Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera

Meganathan, P. R.; Pagán, Heidi J. T.; McCulloch, Eve S.; Stevens, Richard D.; Ray, David A.

doi:10.1016/j.gene.2011.10.038

Cited by 66 publications

(44 citation statements)

References 65 publications

(68 reference statements)

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“…The accurate annotated mitochondrial genome sequence was submitted to GenBank with accession number MF438265. The arrangement of the multiple genes is in line with other Soricidae species (Nikaido et al 2001;Fontanillas et al 2005;Huang et al 2014Huang et al , 2016Xu et al 2016) and most mammals (Meganathan et al 2012;Xu et al 2012Xu et al , 2013Yoon et al 2013).…”

Section: Introductionsupporting

confidence: 69%

Sequencing and analysis of the complete mitochondrial genome of the Ussuri shrew (Sorex mirabilis) from China

Zhu

Xin-Min

Jin

et al. 2017

Mitochondrial DNA Part B

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Section: Introductionsupporting

confidence: 69%

Sequencing and analysis of the complete mitochondrial genome of the Ussuri shrew (Sorex mirabilis) from China

Zhu

Xin-Min

Jin

et al. 2017

Mitochondrial DNA Part B

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“…The accurate annotated mitochondrial genome sequence was submitted to GenBank with accession number MG983792. The arrangement of the multiple genes is in line with other Soricidae species (Nikaido et al 2001;Fontanillas et al 2005;Xu et al 2012Xu et al , 2013Xu et al , 2016Huang et al 2014Huang et al , 2016Jin et al 2017;Liu, Tian, Jin, Dong, et al 2017;Liu, Wang, et al 2017) and most mammals (Meganathan et al 2012;Yoon et al 2013;Xu et al 2012Xu et al , 2013.…”

supporting

confidence: 62%

Sequencing and analysis of the complete mitochondrial genome of the taiga shrew (Sorex isodon) from China

Zhu

Wei

Ao-Nan

et al. 2018

Mitochondrial DNA Part B

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“…Although, this type of megaBLAST-based mtgenome assembly has been utilized previously [13,15], we compared the megaBLAST-based assembly method with a common de novo assembly approach. Thus, we assembled the 454 survey sequencing data of C. hominivorax using Sequencher 4.7 (Gene Codes Corp.) assembler following the same assembly parameters as used for megaBLAST based sequence assembly (match size -12 and minimum match percentage -70).…”

Section: Mtgenome Assembly Methodology Considerationmentioning

confidence: 99%

“…The Illumina sequencing technology has already been shown to be useful for generating insect mtgenomes without using conventional PCRs and cloning techniques [7,8]. The 454 sequencing approach has also been utilized to generate mtgenomes for some species [9][10][11][12][13]. However, this approach has only been attempted in two dipterans [14,15] and the authors of both the studies used PCR and Sanger's sequencing to assemble the complete mtgenome sequences from 454 data.…”

Section: Introductionmentioning

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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Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera

Cited by 66 publications

References 65 publications

Sequencing and analysis of the complete mitochondrial genome of the Ussuri shrew (Sorex mirabilis) from China

Sequencing and analysis of the complete mitochondrial genome of the Ussuri shrew (Sorex mirabilis) from China

Sequencing and analysis of the complete mitochondrial genome of the taiga shrew (Sorex isodon) from China

A 454 sequencing approach to dipteran mitochondrial genome research

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