Filipović Igor, Hereward James P, Rašić Gordana, Devine Gregor J, Furlong Michael J, Etebari Kayvan
School of Biological Sciences, The University of Queensland, St. Lucia, Australia.
Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
PeerJ. 2021 Jan 13;9:e10552. doi: 10.7717/peerj.10552. eCollection 2021.
The coconut rhinoceros beetle (CRB, ) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, (OrNV), has successfully suppressed populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial 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.
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 mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from , 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.
The complete circular mitogenome of 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 and ) 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 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 mitogenome sequence and annotation.
椰心叶甲是亚洲和太平洋地区椰子及其他棕榈树的一种严重入侵害虫。生物防治剂椰心叶甲杆状病毒（OrNV）几十年来成功抑制了椰心叶甲种群数量，但2007年后新的椰心叶甲入侵开始出现。线粒体细胞色素氧化酶亚基I（COI）基因内的一个单核苷酸多态性变异用于区分最近入侵的CRB - G谱系与其他单倍型，但该物种缺乏线粒体基因组序列阻碍了针对椰心叶甲的生物安全和管理计划分子工具集的进一步开发。在此，我们报告椰心叶甲线粒体基因组的完整环状序列及注释，以支持此类工作。
使用长读长纳米孔技术从一只CRB - G雌性个体分离的基因组DNA中生成测序数据。线粒体基因组用Flye v.2.5进行组装，使用短读长Illumina序列通过Pilon去除同聚物，并使用MITOS进行注释。独立生成的转录组数据用于评估椰心叶甲线粒体基因组注释和转录情况。来自椰心叶甲、其他13个金龟子科分类单元和两个外类群分类单元的13个蛋白质编码基因（PCGs）（第三密码子位置简并）的比对序列用于在IQ - TREE中采用最大似然（ML）方法和在MrBayes中采用贝叶斯（BI）方法进行系统发育重建。
椰心叶甲完整的环状线粒体基因组长度为20,898 bp，具有昆虫典型的基因组成（13个PCGs、两个rRNA基因和22个tRNA基因），以及一个结构变异（trnW和trnC的重排）和一个长控制区（6,204 bp）。在所有37个基因中均检测到转录，有趣的是，在控制区的三个结构域内也有转录。ML和BI系统发育树具有相同的拓扑结构，正确地将椰心叶甲与另一个丽金龟亚科分类单元归为一组，并恢复了先前报道的金龟子科各谱系之间的关系。在计算机上进行的PCR - RFLP分析得到了对CRB - G单倍型具有诊断性的正确片段集。这些结果验证了椰心叶甲线粒体基因组序列和注释的高质量。
