Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)

Abstract

Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome of N. lugens biotype 4 from the Indian population for the first time. The mitogenomes of N. lugens are 16,072 and 16,081 bp long with 77.50% and 77.45% A + T contents, respectively, for both of the samples. The mitochondrial genome of N. lugens contains 37 genes, including 13 protein-coding genes (PCGs) (cox1-3, atp6, atp8, nad1-6, nad4l, and cob), 22 transfer RNA genes, and two ribosomal RNA (rrnS and rrnL) subunits genes, which are typical of metazoan mitogenomes. However, both samples of N. lugens mitogenome in the present study retained one extra copy of the trnC gene. Additionally, we also found 93 bp lengths for the atp8 gene in both of the samples, which were 60-70 bp less than that of the other sequenced mitogenomes of hemipteran insects. The phylogenetic analysis of the 19 delphacids mitogenome dataset yielded two identical topologies when rooted with Ugyops sp. in one clade, and the remaining species formed another clade with P. maidis and M. muiri being sisters to the remaining species. Further, the genus Nilaparvata formed a separate subclade with the other genera (Sogatella, Laodelphax, Changeondelphax, and Unkanodes) of Delphacidae. Additionally, the relationship among the biotypes of N. lugens was recovered as the present study samples (biotype-4) were separated from the three biotypes reported earlier. The present study provides the reference mitogenome for N. lugens biotype 4 that may be utilized for biotype differentiation and molecular-aspect-based future studies of N. lugens.

Keywords: NGS; mitochondria; phloem feeder; phylogeny; sucking pest.

Figure 1

Nilaparvata lugens mitochondrial genome map (PCGs, rRNA, tRNAs, and CR) is indicated in the first outer circle. GC content and GC skew are represented in second and third circle, respectively, and inner circles are previously submitted sequences biotype 1 (JN563995) and L (KC333653) genome map.

Figure 2

Linearized depiction of the mitogenome gene arrangements in Nilaparvata lugens in comparison with putative ancestral arthropod, and N. lugens in previous study [27,36]. Shaded boxes indicate genes concerning mitogenome rearrangement.

Figure 3

The AT content percentage of 0-fold degenerate sites, 2-fold degenerate sites, and 4-fold degenerate sites in each protein-coding gene of 19 Delphacidae species from this study, including two Nilaparvata lugens species. The black line at the top of each bar represents the standard deviation value (SD).

Figure 4

Secondary clover-leaf structures for the 23 tRNA genes of N. lugens. Amino acid acceptor arm, TYC arm, the anticodon arm, and dihydrouridine (DHU) arm are given in clockwise direction from the top of the tRNA.

Figure 4

Secondary clover-leaf structures for the 23 tRNA genes of N. lugens. Amino acid acceptor arm, TYC arm, the anticodon arm, and dihydrouridine (DHU) arm are given in clockwise direction from the top of the tRNA.

Figure 5

Sliding window analysis of protein-coding genes in 19 Delphacidae species from this study, including two Nilaparvata lugens species. The value of nucleotide diversity is represented by the red curve.

Figure 6

In the 19 Delphacidae species studied, including two samples of Nilaparvata lugens, GC % vs. GC-skew and AT % vs. AT-skew were compared. For the whole length of mitogenomes, values are determined on J-strands. The skews values are on the X-axis, while the A + T/G + C values are on the Y-axis. Color was assigned to insect species based on their taxonomic classification.

Figure 7

Phylogenetic tree of 19 Delphacidae species obtained from maximum likelihood on the basis of concatenated data of 13 PCGs genes. Colorations of species name and branches are given based on family which they belong. The numbers at nodes indicate branch length. Bootstrap support values are indicated at each node. Accession numbers are given for species obtained from GenBank. * Specimen biotype has not been determined.