Dataset Information

Complete mitochondrial genome of the endangered flower chafer Osmoderma opicum (Coleoptera: Scarabaeidae).

ABSTRACT: The flower chafer Osmoderma opicum (Coleoptera: Scarabaeidae) has been listed in Korea as a class II endangered wild species. The 15?341-bp complete mitochondrial genome (mitogenome) of the species consists of a typical set of genes (13 protein-coding genes [PCGs], two rRNA genes and 22 tRNA genes) and the A?+?T-rich region, with an arrangement typical of insects. The 761-bp long A?+?T-rich region of O. opicum has a microsatellite-like sequence consisting of (TA)₆, along with a poly-T (12?bp) and a poly-A (16?bp) stretch, but does not have a longer repeat sequence often found in other Scarabaeidae. Twelve PCGs started with the typical ATN codon, whereas the COI started with AAC, which has been designated as the start codon for the coleopteran suborder Polyphaga. Phylogenetic analysis using 11 PCGs from Scarabaeidae showed that O. opicum was placed as the sister to the within-subfamilial species Myodermum sp., forming the monophyletic group, the subfamily Cetoniinae, with moderate to high nodal support.

SUBMITTER: Kim MJ

PROVIDER: S-EPMC7799465 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature

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Complete mitochondrial genome of the endangered flower chafer Osmoderma opicum (Coleoptera: Scarabaeidae).

Kim Min Jee MJ Jeong Su Yeon SY Jeong Jong-Chul JC Kim Sung-Soo SS Kim Iksoo I

Mitochondrial DNA. Part B, Resources 20160210 1

The flower chafer Osmoderma opicum (Coleoptera: Scarabaeidae) has been listed in Korea as a class II endangered wild species. The 15 341-bp complete mitochondrial genome (mitogenome) of the species consists of a typical set of genes (13 protein-coding genes [PCGs], two rRNA genes and 22 tRNA genes) and the A + T-rich region, with an arrangement typical of insects. The 761-bp long A + T-rich region of O. opicum has a microsatellite-like sequence consisting of (TA)6, along ...[more]

PMID: 33473440

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Project description:BackgroundThe coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts.MethodsSequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitogenome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes.ResultsThe complete circular mitogenome of O. rhinoceros is 20,898 bp in length, with a gene content canonical for insects (13 PCGs, two rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lineages in the Scarabaeidae. In silico PCR-RFLP analysis recovered the correct fragment set that is diagnostic for the CRB-G haplogroup. These results validate the high-quality of the O. rhinoceros mitogenome sequence and annotation.

Dataset Information

Complete mitochondrial genome of the endangered flower chafer Osmoderma opicum (Coleoptera: Scarabaeidae).

Publications

Complete mitochondrial genome of the endangered flower chafer <i>Osmoderma opicum</i> (Coleoptera: Scarabaeidae).

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