The complete mitochondrial genome of Nilaparvata lugens (stål, 1854) captured in Korea (Hemiptera: Delphacidae)

Abstract

Nilaparvata lugens is one of important pests of rice causing severe damagein early September in Korea after migrating from China. We completed mitogenome of N. lugens captured in Korea. The circular mitogenome of N. lugens is 17,610 bp including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, and a 2424-bp--non-coding region. The base composition was AT-biased (89.5%). 112 single nucleotide polymorphisms (SNPs) and 59 insertions and deletions are identified by comparing with Chinese N. lugens. Phylogenetic trees presented an incongruence of topology in N. lugens clade, suggesting a need for further analyses to classify biotypes based on complete mitochondrial genomes.

Keywords:

• Nilaparvata lugens
• mitochondrial genome
• Delphacidae
• Korea
• biotypes

Nilaparvata lugens, called brown planthoppers, is one of the important pests affecting rice (Sogawa and Cheng 1979). During high infestations, brown planthopper populations cause ‘hopper burn,’ lower infestations reduce the number of tillers and panicles of rice, resulting in the loss of total weight of grains (Bae and Pathak 1970). Nilaparvata lugens is widely distributed in rice cultivated regions including Asia, Northern Australia, and South Pacific archipelago (Hinckley 1963; Abraham and Nair 1975). Three biotypes (biotype 1, 2, and 3), of which mitochondrial genomes were already sequenced (Lv et al. 2015), were distinguished by preference of rice cultivars, TN1, Mudgo, and ASD7, respectively (Claridge and Den Hollander 1980; Diehl and Bush 1984; Tang et al. 2010). Brown planthoppers migrating from China to Korea can infect rice fields in early September (Kim et al. 1985; Saxena and Barrion 1985). To control brown planthoppers in fields effectively, its genetic background is important.

With already published mitochondrial genomes of N. lugens (Zhang et al. 2013; Lv et al. 2015), whole mitochondrial genome of N. lugens captured at Hadong-gun, Gyoungsang-nam province, the Republic of Korea (34°58′34.55ʺN, 127°50′56.40ʺE; Specimen was deposited at InfoBoss Herbarium (IN), Korea; Choi NJ, INH-00017), was completed. Total DNA was extracted using a manual DNA extraction method (Zymo Research, USA). Sequencing was conducted by HiSeqX (Macrogen Inc., Korea) and de novo assembled and confirmation were done by Velvet 1.2.10 (Zerbino and Birney 2008), SOAPGapCloser 1.12 (Zhao et al. 2011), BWA 0.7.17 (Li 2013), and SAMtools 1.9 (Li et al. 2009). Geneious R11 11.1.5 (Biomatters Ltd, Auckland, New Zealand) was used to annotate mitochondrial genome based on N. lugens mitochondrial genome (NC_021748; referred as reference genome; Zhang et al. 2013) together with ARWEN for identifying tRNAs (Laslett and Canbäck 2008).

Nilaparvata lugens mitochondrial genome (Genbank accession is MK590088) is 17,610 bp long, which is shorter than the reference genome by 10 bp. It contains 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. Its nucleotide composition is AT-biased (A + T ratio is 77.1%). The control region, presumably the single largest non-coding AT-rich region, is 2,424 bp (AT ratio is 80.7%). 112 single nucleotide polymorphisms (SNPs) and 59 insertions and deletions are identified against the reference genome, which is lower than that of Chilo suppressallis (Park et al. 2019). Fourteen synonymous SNPs in nine genes and one non-synonymous SNP in ND5 are found.

We inferred phylogenetic relationship from 14 Delphacidae and 1 Fulgoridae complete mitochondrial genomes. They were aligned by MAFFT 7.388 (Katoh and Standley 2013). Neighbor joining (bootstrap repeat is 10,000), minimum evolution (bootstrap repeat is 10,000), and maximum likelihood (bootstrap repeat is 1,000) trees were constructed using MEGA X (Kumar et al. 2018; Figure 1). Phylogenetic trees present that Korean N. lugens is clustered with brown planthopper captured in Hainan, China rather than five biotypes of N. lugens isolated in China (Figure 1); but topology of N. lugens clade is not congruent among three phylogenetic trees (Figure 1). It reflects that Korean N. lugens may have different mitochondrial genotypes from five biotypes, suggesting a need for further analyses to classify biotypes based on mitochondrial genomes.

Figure 1. Neighbor joining (bootstrap repeat: 10,000), minimum evolution (bootstrap repeat: 10,000), and maximum likelihood (bootstrap repeat: 1,000) phylogenetic trees of 14 Delphacidae and 1 Fulgoridae complete mitochondrial genomes, with seven species: Nilaparvata lugens (MK590088 in this study, JX880069, JN563995, KC333653, JN563996, JN563997, and KC333654), Nilaparvata muiri (JN563998), Nilaparvata bakeri (KC333655), Changeondelphax velitchkovskyi (MG049916), Laodelphax striatellus (FJ360695), Sogatella furcifera (KC512914), Peregrinus maidis (MG049917), Ugyops sp. (MH352481), and Laternaria Candelaria (FJ006724), as outgroup species. Phylogenetic tree was shown based on minimum evolution tree. The numbers above branches indicate bootstrap support values of neighbor joining, minimum evolution, and maximum likelihood phylogenetic trees, respectively.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study was carried out with the support of ‘Cooperative Research Program for Agriculture Science & Technology Development (Population analysis and development technology to predict change of white back planthopper population, [PJ01386402])’ Rural Development Administration, Republic of Korea.