Structure and evolution of the mitochondrial genomes of Haematobia irritans and Stomoxys calcitrans: The Muscidae (Diptera: Calyptratae) perspective

Oliveira, Marcos T.; Barau, Joan; Junqueira, Ana Carolina M.; Feijão, Pedro; Rosa, Aline Coelho da; Abreu, Cristina Feix; Azeredo-Espin, Ana Maria Lima de; Lessinger, Ana Cláudia

doi:10.1016/j.ympev.2008.05.022

Cited by 55 publications

(38 citation statements)

References 67 publications

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“…In most metazoan mt genomes, the strand skew biases are found to be weakly positive AT-skew and strongly negative GC-skew for the J-strand. This pattern is consistent across most cyclorrhaphan mt genomes except in three species: Simosyrphus grandicornis (Syrphidae) [12], Spanicelyphus pilosus (Celyphidae, present study) and Stomoxys calcitrans (Muscidae) [31], which have negative AT-skew on the J-strand (Table S1). Three other insect families: Philopteridae (Phthiraptera), Aleyrodidae (Hemiptera) and Braconidae (Hymenoptera)have been found with positive GC-skew and negative AT-skew on the J-strand [55], and a strongly positive AT-skew on the J-strand was detected in Isoptera [56].…”

Section: Base Compositionsupporting

confidence: 80%

“…Most sequenced mt genomes of other cyclorrhaphan flies present a positive AT-Skew for the J-strand with an average of 0.032 (except for in Stomoxys calcitrans (-0.001) [31] and in Simosyrphus grandicornis (-0.004) [12]), ranging from -0.004 (Simosyrphus grandicornis, Syrphidae [12]) to 0.131 (Bactrocera minax, Tephritidae [20]). While, the AT-skew of the lauxanioid mt genomes were relatively low, ranging from -0.009 (Spanicelyphus pilosus, Celyphidae, present study) to 0.007 (Cestrotus liui, Lauxaniidae, present study).…”

Section: Base Compositionmentioning

confidence: 99%

“…While, the AT-skew of the lauxanioid mt genomes were relatively low, ranging from -0.009 (Spanicelyphus pilosus, Celyphidae, present study) to 0.007 (Cestrotus liui, Lauxaniidae, present study). The average GC-skew of other cyclorrhaphan mt genomes was -0.190, ranging from -0.315 (Bactrocera minax, Tephritidae [20]) to -0.124 (Haematobia irritans, Muscidae [31]), while the GC-skew of the lauxanioid mt genomes which ranges from -0.159 (Cestrotus liui, Lauxaniidae, present study) to -0.174 (Spanicelyphus pilosus, Celyphidae, present study) were average amongst reported cyclorrhaphan flies ( Figure 3). In most metazoan mt genomes, the strand skew biases are found to be weakly positive AT-skew and strongly negative GC-skew for the J-strand.…”

Section: Base Compositionmentioning

confidence: 99%

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Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha)

Ding

et al. 2017

Preprint

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Abstract:The superfamily Lauxanioidea is a significant dipteran clade including over 2500 known species in three families: Lauxaniidae, Celyphidae and Chamaemyiidae. We sequenced the first five (three complete and two partial) lauxanioid mitochondrial (mt) genomes, and used them to reconstruct the phylogeny of this group. The lauxanioid mt genomes are typical of the Diptera, containing all 37 genes usually present in bilaterian animals. A total of three conserved intergenic sequences have been reported across the Cyclorrhapha. The inferred secondary structure of 22 tRNAs suggested five substitution patterns among the Cyclorrhapha. The control region in the Lauxanioidea has apparently evolved very fast, but four conserved structural elements were detected in all three complete mt genome sequences. Phylogenetic relationships based on the mt genome data were inferred by Maximum Likelihood and Bayesian methods. The traditional relationships between families within the Lauxanioidea, (Chamaemyiidae + (Lauxaniidae + Celyphidae)), was corroborated, however, the higher level relationships between cyclorrhaphan superfamilies are mostly poorly supported.

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Section: Base Compositionsupporting

confidence: 80%

Section: Base Compositionmentioning

confidence: 99%

Section: Base Compositionmentioning

confidence: 99%

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Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha)

Ding

et al. 2017

Preprint

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“…Complete mtgenome sequences were available for C. hominivorax and H. irritans via Lessinger et al [32] and Oliveira et al [45], respectively. We compared these with the newly obtained sequences to check the reliability of mtgenome sequences generated through our 454 sequencing approach.…”

Section: Reliability Of 454 Sequencing Data To Generate Mtgenomes Of mentioning

confidence: 99%

A 454 sequencing approach to dipteran mitochondrial genome research

et al. 2015

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The availability of complete mitochondrial genome (mtgenome) data for Diptera, one of the largest metazoan orders, in public databases is limited. The advent of high throughput sequencing technology provides the potential to generate mtgenomes for many species affordably and quickly. However, these technologies need to be validated for dipterans as the members of this clade play important economic and research roles. Illumina and 454 sequencing platforms are widely used in genomic research involving non-model organisms. The Illumina platform has already been utilized for generating mitochondrial genomes without using conventional long range PCR for insects whereas the power of 454 sequencing for generating mitochondrial genome drafts without PCR has not yet been validated for insects. Thus, this study examines the utility of 454 sequencing approach for dipteran mtgenomic research. We generated complete or nearly complete mitochondrial genomes for Cochliomyia hominivorax, Haematobia irritans, Phormia regina and Sarcophaga crassipalpis using a 454 sequencing approach. Comparisons between newly obtained and existing assemblies for C. hominivorax and H. irritans revealed no major discrepancies and verified the utility of 454 sequencing for dipteran mitochondrial genomes. We also report the complete mitochondrial sequences for two forensically important flies, P. regina and S. crassipalpis, which could be used to provide useful information to legal personnel. Comparative analyses revealed that dipterans follow similar codon usage and nucleotide biases that could be due to mutational and selection pressures. This study illustrates the utility of 454 sequencing to obtain complete mitochondrial genomes for dipterans without the aid of conventional molecular techniques such as PCR and cloning and validates this method of mtgenome sequencing in arthropods.

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“…The remaining two protein-coding genes ND1 and COI started with 'GTG' and the special quadruplet start codon of 'ATCA', respectively, which corresponded to that of L. trifolii. Besides, COI initiation codons were usually found to use nonstandard start codons in insects and included 'TCG', 'CCG', 'ACC', 'CGA', 'CTA', 'AAA', 'ATG', 'ATTA'and 'ATTTAA' (Sheffield et al, 2008;Fenn et al, 2007;Oliveira et al, 2008;Krzywinski et al, 2006;Yu et al, 2007;Flook et al, 1995;Beard et al, 1993). Consequently, the potential initiation site of COI gene in most species was dependent on the translated amino acid sequence and aligned sequence analysis.…”

Section: Protein-coding Genesmentioning

confidence: 99%

The complete mitochondrial genome of the leafminer Liriomyza sativae (Diptera: Agromyzidae): Great difference in the A+T-rich region compared to Liriomyza trifolii

Yang

Wang

et al. 2011

Gene

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Structure and evolution of the mitochondrial genomes of Haematobia irritans and Stomoxys calcitrans: The Muscidae (Diptera: Calyptratae) perspective

Cited by 55 publications

References 67 publications

Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha)

Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha)

A 454 sequencing approach to dipteran mitochondrial genome research

The complete mitochondrial genome of the leafminer Liriomyza sativae (Diptera: Agromyzidae): Great difference in the A+T-rich region compared to Liriomyza trifolii

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