Identifying copy number variation of the dominant virulence factors msa and p22 within genomes of the fish pathogen Renibacterium salmoninarum.
Identifying copy number variation of the dominant virulence factors msa and p22 within genomes of the fish pathogen Renibacterium salmoninarum.
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DOI：
10.1099/mgen.0.000055
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发表时间：
2016-04
影响因子：
3.9
通讯作者：
Rhodes LD
中科院分区：
文献类型：
--
作者：
Brynildsrud O;Gulla S;Feil EJ;Nørstebø SF;Rhodes LD
鲑鱼肾杆菌是细菌性肾病的病原体，细菌性肾病是全世界养殖和野生鲑鱼的重要疾病。尽管这种疾病具有广泛的时空分布和栖息地压力，从自然环境到水产养殖，从河流到海洋环境，但在鲑鱼基因组中观察到的变异很小。在这里，我们使用实时定量 PCR 证实的基因组测序覆盖深度来检测鲑鱼基因之间的拷贝数变异 (CNV)。 CNV 主要限于已知的显性毒力因子 msa 和 p22。在代表英国、挪威和北美的 68 个分离株中，msa 基因有 2 到 5 个相同拷贝，p22 基因有 1 到 5 个拷贝。这两个基因的 CNV 同时出现，表明它们可能在功能上相关。携带 CNV 的分离株在系统发育上受到限制，主要起源于北美，而不是英国或挪威。虽然系统发育关系和地理起源都被发现与 CNV 状态相关，但地理起源是比系统发育更强的预测因子，这表明局部选择压力在该性状的重复出现和维持中发挥着作用。
Renibacterium salmoninarum is the causative agent of bacterial kidney disease, an important disease of farmed and wild salmonid fish worldwide. Despite the wide spatiotemporal distribution of this disease and habitat pressures ranging from the natural environment to aquaculture and rivers to marine environments, little variation has been observed in the R. salmoninarum genome. Here we use the coverage depth from genomic sequencing corroborated by real-time quantitative PCR to detect copy number variation (CNV) among the genes of R. salmoninarum. CNV was primarily limited to the known dominant virulence factors msa and p22. Among 68 isolates representing the UK, Norway and North America, the msa gene ranged from two to five identical copies and the p22 gene ranged from one to five copies. CNV for these two genes co-occurred, suggesting they may be functionally linked. Isolates carrying CNV were phylogenetically restricted and originated predominantly from sites in North America, rather than the UK or Norway. Although both phylogenetic relationship and geographical origin were found to correlate with CNV status, geographical origin was a much stronger predictor than phylogeny, suggesting a role for local selection pressures in the repeated emergence and maintenance of this trait.