Cargando…

The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing

BACKGROUND: The 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 invas...

Descripción completa

Detalles Bibliográficos
Autores principales: Filipović, Igor, Hereward, James P., Rašić, Gordana, Devine, Gregor J., Furlong, Michael J., Etebari, Kayvan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7811291/
https://www.ncbi.nlm.nih.gov/pubmed/33520439
http://dx.doi.org/10.7717/peerj.10552
_version_ 1783637466418249728
author Filipović, Igor
Hereward, James P.
Rašić, Gordana
Devine, Gregor J.
Furlong, Michael J.
Etebari, Kayvan
author_facet Filipović, Igor
Hereward, James P.
Rašić, Gordana
Devine, Gregor J.
Furlong, Michael J.
Etebari, Kayvan
author_sort Filipović, Igor
collection PubMed
description BACKGROUND: The 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. METHODS: Sequencing 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. RESULTS: The 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.
format Online
Article
Text
id pubmed-7811291
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher PeerJ Inc.
record_format MEDLINE/PubMed
spelling pubmed-78112912021-01-28 The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing Filipović, Igor Hereward, James P. Rašić, Gordana Devine, Gregor J. Furlong, Michael J. Etebari, Kayvan PeerJ Computational Biology BACKGROUND: The 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. METHODS: Sequencing 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. RESULTS: The 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. PeerJ Inc. 2021-01-13 /pmc/articles/PMC7811291/ /pubmed/33520439 http://dx.doi.org/10.7717/peerj.10552 Text en © 2021 Filipović et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Computational Biology
Filipović, Igor
Hereward, James P.
Rašić, Gordana
Devine, Gregor J.
Furlong, Michael J.
Etebari, Kayvan
The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing
title The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing
title_full The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing
title_fullStr The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing
title_full_unstemmed The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing
title_short The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing
title_sort complete mitochondrial genome sequence of oryctes rhinoceros (coleoptera: scarabaeidae) based on long-read nanopore sequencing
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7811291/
https://www.ncbi.nlm.nih.gov/pubmed/33520439
http://dx.doi.org/10.7717/peerj.10552
work_keys_str_mv AT filipovicigor thecompletemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT herewardjamesp thecompletemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT rasicgordana thecompletemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT devinegregorj thecompletemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT furlongmichaelj thecompletemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT etebarikayvan thecompletemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT filipovicigor completemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT herewardjamesp completemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT rasicgordana completemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT devinegregorj completemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT furlongmichaelj completemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing
AT etebarikayvan completemitochondrialgenomesequenceoforyctesrhinoceroscoleopterascarabaeidaebasedonlongreadnanoporesequencing