Haplotype Analysis of Varroa destructor and Deformed Wing Virus Using Long Reads

Abstract

As a phoretic parasite and virus vector, the mite Varroa destructor and the associated Deformed wing virus (DWV) form a lethal combination to the honey bee, Apis mellifera. Routine acaricide treatment has been reported to reduce the diversity of mites and select for tolerance against these treatments. Further, different DWV strains face selective pressures when transmitted via mites. In this study, the haplotypes of Varroa mites and associated DWV variants were quantified using long reads. A single haplotype dominated the mite mitochondrial gene cytochrome oxidase subunit I, reflecting an ancient bottleneck. However, highly polymorphic genes were present across the mite genome, suggesting the diversity of mites could be actively maintained at a regional level. DWV detected in both mites and honey bees show a dominant variant with only a few low-frequency alternate haplotypes. The relative abundances of DWV haplotypes isolated from honey bees and mites were highly consistent, suggesting that some variants are favored by ongoing selection.

Keywords: haplotype; honey bee; long reads; mite; selection; virus.

Figure 1

Venn diagram of the SNVs and genes. (A) Venn diagram of the synonymous and non-synonymous SNVs among the mites of four honey bee colonies. Overall, 892 SNVs were shared among the four colonies. The number of synonymous SNV was significantly higher than random for each honey bee colony (Pearson's Chi-square test, P < 0.001). (B) Venn diagram of the genes with non-synonymous SNVs among the mites of four honey bee colonies. Overall, 437 genes were shared in all four colonies, which was again significantly higher than random (Pearson's Chi-square test, P < 0.001).

Figure 2

Cumulative frequency histogram of haplotypes. (A) Frequency of V. destructor haplotypes. Haplotypes were constructed on five SNVs of the most diversified transcript XP_22662619.1 at 4920, 4947, 4957, 4980, and 5076^th nucleotide. In total, 30 haplotypes were identified, and 25 haplotypes were shared at least in two colonies. The four colonies shared dominant haplotypes (VD-1 to VD-5) and a few low frequency haplotypes (VD-others). VD represents V. destructor dominant haplotype. (B) Frequency of DWV haplotypes. Haplotypes were constructed on three SNVs at the 1809, 1938, and 1977^th nucleotide. In total, 11 haplotypes were identified, and 8 haplotypes were shared at least in two colonies. Three haplotypes were shared among the four honey bee colonies, which accounted for 70% of total haplotypes. DD represents DWV dominant haplotype.

Figure 3

Chord diagram of the DWV haplotype transmission from the mites to honey bees. To quantify the transmission of DWV haplotypes from mites to bees, a controlled mite infestation assay was performed. The larvae were artificially reared in 48-well microtiter plates and a female mite was transplanted to each of the larvae. Then DWV haplotypes was quantified for each bee-mite pair. Two DWV haplotypes dominated in both bee and mites. The dominant haplotype 1 (D1) accounted for 52% of observed haplotypes in mite, which accounted for 57% of observed haplotypes in bees. The dominant haplotype 2 (D2) accounted for 37% of observed haplotypes in mite, which also accounted for 37% of observed haplotypes in bees. A few minor haplotypes were also observed in bees and mites. Overall, the relative haplotype abundance of DWV in bees was highly consistent with the mites (Fisher's exact test, P < 0.001).