基于3种原噬菌体基因的赣南地区黄龙病菌种群动态分析

柑橘黄龙病(citrus Huanglongbing,HLB)对全球柑橘产业造成了重大经济损失。为明确赣南地区柑橘黄龙病菌基因组上原噬菌体的分子特征和传播动态,本研究对采自赣南10个市县区的470份样品进行HLB检测,并对阳性样品中3种类型的原噬菌体（SC1、SC2和P-JXGC-3）上的SC1_gp050、SC2_gp040和PJXGC_gp08基因序列进行遗传多样性分析和谱系地理学分析。结果显示,共检出74份HLB阳性样品,包括7种原噬菌体组合类型:SC1、SC2、P-JXGC-3、SC1+SC2、SC1+P-JXGC-3、SC2+P-JXGC-3和SC1+SC2+P-JXGC-3,含SC2类型的原噬菌体检出41份,检出率为55.41%,说明赣南地区含SC2类型的原噬菌体菌株最为普遍。遗传多样性分析结果表明，赣南地区的3种原噬菌体的基因交流频繁,遗传分化现象不明显。选择压力分析结果显示,SC1和P-JXGC-3类型的原噬菌体均处于负向选择,SC2类型的原噬菌体处于正向选择。基于3种原噬菌体上的基因构建的中介网络图和单倍型分布表结果显示,3种原噬菌体均存在1个祖先单倍型,其他独有单倍型均是由该祖先单倍型经多次突变而来,其中PJXGC_gp08基因产生的独有单倍型最多。时空动态分析结果显示,SC1类型原噬菌体存在2条传播路径,分别为安远和全南地区间的相互传播(3

Analysis of population dynamics of citrus Huanglongbing in Gannan based on three prophage genes

Citrus Huanglongbing (HLB) has caused significant economic losses to the global citrus industry. This study aimed to elucidate the molecular characteristics and transmission dynamics of prophages region on genome of pathogen causing citrus Huanglongbing disease in Gannan. A total of 470 samples collected from ten counties and urban areas in Gannan were tested for HLB. The sequences of SC1_gp050, SC2_gp040 and PJXGC_gp08 genes on three types of prophages (SC1, SC2 and P-JXGC-3) were analyzed for genetic diversity and genealogical geography. The results showed that 74 samples were HLB-positive, including seven prophage combination types: SC1, SC2, P-JXGC-3, SC1+SC2, SC1+P-JXGC-3, SC2+P-JXGC-3 and SC1+SC2+P-JXGC-3. The prophages containing SC2 type (41) were the most prevalent in Gannan, with a detection rate of 55.41%. The results of genetic diversity analysis showed that the genes of the three types of prophages in the Gannan region were frequently exchanged, and genetic differentiation was not obvious. The results of selection pressure analysis showed that both SC1 and P-JXGC-3 type prophages were under negative selection, while SC2 type prophage was under positive selection. An intermediary network and haplotype distribution table based on the prophage genes revealed that three prophages were derived from one ancestral haplotype, respectively, and mutated multiple times, with the PJXGC_gp08 gene producing the most unique haplotypes. The results of spatio-temporal dynamic analysis showed that there were two transmission pathways for SC1 type prophage, involving mutual transmission between Anyuan and Quannan areas (3