基于全基因序列的中国北方3省(区)马铃薯Y病毒遗传多样性分析

本研究以马铃薯Y病毒(PVY)全基因组为基础,分析吉林、黑龙江和内蒙古3省(区)PVY群体遗传多样性和群体分化,并评估突变、重组、选择等遗传力所起的作用。根据已报道的PVY全基因序列保守区设计4对引物,采用片段重叠法对来自内蒙古和吉林的24个PVY分离物全基因序列进行测定,并联合NCBI中已登录的9个黑龙江分离物全基因组序列进行遗传多样性参数评估、群体分化检验和分子变异等分析。结果显示,我国北方3省(区)PVY群体遗传多样性高,其中内蒙古和黑龙江PVY群体遗传多样性高于吉林群体,并且3个群体之间呈现一定程度的遗传分化。分子变异分析发现在PVY基因组中存在1 786个变异位点,表明我国北方3省(区)PVY群体变异程度较高,并且这种高变异度有85.54%来自各个马铃薯种植区内PVY个体的遗传变异。重组分析和系统发育分析发现,我国北方3省(区)PVY群体中重组株系占比高达90.3%,并具有明显的株系多样性,表明PVY重组株系已成为我国北方3省(区)马铃薯种植区的流行株系。选择压力分析显示,使用FEL和IFEL法分别检测出501个和315个净化压力选择位点,这表明3省(区)PVY群体受净化选择压力为主。以上结果表明,中国北方3省(区)PVY群体遗传多样性高,突变、重组和自然选择都对遗传多样性和群体分化存在一定影响。

Genetic diversity analysis of Potato virus Y in three provinces of north China based on the full genomic sequences

Complete genome sequences of Potato virus Y (PVY) from three provinces (Jilin, Heilongjiang and Inner Mongolia) of north China were used to investigate its genetic diversity and population differentiation. Meanwhile, the effects of mutations, recombination and selection on population genetic dynamics were evaluated. The complete genomes of 24 PVY isolates from Jilin and Inner Mongolia were amplified and sequenced using 4 pairs of primers designed according to the conserved regions of the reported PVY isolates, and were then combined with complete genome sequences of 9 Heilongjiang isolates for estimation of genetic variation, population differentiation, molecular variation, etc. The genetic diversity of the PVY populations in the three provinces was high. Furthermore, the genetic diversities of PVY isolates from Heilongjiang and Inner Mongolia were higher than that of PVY from Jilin and there was a certain degree of genetic differentiation among the three populations. Analysis of molecular variation revealed that there were 1 786 mutation sites in PVY genomes, which indicated that the degree of variation in PVY populations in the three provinces was high; 85.54% of the variation was from individuals of different potato planting areas. Recombination and phylogenetic analysis showed that 90.3% strains were recombinant and there was obvious strain diversity in the PVY populations, indicating that the recombinant strains had become the epidemic strain in the potato cropping regions of the three provinces. Totally 501 and 315 purifying selection sites were detected by using FEL and IFEL methods, respectively, suggesting that the PVY populations in the three provinces were mainly affected by purifying selection pressure. In summary, the PVY populations in the three provinces of northern China had high genetic diversity, and mutations, recombination and selection all contributed to the genetic diversity and population differentiation.