Characterization of the mitochondrial genome of the lawn cutworm Spodoptera depravata (Lepidoptera: Noctuidae)

Abstract

The lawn cutworm, Spodoptera depravata, is one of the most important pests that causes economic damage to grass crops. This study reports the complete mitochondrial genome of an S. depravata sample collected in China. The genome is a circular molecule 15,460 bp in length with an overall A + T content of 81.6%. It contains 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The gene content and organization of the mitogenome of S. depravata are identical to those of other Spodoptera species. Maximum-likelihood phylogenetic analysis based on mitogenomes showed a close evolutionary relationship between S. depravata and S. exempta. This study provides new molecular data for the identification and further phylogenetic analyses of Spodoptera species.

Keywords:

• Spodoptera depravata
• mitochondrial genome
• phylogenetic analysis
• Noctuidae

Introduction

The lawn cutworm, Spodoptera depravata (Butler, 1879), is a major lepidopteran pest exclusively distributed in northeastern Asian countries, such as China, Japan, and the Republic of Korea (Oku et al. 1978; Kang et al. 2004). The larvae of S. depravata attack the linear leaves of Gramineae crops, resulting in yellowish grasses and brown patches on the ground (Kang et al. 2004). Previous studies on this pest have focused on ecological research, including their flight activity, reproductive capacity, life cycle, and control methods (Saito 2000; Qian et al. 2003; Huang et al. 2004; Huang and Xu 2004; Zhou et al. 2008). To date, few molecular biological studies of this pest have been conducted. As a member of the Spodoptera genus of moths, which includes pest insects comprising approximately 30 species, S. depravata causes severe damage to multiple agricultural crop species globally (Kergoat et al. 2021). The comprehensive identification and phylogenetic analysis of this genus will help clarify the relationships between different species and help prevent potential crop damage. However, mitochondrial genome data have been published for only five species of Spodoptera, and the genetic relationship between species requires more in-depth investigation. In this study, the complete mitochondrial genome of S. depravata (Figure 1) was sequenced.

Figure 1. Species reference image of Spodoptera depravata. The image is referenced from the Bold Systems (Ratnasingham and Hebert 2007). Sample ID is SDNU-INS-04111. This figure is attribution noncommercial sharing. http://v3.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxon=Spodoptera+depravata&searchTax=.

Materials

The S. depravata sample used in this study was a moth collected from Changchun (43°48′38″N, 125°24′14″E), Jilin Province, China in 2020. The specimen was initially identified as belonging to the genus Spodoptera, based on its morphological appearance (Chen 1999), and was further identified as S. depravata based on the mitochondrial cytochrome oxidase subunit 1 (COI) sequence (Folmer et al. 1994). A nucleotide BLAST search in GenBank showed that the COI sequence of the specimen had 99.51–100.00% sequence similarity with the COI sequence of S. depravata. The phylogenetic tree constructed using the neighbor-joining method also showed that the specimen was grouped with S. depravata samples, including three previously published samples (Watabiki et al. 2013; Kergoat et al. 2021). The voucher specimen and DNA were deposited at the Agricultural Genomics Institute in Shenzhen, China (https://www.agis.org.cn/, contact Lei Zhang, [email protected]) under voucher number AGIS-SD-202011.

Methods

Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Cat. no. 69506; Qiagen, Hilden, Germany). DNA quality and concentration were determined using a NanoDrop One UV-Vis spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). A total of 0.5 μg of genomic DNA was used to construct a library with a 350 bp insert size. The library was sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA) with 150 bp paired-end reads, resulting in a total of 144,834,262 reads (the percentage of reads with ≥ Q30 score was 95.88%). Moreover, we further evaluated the sequencing depth of mitochondrial genome using mosdepth software (Pedersen and Quinlan 2018).

The complete mitochondrial genome sequence was assembled using the software NOVOPlasty v2.5.6 (Dierckxsens et al. 2017), and the mitogenome was annotated using MITOS2 (http://mitos2.bioinf.uni-leipzig.de/index.py) (Donath et al. 2019). A mitochondrial genome map of S. depravata was generated using OGDRAW v1.3.1 software (Greiner et al. 2019). Multiple mitochondrial genome sequence alignments were conducted using MAFFT v7.455 (Katoh and Standley 2013). A phylogenetic tree was constructed based on the maximum-likelihood method using the best-fit model (GTR + F+I + G4) estimated using IQ-TREE v1.6.10 (Nguyen et al. 2015). One thousand bootstrap replicates were used, and the tree was visualized using iTol v6.5.2 (https://itol.embl.de/).

