https://orcid.org/0000-0002-5838-8429
Abstract
The chinaberry yellow-banded longhorn beetle, Anoplophora horsfieldi Hope 1842 (Coleoptera: Cerambycidae) is an important pest on many economic tree species. In this study, the complete mitochondrial genome of A. horsfieldi was determined, which was 15,837 bp in length and contained 37 genes, including 13 protein-coding genes (PCGs), two rRNA, 22 tRNA genes, and a non-coding A + T-rich region. The phylogenetic analysis based on mitochondrial genomes showed that A. horsfieldi is sister to a clade formed by A. chinensis and A. glabripennis.
The chinaberry yellow-banded longhorn beetle, Anoplophora horsfieldi Hope 1842 (Coleoptera: Cerambycidae), is widely distributed in south China, Vietnam and India. It is an important pest on many economic tree species (Hua et al. Citation2009; Wang Citation2014). Here, we sequenced and annotated the complete mitochondrial genome of A. horsfieldi. The studied adult specimen was collected from Wenjiang District, Chengdu City, Sichuan Province, China (N30°41′47″, E103°50′45″) in 20 June 2020 and deposited at The Insect Specimen Room of Chengdu Academy of Agricultural and Forestry Sciences (http://www.cdnky.com/, Bo-Long Zhang and [email protected]) under the voucher no. D015016.1. Genomic DNA was extracted from A. horsfieldi legs using 2xCTAB method, and then sequenced using the Illumina NovaSeq platform. The Illumina sequencing generated 44 million of high-quality 150 bp paired-end reads, which were mapped to the published A. chinensis mitochondrial genome as the reference using mummer v3.1 (Kurtz et al. Citation2004). Then, A5-miseq v20150522 (Coil et al. Citation2014) and SPAdes v3.9.0 (Bankevich et al. Citation2012) were employed to assemble these reads into complete mitochondrial genome, of which the protein-coding genes (PCGs), transfer RNA genes (tRNAs), and ribosomal RNA genes (rRNAs) were predicted using the MITOZ software (https://github.com/linzhi2013/MitoZ) (Meng et al. Citation2019).
The circular mitochondrial genome of A. horsfieldi was 15,837 bp in length (GenBank accession number MW364565), and the nucleotide composition was significantly AT-biased (A: 39.65%, G: 12.44%, C: 8.16%, and T: 39.75%). The AT-skew and GC-skew of this genome were −0.001 and 0.207, respectively. The genome consisted of 37 genes, including 13 PCGs, two rRNAs, 22 tRNAs, and a non-coding A + T-rich region. Twenty-three genes were transcribed on the J-strand, whereas the others were oriented on the N-strand. The PCGs used four different start codons: ATT, ATG, ATA, or ATC, and two stop codons: TAA or TAG, except that ND4 and ND5 ended with TA, T completed by post transcriptional addition of 3′ A residues. The gene arrangement of A. horsfieldi mitochondrial genome was identical to that of other coleopterans. In order to validate the phylogenetic position of A. horsfieldi, the mitochondrial genomes of 13 representatives of the family Cerambycidae were used to construct a maximum-likelihood (ML) tree with Aclees cribratus (Curculionidae) as the outgroup. The nucleotide sequences of the 13 PCGs, aligned and concatenated in PhyloSuite v1.2.2 (Zhang et al. Citation2020) were used to perform the ML inference in IQ-TREE Multicore version 1.6.12 (Gao et al. Citation2018). The result indicated that A. horsfieldi is sister to a clade formed by A. chinensis and A. glabripennis ().
Figure 1. Maximum-likelihood phylogenetic analysis of 13 species of Cerambycidae and Aclees cribratus as outgroup based on the nucleotide sequences of the 13 PCGs from the mitochondrial genomes by IQ-TREE multicore version 1.6.12 under GTR + R6 model for 5000 ultrafast bootstraps and 5000 SH-aLRT test. Bootstrap values were shown next to nodes. GenBank accession numbers of each species were listed in the tree.
Disclosure statement
The authors report no conflicts of interest and are solely responsible for this paper. There are no relevant financial or non-financial competing interests to report.
Data availability statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession no. MW364565. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA693416, SRR13508141, and SAMN17386627, respectively.
Additional information
Funding
References
- Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477.
- Coil D, Jospin G, Darling AE. 2014. A5-MiSeq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics. 31(4):587–589.
- Gao FL, Shen JG, Liao FR, Cai W, Lin SP, Yang HK, Chen SL. 2018. The first complete genome sequence of narcissus latent virus from Narcissus. Arch Virol. 163:1383–1386.
- Hua LZ, Nara H, Saemulson GA, Steven WL. 2009. Iconography of Chinese longicorn beetles (1406 species) in color. Vol. 197. Guangzhou: Sun Yat-sen University Press; p. 336.
- Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5(2):R12.
- Meng GL, Li YY, Yang CT, Liu SL. 2019. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Res. 47(11):e63.
- Wang ZC. 2014. Monographia of original colored longicorn beetles of China (basics volume 1). Beijing: Scientific and Technical Documentation Press; p. 587.
- Zhang D, Gao FL, Jakovlic I, Zou H, Zhang J, Li WX, Wang GT. 2020. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 20(1):348–355.