Evolutionary origin and distribution of amino acid mutations associated with resistance to sodium channel modulators in onion thrips, Thrips tabaci

Abstract

In onion thrips Thrips tabaci, reduced sensitivity of the sodium channel caused by several sodium channel mutations have been correlated with pyrethroid resistance. For this study, using mitochondrial cytochrome c oxidase subunit I gene sequences, we examined the phylogenetic relation among a total of 52 thelytokous and arrhenotokous strains with different genotypes of the sodium channel mutations. Then, we used flow cytometry to estimate their ploidy. Results showed that the strains are divisible into three groups: diploid thelytoky, triploid thelytoky, and diploid arrhenotoky. Using 23 whole genome resequencing data obtained from 20 strains out of 52, we examined their genetic relation further using principal component analysis, admixture analysis, and a fixation index. Results showed that diploid and triploid thelytokous groups are further classifiable into two based on the sodium channel mutations harbored by the respective group members (strains). The greatest genetic divergence was observed between thelytokous and arrhenotokous groups with a pair of T929I and K1774N. Nevertheless, they shared a genomic region with virtually no polymorphism around the sodium channel gene loci, suggesting a hard selective sweep. Based on these findings, we discuss the evolutionary origin and distribution of the sodium channel mutations in T. tabaci.

Figure 1

Phylogenetic tree of 52 Thrips tabaci strains using the COI gene sequences. The COI gene sequences were obtained through nucleotide sequencing of the PCR products (42 strains other than HKD1, HKD2, HKD3, ANO, TOK6, WKY-M918T, TKO, TKO-SPRR, KTF-SPSS, and KTF-SPRR) and whole genome resequencing data (10 strains other than 42 strains examined using the PCR products). The tree was constructed with the Neighbor-Joining tree method using Molecular Evolutionary Genetics Analysis (MEGA) ver. 10.0. Bootstrap values on nodes were obtained by 1000 replications.

Figure 2

Flow cytometric histogram showing the relative fluorescence of nuclei prepared from haploid males, diploid females, and triploid females of Thrips tabaci. Ploidy determination using flow cytometry was conducted for 46 strains, as shown in Table 1.

Figure 3

PCA plot of 20 strains (23 analyses) of Thrips tabaci using biallelic linkage disequilibrium (LD) pruned SNP data: (a) PCA plot based on 185,335 SNPs in the whole genome; (b) PCA plot based on 36 SNPs in the voltage-gated sodium channel gene locus (TTG013117).

Figure 4

Estimated ancestry proportion of 20 strains (23 analyses) of Thrips tabaci by admixture analysis. LD-pruned 185,335 SNPs were used. Results from K = 2 to 7 (the number of ancestral populations) were evaluated. K = 3 with the lowest CV error value (Fig. S2) was regarded as the best K value. Each column represents one strain (corresponding to one pooled whole genome resequencing data). Each T. tabaci subgroup (L1-TKB, L1-KYT, L1-SKK, L2-II-T929I, L2-II-SS/M918T, L2-III-SS/M918L, and L2-III-SS) is separated by each vertical bar.

Figure 5

Selective-sweep region including the sodium channel gene. Distribution of the expected heterozygosity (H) and fixation index (F_ST) for non-overlapping 10 kb sliding windows in 1,588,560 bp genomic region with estimated conserved synteny to the part of chromosome 15 in Thrips palmi (upper row) and in the 264 kb hard selective sweep region (lower row). Three regions surrounded with dotted black vertical bars represent selective sweep regions (P₁, P₂, and P₃). Thin solid black bars represent border lines of scaffolds. One region surrounded with a green dotted vertical bar represents a genomic region of the sodium channel gene. Overlapped regions with scaffold572 were removed manually in scaffold1303M and scaffold456M. The three scaffolds were concatenated manually (scaffold1303M and scaffold527 were aligned to minus strand). The order of scaffold 99, scaffold232, scaffold973, and the concatenated three scaffolds was estimated based on the conserved synteny among the predicted genes in these scaffolds and genes in the chromosome 15 of Thrips palmi (Table S7).