Genome Re-sequencing: Unveiling the Origins of Pesticide Resistance
In a recent study, DNA was successfully extracted from 258 adult female individuals of Tetranychus urticae collected from 25 field populations across China. Following extraction, the entire genome was amplified and re-sequenced using the BGI MGISEQ-2000 platform, achieving an average sequencing depth of 42.1 X. An additional dataset comprising 64 re-sequenced reference genomes from diverse geographical locations such as Africa, Asia, Europe, and America was integrated for comprehensive analysis.
The study undertook a comparative analysis of two sequencing methods to ensure the reliability of the results. While the reference genomes were derived from pooled samples, the Chinese samples involved amplifying the whole genome of each single individual before sequencing. This approach allowed for a nuanced comparison between individual and pooled sequencing methodologies.
Comparative Sequencing Analysis
Two iso-female lines were constructed for comparative analysis. DNA was extracted and amplified from the initial female founders, while their offspring, expanded to a size of 400, were pooled for sequencing. Results suggested minimal differences between the two methods in terms of sequencing coverage and SNP similarities.
The SNP missing rates were slightly higher for the whole-genome amplification samples (5.98%) compared to the pool sequencing samples (4.08%). Despite these minor discrepancies, heterozygosity rates were slightly elevated in single female samples compared to offspring pool sequencing samples.
Population Structure of T. urticae
Initial characterization of T. urticae’s global population structure revealed insights into its evolutionary journey. The European lineage appeared to be the oldest, portraying significant genetic divergence. Analyzing 304,709 nuclear SNPs, the Neighbor-Joining tree suggested that T. urticae might have originated in Europe, with Asian samples forming a monophyletic lineage, indicating more recent divergence.
Principal component analysis corroborated these findings, further illustrating genetic clustering based on geographical origins. A particularly distinct Romanian sample was noted, potentially due to interspecific hybridization, pointing towards complex evolutionary dynamics.
Genomic Insights into Chinese Populations
A distinct mitochondrial SNP network analysis of 322 samples further supported the nuclear findings, showing significant haplotype divergence. The Chinese samples, however, exhibited high haplotype similarity, indicative of a founder effect. Delving deeper, the Chinese populations were categorized into two primary haplogroups, marked by low divergence, indicating recent genetic diversification.
Chinese populations demonstrated lower heterozygosity and SNP diversity compared to their European counterparts. This diversity pattern strongly suggests a founder effect has influenced the genetic landscape in China.
Geographical and Genetic Structure
Utilizing a dataset of 19,480 unlinked SNPs, the genetic structure of Chinese populations was further characterized. A significant correlation between geographic and genetic distances was detected, indicating geographical isolation’s impact on shaping genetic differentiation.
Principal component analysis differentiated Chinese populations into three primary groups, correlating somewhat with geographical distribution. However, genetic analysis also highlighted significant gene flow among these groups, particularly within strawberry-associated populations, suggesting anthropogenic factors in dispersal.
Pesticide Resistance Mutations
The study identified 18 target-site mutations across 10 genes associated with pesticide resistance in T. urticae. Notably, the mutation F331W/Y/C in acetylcholinesterase gene was prevalent in 95.3% of Chinese samples, likely reflecting extensive historical pesticide use.
Other prevalent mutations included A1215D in VGSC and significant linkage between mutations in GluCl1 and GluCl3, which contribute to abamectin resistance. The genetic differences between the two defined Chinese genetic groups were highlighted, with significant variation in resistance mutations.
Evolutionary Implications and Global Spread
The study unveiled that most resistance mutations have multiple independent origins, contributing to a complex pattern of genetic adaptability. However, shared haplotypes across global samples reflect a degree of gene flow contributing to the spread of resistance mutations.
Geographical distribution of haplotypes across Chinese populations showcased significant resistance gene flow, despite the mutations arising independently. This has implications for understanding how anthropogenic factors might influence the spread of resistance, particularly in crops like strawberries.
Conclusion
This comprehensive genomic study provides valuable insights into the evolutionary pathways of T. urticae and its adaptive responses to pesticide pressure. By elucidating the global population structure and pinpointing genetic similarities and divergences, the study emphasizes the importance of understanding pest genetics for effective pest management strategies globally.
