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Comparative Mt Genomics of the Tipuloidea (Diptera: Nematocera: Tipulomorpha) and Its Implications for the Phylogeny of the Tipulomorpha.

Zhang X, Kang Z, Mao M, Li X, Cameron SL, Jong Hd, Wang M, Yang D - PLoS ONE (2016)

Bottom Line: We did a comparative analysis of these mt genomics and used them, along with some other representatives of the Nematocera to construct phylogenetic trees.Tipulomorpha are not supported as the earliest branch of the Diptera.Furthermore, phylogenetic trees indicate that the family Limoniidae is a paraphyletic group.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, China Agricultural University, Beijing, 100193, China.

ABSTRACT
A traditionally controversial taxon, the Tipulomorpha has been frequently discussed with respect to both its familial composition and relationships with other Nematocera. The interpretation of internal relationships within the Tipuloidea, which include the Tipulidae sensu stricto, Cylindrotomidae, Pediciidae and Limoniidae, is also problematic. We sequenced the first complete mitochondrial (mt) genome of Symplecta hybrida (Meigen, 1804), which belongs to the subfamily Chioneinae of family Limoniidae, and another five nearly complete mt genomes from the Tipuloidea. We did a comparative analysis of these mt genomics and used them, along with some other representatives of the Nematocera to construct phylogenetic trees. Trees inferred by Bayesian methods strongly support a sister-group relationship between Trichoceridae and Tipuloidea. Tipulomorpha are not supported as the earliest branch of the Diptera. Furthermore, phylogenetic trees indicate that the family Limoniidae is a paraphyletic group.

No MeSH data available.


Inferred secondary structure of the lrRNA gene in Symplecta hybrida.The short line indicated the inferred Watson-Crick bonds, and the dark dots indicated GU bonds.
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pone.0158167.g004: Inferred secondary structure of the lrRNA gene in Symplecta hybrida.The short line indicated the inferred Watson-Crick bonds, and the dark dots indicated GU bonds.

Mentions: The mt rRNA genes have frequently not been annotated via the use of functional features, so it is hard to annotate them from their DNA sequences alone [56, 60–61]. Beckenbach has proposed that the start of srRNA is AARGUUUU based on an alignment across dipteran and mecopteran sequences [6]. Hence, we annotated the lrRNA gene as in other dipteran species, where it is between tRNALeu (CUN) and tRNAVal, while the srRNA gene is flanked at the 3’ end by tRNAVal and the motif AARGUUUU. Furthermore, we inferred the secondary structures for lrRNA and srRNA in the Tipuloidea using the sequences of S. hybrida based on the published lrRNA and srRNA secondary structures, the sepsid fly Nemopoda mamaevi Ozerov, 1997 [56]. The secondary structures of lrRNA and srRNA are similar to those in N. mamaevi and other Dipteran species [56, 62]. The lrRNA has five structural domains (domain III absent as in other insects) and 42 helices while the srRNA includes 3 domains and 25 helices (Figs 4 and 5).


Comparative Mt Genomics of the Tipuloidea (Diptera: Nematocera: Tipulomorpha) and Its Implications for the Phylogeny of the Tipulomorpha.

Zhang X, Kang Z, Mao M, Li X, Cameron SL, Jong Hd, Wang M, Yang D - PLoS ONE (2016)

Inferred secondary structure of the lrRNA gene in Symplecta hybrida.The short line indicated the inferred Watson-Crick bonds, and the dark dots indicated GU bonds.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920351&req=5

pone.0158167.g004: Inferred secondary structure of the lrRNA gene in Symplecta hybrida.The short line indicated the inferred Watson-Crick bonds, and the dark dots indicated GU bonds.
Mentions: The mt rRNA genes have frequently not been annotated via the use of functional features, so it is hard to annotate them from their DNA sequences alone [56, 60–61]. Beckenbach has proposed that the start of srRNA is AARGUUUU based on an alignment across dipteran and mecopteran sequences [6]. Hence, we annotated the lrRNA gene as in other dipteran species, where it is between tRNALeu (CUN) and tRNAVal, while the srRNA gene is flanked at the 3’ end by tRNAVal and the motif AARGUUUU. Furthermore, we inferred the secondary structures for lrRNA and srRNA in the Tipuloidea using the sequences of S. hybrida based on the published lrRNA and srRNA secondary structures, the sepsid fly Nemopoda mamaevi Ozerov, 1997 [56]. The secondary structures of lrRNA and srRNA are similar to those in N. mamaevi and other Dipteran species [56, 62]. The lrRNA has five structural domains (domain III absent as in other insects) and 42 helices while the srRNA includes 3 domains and 25 helices (Figs 4 and 5).

Bottom Line: We did a comparative analysis of these mt genomics and used them, along with some other representatives of the Nematocera to construct phylogenetic trees.Tipulomorpha are not supported as the earliest branch of the Diptera.Furthermore, phylogenetic trees indicate that the family Limoniidae is a paraphyletic group.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, China Agricultural University, Beijing, 100193, China.

ABSTRACT
A traditionally controversial taxon, the Tipulomorpha has been frequently discussed with respect to both its familial composition and relationships with other Nematocera. The interpretation of internal relationships within the Tipuloidea, which include the Tipulidae sensu stricto, Cylindrotomidae, Pediciidae and Limoniidae, is also problematic. We sequenced the first complete mitochondrial (mt) genome of Symplecta hybrida (Meigen, 1804), which belongs to the subfamily Chioneinae of family Limoniidae, and another five nearly complete mt genomes from the Tipuloidea. We did a comparative analysis of these mt genomics and used them, along with some other representatives of the Nematocera to construct phylogenetic trees. Trees inferred by Bayesian methods strongly support a sister-group relationship between Trichoceridae and Tipuloidea. Tipulomorpha are not supported as the earliest branch of the Diptera. Furthermore, phylogenetic trees indicate that the family Limoniidae is a paraphyletic group.

No MeSH data available.