Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia

Meganathan, P. R.; Dubey, Bhawna; Batzer, Mark A.; Ray, David A.; Haque, Ikramul

doi:10.1016/j.gene.2011.01.012

Cited by 26 publications

(25 citation statements)

References 54 publications

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“…The Ka/Ks ratio is a measure of selective pressures acting on gene that indicates neutral mutation (ka/ks = 1), negative or purifying selection (Ka/Ks of <1), and positive or diversifying selection (Ka/Ks of >1) [38], [39]. Here, nad 2 showed the highest ratio, followed by nad 3, while cox 1 appeared to have the lowest ratio (Figure 2).…”

Section: Resultsmentioning

confidence: 97%

Mitochondrial Genome of the Eyeworm, Thelazia callipaeda (Nematoda: Spirurida), as the First Representative from the Family Thelaziidae

Gasser

Otranto

et al. 2013

PLoS Negl Trop Dis

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Human thelaziosis is an underestimated parasitic disease caused by Thelazia species (Spirurida: Thelaziidae). The oriental eyeworm, Thelazia callipaeda, infects a range of mammalian definitive hosts, including canids, felids and humans. Although this zoonotic parasite is of socio-economic significance in Asian countries, its genetics, epidemiology and biology are poorly understood. Mitochondrial (mt) DNA is known to provide useful genetic markers to underpin fundamental investigations, but no mt genome had been characterized for any members of the family Thelaziidae. In the present study, we sequenced and characterized the mt genome of T. callipaeda. This AT-rich (74.6%) mt genome (13,668 bp) is circular and contains 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes, but lacks an atp8 gene. All protein-coding genes are transcribed in the same direction; the gene order is the same as those of Dirofilaria immitis and Setaria digitata (Onchocercidae), but distinct from Dracunculus medinensis (Dracunculidae) and Heliconema longissimum (Physalopteridae). Phylogenetic analyses of the concatenated amino acid sequence data for all 12 protein-coding genes by Bayesian inference (BI) showed that T. callipaeda (Thelaziidae) is related to the family Onchocercidae. This is the first mt genome of any member of the family Thelaziidae and should represent a new source of genetic markers for studying the epidemiology, ecology, population genetics and systematics of this parasite of humans and other mammals.

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Section: Resultsmentioning

confidence: 97%

Mitochondrial Genome of the Eyeworm, Thelazia callipaeda (Nematoda: Spirurida), as the First Representative from the Family Thelaziidae

Gasser

Otranto

et al. 2013

PLoS Negl Trop Dis

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“…Interestingly, heat map analyses show that dipterans exhibit similar patterns of synonymous codon usage for particular amino acids and prefer codons ending with A/T over G/C. Studies of animal and plant mtgenomes suggest that codon usage bias is influenced by strong mutational and weak selection pressures [52][53][54], which suggest that mtgenomes within Diptera are under the influence of these pressures. However, this interpretation needs to be studied in detail to reveal the specifics.…”

Section: Structure and Organization Of The P Regina And S Crassipalmentioning

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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“…mtDNA sequences have been extensively used as genetic markers not only for studying population or ecological genetics, but also for phylogenetic, phylogeographical and evolutionary analyses, due to its conservation in protein-coding sequences, rapid evolutionary rate, and lack of genetic recombination (eg., Lei et al, 2010;Lin et al, 2011;Xie et al, 2011;Zhou et al, 2011). Comparison of complete mitochondrial sequences can reveal information about gene order and its variation, as well as gene and genome evolution (Meganathan et al, 2011;Uda et al, 2011). In spite of the availability of advanced DNA technologies, there is still a paucity of knowledge of the mt genomes for many parasitic nematodes of public health significance, such as A. lumbricoides, which is a major nematode species that parasitizes humans.…”

Section: Introductionmentioning

confidence: 99%

Comparative analyses of the complete mitochondrial genomes of Ascaris lumbricoides and Ascaris suum from humans and pigs

Song

et al. 2012

Gene

107

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Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia

Cited by 26 publications

References 54 publications

Mitochondrial Genome of the Eyeworm, Thelazia callipaeda (Nematoda: Spirurida), as the First Representative from the Family Thelaziidae

Mitochondrial Genome of the Eyeworm, Thelazia callipaeda (Nematoda: Spirurida), as the First Representative from the Family Thelaziidae

A 454 sequencing approach to dipteran mitochondrial genome research

Comparative analyses of the complete mitochondrial genomes of Ascaris lumbricoides and Ascaris suum from humans and pigs

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