Assembly and annotation of the first complete mitochondrial genome of Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae)

Year 2024, , 67 - 71, 02.08.2024

Payman Ehsas , Merve Aygün , Cengiz İkten , Hilal Şule Tosun

https://doi.org/10.29136/mediterranean.1494881

Abstract

The cotton mealybug, Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), is a significant economic pest with a global distribution. Despite the increasing volume of literature on mitochondrial genome sequencing, complete mitochondrial genome sequences have not been reported for P. solenopsis yet. Here, we assembled the complete mitochondrial genome of P. solenopsis using high throughput DNA sequencing technology. The genome is 14,831 bp in length and is comprised of 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The total length of all PCGs is 9,678 bp, accounting for 65.2% of the overall mitogenome. Among the PCGs, atp8 is the smallest gene (99 bp) and nad5 is the largest (1,593 bp). Of the 13 PCGs, seven (nad3, cox3, atp6, atp8, cox2, cox1, nad2) are encoded on the majority strand (J-strand), while six (nad1, nad6, cob, nad4L, nad4, nad5) are on the minority strand (N-strand). The analysis revealed a predominant A+T base composition, making up 90.3% of the total genome. However, the non-coding regulatory control region (CR) is missing due to the non-overlapping endpoints of the linear assembly. This assembly provides comprehensive information for investigating the evolutionary relationships between scale insects and for the precise identification of insects.

Keywords

Phenacoccus solenopsis, Mitochondrial genome assembly, High-throughput DNA sequencing

References

• Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution 69(2): 313-319. doi: org/10.1016/j.ympev.2012.08.023.
• Bushnell B (2020) BBDuk. Jt Genome Inst. Available online: https://jgi.doe.gov/data-and-tools/bbtools/bb-toolsuserguide/bbduk-guide. Accessed 10 May, 2024.
• Cameron SL (2014) Insect mitochondrial genomics: Implications for evolution and phylogeny. Annual Review of Entomology 59(1): 95-117. doi: org/10.1146/an- nurev-ento-011613-162007.
• Deng J, Lu C, Huang X (2019) The first mitochondrial genome of scale insects (Hemiptera: Coccoidea). Mitochondrial DNA Part B Resources 4: 2094-2095. doi: org/10.1080/23802359.2019.1622464.
• Domes K, Maraun M, Scheu S, Cameron SL (2008) The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: Genome rearrangements and loss of tRNAs. BMC Genomics 9: 532. doi: org/10.1186/1471-2164-9-532.
• Doyle JJ, Doyle JL (1987) A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue. Phytochemical Bulletin 19: 11-15.
• EPPO (2024) Statistical database. https://gd.eppo.int/taxon/PHENSO/distribution. Accessed 31 May, 2024.
• García Morales M, Denno BD, Miller DR, Miller GL, Ben Dov Y, Hardy NB (2016) ScaleNet: a literature-based model of scale insect biology and systematics. Database doi: org/10.1093/database/bav118, https://scalenet.info/. Accessed 25 May, 2024.
• Girardot C, Scholtalbers J, Sauer S, Su SY, Furlong, EE (2016) Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinformatics 17: 419. doi: org/10.1186/s12859-016-1284-2.
• Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Research 36(2): 181-184. doi: org/10.1093/nar/gkn179.
• Gullan PJ, Cook LG (2007) Phylogeny and higher classification of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea). Zootaxa 1668: 413-425.
• Han Xu, Xiaochen Liu, Hu L, Sanan Wu (2021) The mitogenome of the scale insect Didesmococcus koreanus Borchsenius, 1955 (Coccoidea: Coccidae). Mitochondrial DNA Part B 6(4): 1298-1299.
• Lavrov DV, Brown WM, Boore JL (2000) A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proceedings of the National Academy of Sciences 97(25): 13738-13742. doi: org/10.1073/pnas.250402997.
• Li D, Liu C, Luo R, Sadakane K, Lam T (2015) Application note MEGAHIT: an ultra-fast single-node solution for large and com- plex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31(10): 1674-1676.
• Lu C, Huang X, Deng J (2020) The challenge of Coccidae (Hemiptera: Coccoidea) mitochondrial genomes: The case of Saissetia coffeae with novel truncated tRNAs and gene rearrangements. International Journal of Biological Macromolecules 158: 854-864. doi: org/10.1016/j.ijbiomac.2020.04.257.
• Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal 17: 10-12. doi: org/10.14806/ej.17.1.200.
• Nurk S, Meleshko D, Korobeynikov A, Pevzner PA (2017) metaSPAdes: a new versatile metagenomic assembler. Genome Research 27(5): 824-834. doi: org/10.1101/gr.213959.116.
• Segovia R, Pett W, Trewick S, Lavrov DV (2011) Extensive and evolutionarily persistent mitochondrial tRNA editing in velvet worms (phylum Onychophora). Molecular Biology and Evolution 28(10): 2873-2881. doi: org/10.1093/molbev/msr113.
• Shen J, Cong Q, Grishin NV (2015) The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications. Meta Gene 5: 68-83. doi: org/10.1016/j.mgene.2015.05.002.
• Wolstenholme DR, Macfarlane JL, Okimoto R, Clary DO, Wahleithner JA (1987) Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms. Proceedings of the National Academy of Sciences 84(5): 1324-1328. doi: org/10.1073/pnas.84.5.1324.
• Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. International review of cytology 141: 173-216. doi: org/10.1016/S0074-7696(08)62066-5.