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

Abstract

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.

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

“…7). By contrast, Stegobium paniceum had 70 SSRs (Park et al 2022b), S. furcifera had 101 and 103 SSRs (Park et al, 2021e), and Figulus binodulus had only 50 SSRs (Lee et al 2020b). Eight normal, seven extended, and 45 potential SSRs were also detected in the two partial Melanoplus mitochondrial genomes (GenBank accession Nos.…”

“…Simple sequence repeats (SSRs) were identified on the mitochondrial genome sequence with the SSR database pipeline utilized in previous studies (Choi et al 2021; Kim et al 2019; Kim et al 2021e; Park et al 2020c; Park et al 2022a). We conducted this analysis according to usual definition of an SSR on the circular genome (mitochondria and chloroplast): monoSSR (1 bp), hexaSSR (6 bp), and decaSSR (10 bp) (Lee et al 2020b; Park et al, 2021e).…”

The complete chloroplast genome of Campsis grandiflora (Bignoniaceae)

“…Simple sequence repeats (SSRs) were identified on the chloroplast genome sequence using the pipeline of the SSR database (SSRDB; http://ssrdb.infoboss.co.kr/) which has been utilized in several organelle genomic studies (Lee et al, 2020;Choi et al, 2021;Park et al, 2021dPark et al, , 2022. The SSR is conventionally recognized as the nucleotide array composed of repeats with one or up to six base pair units.…”

The complete mitochondrial genome of Aclees taiwanensis Kôno, 1933 (Coleoptera: Curculionidae)

“… 2021 ), and Stegobium paniceum (Linnaeus, 1761) (Coleoptera: Ptinidae; Anobiinae) (Park et al. 2022 ).…”