The complete mitochondrial genome of Aphis gossypii Glover, 1877 (Hemiptera: Aphididae) collected in Korean peninsula

Abstract

Aphid gosypii Glover, 1877 is a widely recognized economically important aphid species in the world. We have determined mitochondrial genome of A. gossypii collected in Korean peninsula. The circular mitogenome of A. gossypii is 15,872 bp including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single control region of 627 bp. The base composition was AT-biased (83.8%). In comparison of Chinese A. gossypii mitochondrial genomes with that of Korean sample, 61 single nucleotide polymorphisms and 3 insertions and deletions were identified, presenting lower level of those of Nilaparvata lugens, Laodelphax striatellus, and Chilo suppresallis.

Aphis gossypii Glover, 1877 is a cosmopolitan aphid species found from the temperate to the tropics. The species is notorious as agricultural pests not only for sucking sap from plants, but also a vector of more than 50 plant viruses spreading many viral diseases (Blackman and Eastop 2000). Aphis gossypii is extremely polyphagous, polymorphic, and can reproduce parthenogenetically (Zhang and Tong 1990), enabling it to feed on various crops (Cucurbitaceae, Rutaceae, and Malvaceae families; Schirmer et al. 2008) and multiply rapidly resulting difficult to control.

Here we present mitogenome collected in Seoul, Republic of Korea (37°45′74″N, 126°94′84″E; the specimen is stored in Gyeongsang National University, Korea, Accession number: Coll#WH0003). DNA was extracted using CTAB-based DNA extraction method manually (iNtRON biotechnology, INC., Korea). Raw sequences obtained from Illumina HiSeq2000 (Macrogen Inc., South Korea) were filtered by Trimmomatic 0.33 (Bolger et al. 2014) and de novo assembled by Velvet 1.2.10 (Zerbino and Birney 2008) and gaps including 548-bp-AT-rich region were closed with SOAPGapCloser 1.12 (Zhao et al. 2011), BWA 0.7.17, and SAMtools 1.9 (Li et al. 2009; Li 2013). Geneious R11 11.1.5 (Biomatters Ltd, Auckland, New Zealand) was used to annotate mitogenome based on that of Chinese A. gossypii (NC_024581; Zhang et al. 2016) with considering those of other aphid species.

Aphis gossypii mitogenome (Genbank accession is MN102349) is 15,872 bp long, which is longer than that of Chinese A. gossypii (NC_024581) by 3 bp. Its nucleotide composition is AT-biased (A + T is 83.8%) and contains 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The control region, presumably corresponding to single largest non-coding AT-rich region (627 bp, A + T is 84.5%), is same to that of Chinese A. gossypii (NC_024581).

In comparison of two A. gossypii mitogenomes, 61 single nucleotide polymorphisms (SNPs) and 3 insertions and deletions (INDELs) were identified. Three INDELs contribute 3-bp increase of length of Korean A. gossypii mitogenome. Level of intraspecies variations identified from samples between Korean and China is smaller than those of Nilaparvata lugens (Choi et al. 2019; Park, Kwon, et al. 2019), Laodelphax striatellus (Park, Jung, et al. 2019; Seo et al. 2019), and Chilo suppresallis (Park, Xi, et al. 2019).

We inferred the phylogenetic relationship of 35 mitogenomes, including two A. gossypii genomes and one outgroup species, Bemisia tabaci (Tay et al. 2016). Multiple sequence alignment was conducted by MAFFT 7.388 (Katoh and Standley 2013). Neighbor joining (10,000 bootstrap repeats) and maximum likelihood (1000 bootstrap repeats) phylogenetic trees were constructed using MEGA X (Kumar et al. 2018). Korean A. gossypii is clustered with Chinese A. gossypii (Figure 1), as expected, and all mitogenomes of Aphis genus form one clade, presenting monophyletic manner (Figure 1). In addition, it also presents that branch lengths of more than one mitogenome originated from A. craccivora and Nurudea yanoniella are similar to that of A. gossypii (Figure 1), indicating level of their intraspecies variations may be similar to each other. This mitogenome will be helpful to understand geographical intraspecies variations of A. gossypii.

Figure 1.

Neighbor joining (10,000 bootstrap repeats) and maximum likelihood (1,000 bootstrap repeats) phylogenetic trees of 35 mitochondrial genomes of Aphididae and one outgroup: two Aphis gossypii (MN102349 in this study and NC_024581), Myzus persicae (NC_029727, KU877171), Acyrthosiphon pisum (NC_011594), Sitobion avenae (NC_024683), Diuraphis noxia (NC_022727), Cavariella salicicola (NC_022682), Schizaphis graminum (NC_006158), Aphis fabae mordvilkoi (NC_039988), Aphis craccivora (NC_031387, KX447142), Hormaphis Betula (NC_029495), Cervaphis quercus (NC_024926), Greenidea psidii (NC_041198), Eriosoma lanigerum (NC_033352), Paracolopha morrisoni (MN167467), Baizongia pistaciae (NC_035314), Nurudea yanoniella (NC_035313 and MK435595), Nurudea shiraii (NC_035301), Nurudea ibofushi (NC_035311), Schlechtendalia chinensis (NC_032386), Schlechtendalia peitan (NC_035302), Melaphis rhois (NC_036065), Schlechtendalia elongallis (NC_035315), Nurudea choui (NC_035310), Nurudea meitanensis (NC_035316), Schlechtendalia flavogallis (NC_035312), Kaburagia rhusicola ovatirhusicola (MF043985), Kaburagia rhusicola ensigallis (MF043984), Kaburagia rhusicola ovagallis (MF043986), Kaburagia rhusicola rhusicola (MF043987), Mindarus keteleerifoliae (NC_033410), Appendiseta robiniae (NC_042165), and Bemisia tabaci (NC_006279) as an outgroup. Phylogenetic tree was drawn based on neighbour joining tree. The numbers above branches indicate bootstrap support values of neighbor joining and maximum likelihood phylogenetic trees, respectively.

Disclosure statement

No potential conflict of interest was reported by the authors.