Results

The mitogenome of S. depravata (GenBank Accession Number OK053108) is a circular molecule 15,460 bp in length, with an A + T content of 81.6%. The mitogenome consensus sequence average coverage was 5866× (Figure S1). However, the differences in length between species are primarily in the non-coding regions. The mitogenome encodes a standard set of 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, and 22 transfer RNAs, and a control region (Figure 2). All 13 PCGs begin with ATN codons, except for cox1, which begins with CGA. Most PCGs are terminated with TAA or TAG stop codons, except for three genes (cox1, cox2, and nad4), which have an incomplete stop codon (T), as seen in S. exempta and S. littoralis. In contrast, five genes (nad2, cox1, cox2, nad3, and nad4) have incomplete stop codons (T) in S. exigua, S. frugiperda, and S. litura. Twenty-two complete mitogenomes (21 lepidopteran species and one species from the family Erebidae) were used for phylogenetic analysis (Figure 3). The phylogenetic tree showed that all six Spodoptera species formed a clade, in which four species were clustered into one branch ([{S. littoralis + S. litura} + S. frugiperda] + S. exigua), which is consistent with the findings of previous studies (Li, Wang, Xiao, et al. 2021). The other branch consisted of S. depravata and S. exempta, indicating the close evolutionary relationship between S. depravata and S. exempta.

Figure 2. Gene map of S. depravata mitochondrial genome. Genes belonging to different functional groups are color-coded. Genes are shown outside and inside the outer circle are transcribed counterclockwise and clockwise, respectively. The grey in the inner circle corresponds to the GC% along the mitochondrion.

Figure 3. Phylogenetic tree of 21 lepidopteran species based on their mitochondrial genomes. Eudocima phalonia from the family Erebidae was used as the outgroup. The following sequences were used: Eudocima phalonia NC_032382.1 (Seo et al. 2019), Diachrysia nadeja MT916722.1 (Gao et al. 2021), Trichoplusia ni MK358044.1 (Zhao et al. 2022), Ctenoplusia albostriata NC_053742.1 (Xue et al. 2019), Helicoverpa assulta NC_014668.1 (Seo et al. 2019), Helicoverpa armigera NC_014668.1 (Yin et al. 2010), Spodoptera exempta NC_054179.1 (Li, Wang, Xiao, et al. 2021), Spodoptera exigua JX316220.1 (Wu et al. 2013), Spodoptera frugiperda MN385596.1 (Li, Wang, Xiao, et al. 2021), Spodoptera litura NC_022676.1 (Wan et al. 2013), Spodoptera littoralis MT816470.1 (Li, Wang, and Zhang 2021), Agrotis segetum KC894725.1 (Wu et al. 2014), Agrotis ipsilon KF163965 (Zhao et al. 2022), Athetis pallidipennis NC_046525.1 (Li, Wang, and Zhang 2021), Sesamia nonagrioides CM030612.1 (Muller et al. 2021), Sesamia inferens JN039362.1 (Wu et al. 2019), Anarta trifolii NC_046049.1 (Li, Wang, and Zhang 2021), Protegira songi NC_034938.1 (Guo et al. 2017), Mythimna loreyi NC_057500.1 (Nam et al. 2020), Mythimna separata KM099034.1 (Li, Wang, and Zhang 2021).

Discussion and conclusion

We assembled and annotated the first complete mitochondrial genome sequence of S. depravata, which is 15,460 bp in length. It is longer than the mitogenomes of the other five published Spodoptera species, which range from 15,365 to 15,457 bp (Wan et al. 2013; Wu et al. 2013; Seo et al. 2019; Li, Wang, and Zhang 2021; Li et al. 2021). The gene composition and gene order are the same for all six Spodoptera mitogenomes and are identical to those of the majority of lepidopteran species (Wan et al. 2013). We also conducted a phylogenetic analysis of the Spodoptera species. It provides useful information and lays a foundation for the subsequent genetic evolution and phylogenetic analyses of Spodoptera species.

Ethical approval

Spodoptera depravata is a common pest on grass crops in China. Therefore, no ethical approval or other relevant permission can be provided for the study.

Authors’ contributions

Xinyue Liang and Lei Zhang collected and identified the specimens; Xinyue Liang and Zaiyuan Li analyzed the data; Xinyue Liang wrote the manuscript; Lei Zhang and Zaiyuan Li revised the manuscript. Yutao Xiao conceived and designed the project, and finally approved the version to be published. All authors agree to be accountable for all aspects of the work.

Disclosure statement

No potential conflict of interest is reported by the author(s).

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 accession no. OK053108. The associated BioProject, BioSample, and SRA numbers are PRJNA809185, SAMN26149759, and SRS12076762 respectively.

Additional information

Funding

This work was supported by the Shenzhen Natural Science Foundation under Grant number [JCYJ20200109150629266]; the Science and Technology Innovation Program of the Chinese Academy of Agricultural and Sciences.