remaining Cyclorrhapha) was weaker than that found here. Although only moderately supported (posterior probability = 0.86/0.70/0.98/0.79, ML bootstrap = 78/14/95/82), the position of superfamily Opomyzoidea (Fergusoninidae + Agromyzidae) was sister to the remaining Cyclorrhapha. Wiegmann et al. [77] did not find a monophyletic Opomyzoidea, nor did they find a sister-group relationship between the two representative families included in the present study. Given that there are 14 families recognized within the Opomyzoidea considerable additional data is necessary to firmly resolve their monophyly and relationships to other schizophoran superfamilies. Sepsidae is sister taxon to Tephritoidea (posterior probability = 1.00/1.00/0.92/1.00, ML bootstrap = 33/100/91/99), while Ephydroidea + Calyptratae formed a monophyletic group (posterior probability = 1.00, ML bootstrap = 41/73/87/84). Both relationships have previously been found in Wiegmann et al. [77], however neither had significant nodal support in that study.


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)

Phylogenetic tree of Brachycera families based on mt genome data.Cladogram of relationships resulting from Bayesian analyses with datasets PCG12 and PCG12RNA, with Cydistomyia duplonotata (Nemestrinidae) and Trichophthalma punctata (Tabanidae) as outgroups. Squares at the nodes are Bayesian posterior probabilities for 1, 2, 5 and 6, ML bootstrap values for 3, 4, 7 and 8. Dataset of PCG123, 1 and 3, PCG123RNA, 2 and 4, PCG12, 5 and 7, PCG12RNA, 6 and 8. Black indicates posterior probabilities = 1.00 or ML bootstrap = 100, gray indicates posterior probabilities ≥ 0.90 or ML bootstrap ≥ 70, white indicates posterior probabilities < 0.90 or ML bootstrap < 70, ‘ns’ indicates not support, * indicates posterior probabilities = 1.00 or ML bootstrap = 100 in eight trees. A. Part of the Bayesian tree of datasets PCG123 and PCG123RNA as well as ML tree of datasets PCG123, PCG12 and PCG12RNA. B. Part of the ML tree of dataset PCG123RNA.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4380458&req=5

pone.0123594.g010: Phylogenetic tree of Brachycera families based on mt genome data.Cladogram of relationships resulting from Bayesian analyses with datasets PCG12 and PCG12RNA, with Cydistomyia duplonotata (Nemestrinidae) and Trichophthalma punctata (Tabanidae) as outgroups. Squares at the nodes are Bayesian posterior probabilities for 1, 2, 5 and 6, ML bootstrap values for 3, 4, 7 and 8. Dataset of PCG123, 1 and 3, PCG123RNA, 2 and 4, PCG12, 5 and 7, PCG12RNA, 6 and 8. Black indicates posterior probabilities = 1.00 or ML bootstrap = 100, gray indicates posterior probabilities ≥ 0.90 or ML bootstrap ≥ 70, white indicates posterior probabilities < 0.90 or ML bootstrap < 70, ‘ns’ indicates not support, * indicates posterior probabilities = 1.00 or ML bootstrap = 100 in eight trees. A. Part of the Bayesian tree of datasets PCG123 and PCG123RNA as well as ML tree of datasets PCG123, PCG12 and PCG12RNA. B. Part of the ML tree of dataset PCG123RNA.
Mentions: The phylogenetic trees conducted from both Bayesian and ML analyses have very similar topologies across four datasets (Fig 10). The monophyly of Cyclorrhapha, Opomyzoidea, Tephritoidea and Ephydroidea were consistently supported (posterior probability = 1.00, ML bootstrap = 100), as was the monophyly of Schizophora (posterior probability = 1.00, ML bootstrap = 85/100/100/100) and Calyptratae (posterior probability = 1.00, ML bootstrap = 41/73/87/84). Several recent researchers have concluded that ‘Aschiza’ is not monophyletic [71–76], here we add support for this conclusion from mt genome data. Phoridae was sister group of other Cyclorrhapha (posterior probability = 1.00, ML bootstrap = 100), and Syrphoidea was sister group of the Schizophora (posterior probability = 1.00, ML bootstrap = 85/100/100/100). This supports Wiegmann et. al’s findings regarding basal branching events within the Cyclorrhapha [77], however their nodal support for the relationship Phoridae + (remaining Cyclorrhapha) was weaker than that found here. Although only moderately supported (posterior probability = 0.86/0.70/0.98/0.79, ML bootstrap = 78/14/95/82), the position of superfamily Opomyzoidea (Fergusoninidae + Agromyzidae) was sister to the remaining Cyclorrhapha. Wiegmann et al. [77] did not find a monophyletic Opomyzoidea, nor did they find a sister-group relationship between the two representative families included in the present study. Given that there are 14 families recognized within the Opomyzoidea considerable additional data is necessary to firmly resolve their monophyly and relationships to other schizophoran superfamilies. Sepsidae is sister taxon to Tephritoidea (posterior probability = 1.00/1.00/0.92/1.00, ML bootstrap = 33/100/91/99), while Ephydroidea + Calyptratae formed a monophyletic group (posterior probability = 1.00, ML bootstrap = 41/73/87/84). Both relationships have previously been found in Wiegmann et al. [77], however neither had significant nodal support in that study.

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.