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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.


Start and stop codons usage in nematoceran mt genomes.a: Start codons usage of PCGs in Nematocera; b: Stop codons usage of PCGs in Nematocera.
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pone.0158167.g002: Start and stop codons usage in nematoceran mt genomes.a: Start codons usage of PCGs in Nematocera; b: Stop codons usage of PCGs in Nematocera.

Mentions: Among all sequenced nematoceran flies, the most commonly used start codons are the canonical start codons ATN (Met/Ile), found in every PCG. Among them, ATG (Met) and ATT (Ile) are the mostly common used start codons. ATG (Met) is used in ATP6, CO2, CO3, CYTB, ND4 and ND4L for almost all nematoceran flies. This pattern is also observed in cyclorrhaphan flies [56]. ATT (Met) is found in 10 of the 13 PCGs (ATP6, ATP8, CO1, CO3, ND2, ND4L, and ND6) for almost all nematoceran flies, especially used for ND2, ATP8, ND3, and ND6. However, another two conventional start codons ATA (Met) and ATC (Ile) are found in a minority of the nematoceran species. GTG (Val), TCG (SerUCN) and TTG (LeuUUR) are used for ND5, CO1 and ND1 respectively in most species. CCG (Pro) is identified as the start codon for CO1 in C. arakawae (Ceratopogonidae) and Dixella sp. (Dixidae). TTA (LeuUUR) is the start codon of CO3 in R. pomum (Cecidomyiidae) (Fig 2, S6 Table).


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)

Start and stop codons usage in nematoceran mt genomes.a: Start codons usage of PCGs in Nematocera; b: Stop codons usage of PCGs in Nematocera.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0158167.g002: Start and stop codons usage in nematoceran mt genomes.a: Start codons usage of PCGs in Nematocera; b: Stop codons usage of PCGs in Nematocera.
Mentions: Among all sequenced nematoceran flies, the most commonly used start codons are the canonical start codons ATN (Met/Ile), found in every PCG. Among them, ATG (Met) and ATT (Ile) are the mostly common used start codons. ATG (Met) is used in ATP6, CO2, CO3, CYTB, ND4 and ND4L for almost all nematoceran flies. This pattern is also observed in cyclorrhaphan flies [56]. ATT (Met) is found in 10 of the 13 PCGs (ATP6, ATP8, CO1, CO3, ND2, ND4L, and ND6) for almost all nematoceran flies, especially used for ND2, ATP8, ND3, and ND6. However, another two conventional start codons ATA (Met) and ATC (Ile) are found in a minority of the nematoceran species. GTG (Val), TCG (SerUCN) and TTG (LeuUUR) are used for ND5, CO1 and ND1 respectively in most species. CCG (Pro) is identified as the start codon for CO1 in C. arakawae (Ceratopogonidae) and Dixella sp. (Dixidae). TTA (LeuUUR) is the start codon of CO3 in R. pomum (Cecidomyiidae) (Fig 2, S6 Table).

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.