The complete mitochondrial genome of <i>Cervus canadensis</i> (Erxleben, 1777), as a model species of Chronic Wasting Disease (CWD)

Kim, Hyojin; Hwang, Jeong Hyun; Park, Kyung-Je; Park, Hoo-Chang; Kang, Hae‐Eun; Park, Jongsun; Sohn, Hyun‐Joo

doi:10.1080/23802359.2020.1780983

Cited by 4 publications

(3 citation statements)

References 15 publications

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“…Intraspecific variations such as SNPs and INDELs on the mitochondrial genomes were identified with the ‘Find variations/SNPs’ function in Geneious Prime® v. 2020.2.4 (Biomatters Ltd., Auckland, New Zealand). This application has been utilized in previous mitochondrial genomic studies (Kim et al 2020; Kim et al 2021a; Lee et al 2020a; Park et al 2019e). The INDELs were enumerated and continuous INDEL bases were considered a single INDEL region.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of the complete mitochondrial genome of Melanoplus differentialis (Acrididae: Melanoplinae) captured in Korea

Kim

Lee

et al. 2023

Entomological Research

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In this study, we determined the complete mitochondrial genome of the invasive insect species Melanoplus differentialis captured in Korea. The complete mitochondrial genome of M. differentialis is 15,625 bp long and comprises 13 protein‐coding genes, two ribosomal RNA genes, and 22 transfer RNAs, with a GC ratio of 25.2%. In total, 353 SNPs and 11 INDEL regions (total length 67 bp) were found against the previously sequenced M. differentialis mitochondrial genome recorded as public genome data. The number of interspecific variations was greater than the number of intraspecific variations in this insect. Phylogenetic tree analysis showed that the mitochondrial genome clustered the Melanoplus clade with two previously reported Melanoplus sequences. However, the sequences were not divided at the species‐level clade possibly as a consequence of misidentification caused by an error in the public database. Our results extend the molecular database status of Melanoplus by providing a novel complete mitochondrial genome sequence for M. differentialis that could serve as reference for further molecular studies.

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Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of the complete mitochondrial genome of Melanoplus differentialis (Acrididae: Melanoplinae) captured in Korea

Kim

Lee

et al. 2023

Entomological Research

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“…NGS raw reads of truffle (SRA accession: SRR5005499) were downloaded from NCBI and processed under the Genome Information System (GeIS, http://geis.infoboss.co.kr) which has been utilized in various genomics studies. 7–9,13,14,17,19,20,25–83 SRR5005499 dataset used in this study contains 29,010,538 100-bp-reads (2,901,053,800 bp). In the pipeline, de novo assembly and confirmation were done by Velvet v1.2.10…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The investigation of intraspecific characteristics and comparative analyses of the complete mitochondrial genome of Stegobium paniceum (Linnaeus, 1758) (Coleoptera: Ptinidae) assembled from public NGS raw reads of the black truffle, Tuber melanosporum

Park¹,

Lee²,

Park³

2022

Science Progress

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Due to the rapid development of NGS technologies, a huge amount of NGS raw reads have been accumulated in public repositories, such as the Short Read Archive of NCBI. We successfully rescued the complete mitochondrial genome of Stegobium paniceum, a drug store beetle, from public NGS raw reads of truffle generated from the whole genome project. The circular mitogenome of S. paniceum is 15,474 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 803 bp. Intraspecific transfer RNAs structure and sequence variations were investigated and simple sequence repeats identified from three S. paniceum mitochondrial genomes were compared showing their diversities as fundamental data to utilize them in various aspects including developing efficient molecular markers in the family, Ptinidae. Phylogenetic analysis of 23 Bostrichoidea mitochondrial genomes presented better species identification based on phylogenetic analyses and the optimal options for constructing phylogenetic trees based on Bostrichoidea mitochondrial genomes. Our results present not only utilization of public NGS raw read sequences but also intraspecific features of S. paniceum mitochondrial genomes and comparative analysis of Bostrichoidea mitochondrial genomes in various aspects.

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Cervidae antlers exploited to manufacture prehistoric tools and hunting implements as a reliable source of ancient DNA

Tejero,

Cheronet,

Gelabert

et al. 2024

Heliyon

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The complete mitochondrial genome of Cervus canadensis (Erxleben, 1777), as a model species of Chronic Wasting Disease (CWD)

Cited by 4 publications

References 15 publications

Comprehensive analysis of the complete mitochondrial genome of Melanoplus differentialis (Acrididae: Melanoplinae) captured in Korea

Comprehensive analysis of the complete mitochondrial genome of Melanoplus differentialis (Acrididae: Melanoplinae) captured in Korea

The investigation of intraspecific characteristics and comparative analyses of the complete mitochondrial genome of Stegobium paniceum (Linnaeus, 1758) (Coleoptera: Ptinidae) assembled from public NGS raw reads of the black truffle, Tuber melanosporum

Cervidae antlers exploited to manufacture prehistoric tools and hunting implements as a reliable source of ancient DNA

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