The complete mitochondrial genome of Nilaparvata lugens (Stål, 1854) captured in China (Hemiptera: Delphacidae): investigation of intraspecies variations between countries

Abstract

Nilaparvata lugens, called as brown planthoppers (BPH), is one of the important pests on rice. To identify the origin of Korean N. lugens, we completed the mitochondrial genome of N. lugens captured in Guangdong province, China. The circular mitogenome of N. lugens is 17,606 bp including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, and a single large non-coding region of 2,424 bp. The base composition was AT-biased (89.5%). Ninety single nucleotide polymorphisms and ten insertions and deletions are identified by comparing with Korean N. lugens. Phylogenetic trees present that Guangdong may not be an origin of Korean BPH based on the distance of two mitochondrial genomes.

Keywords:

• Nilaparvata lugens
• mitochondrial genome
• Delphacidae
• China
• intraspecies variation

Nilaparvata lugens (Stål, 1854) is one of the important rice pests, called brown planthoppers (BPH; Sogawa and Cheng 1979). It is widely distributed in Asia, Northern Australia, and South Pacific archipelago, where rice has been cultivated widely (Hinckley 1963; Abraham and Nair 1975). In 2013, the first BPH mitochondrial genome was analyzed together with Laodelphax striatellus, displaying short Atp8 and rearrangement of tRNAs (Zhang et al. 2013). Additional mitochondrial genomes of biotype 1, 2, and 3, and Nilaparvata muiri were sequenced, showing Nad2 is the most variables among N. lugens mitochondrial genomes (Lv et al. 2015). Consequently, mitochondrial genomes of two more biotypes, Y and L, were also sequenced. Moreover, N. lugens captured in Korea was analyzed to find its origin due to periodic migration from China to Korea (Kim et al. 1985; Saxena and Barrion 1985), presenting its mitochondrial genome that is positioned outside of clade of N. lugens (Park et al., under review).

To understand intra-species variations of mitochondrial genome of N. lugens more, total DNA of N. lugens captured at Guangdong province (23°03′18.74′N, 114°35′11.58′E), China, was obtained (Specimen was deposited at InfoBoss Herbarium (IN), Korea; Choi NJ, INH-00015) was extracted using DNA extraction method manually (Zymo Research, DNA extraction kit, USA). Sequencing was conducted by HiSeqX (Macrogen Inc., Korea) and de novo assembly 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 (MK590088; Park et al., under revision) together with ARWEN for tRNAs (Laslett and Canbäck 2008).

Nilaparvata lugens mitochondrial genome (Genbank accession is MK606371) is 17,606 bp, which is shorter than that of N. lugens captured in Korea (MK590088; Park et al., under review) by 4 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 single largest non-coding AT-rich region, is 2,424 bp (AT ratio is 80.7%). Ninety single nucleotide polymorphisms (SNPs) and 10 insertions and deletions are identified by comparing with that of Korean BPH, which is a similar level of variation between Korean BPH and its first mitochondrial genome (Park et al., under review) and is lower than those of Chilo suppressalis (Park et al. 2019). Seventeen synonymous SNPs in eight genes and two non-synonymous SNPs and one deletion in ND5, CTYB, and ND1, respectively, are identified.

We inferred the phylogenetic relationship from 11 Delphacidae complete mitochondrial genomes aligned by MAFFT 7.388 (Katoh and Standley 2013). Neighbor joining, minimum evolution, and maximum likelihood bootstrapped phylogenetic trees were constructed using MEGA X (Kumar et al. 2018). Phylogenetic trees present that five mitochondrial genomes with identified biotypes are not clustered in one clade with those of Guangdong and Korean BPHs, presenting distance between the two mitochondrial genomes and the rest six (Figure 1). In addition, Guangdong BPH is also distinct from Korean PBH, suggesting that the origin of Korean BHP may not be Guangdong area, China (Figure 1).

Figure 1. Neighbor joining (bootstrap repeat: 10,000), minimum evolution (bootstrap repeat: 10,000), and maximum likelihood (bootstrap repeat: 1,000) phylogenetic trees of fifteen Delphacidae and one Fulgoridae complete mitochondrial genomes: Eight Nilaparvata lugens (MK606371 in this study, MK590088, JX880069, JN563995, KC333653, JN563996, JN563997, and KC333654), Nilaparvata muiri (JN563998), Nilaparvata bakeri (KC333655), and Changeondelphax velitchkovskyi (MG049916) as an outgroup species. Phylogenetic tree was shown based on neighbor joining 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.