Yam Jerald, Bogema Daniel R, Micallef Melinda L, Djordjevic Steven P, Jenkins Cheryl
NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia.
Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia.
Pathogens. 2022 Jul 15;11(7):801. doi: 10.3390/pathogens11070801.
causes losses to cattle producers in Eastern Asia, Oceania and, more recently, North America. One pathogenic genotype (Ikeda) has been sequenced to the chromosomal level, while only draft genomes exist for globally distributed Chitose and Buffeli genotypes. To provide an accurate comparative gene-level analysis and help further understand their pathogenicity, we sequenced isolates of the Chitose and Buffeli genotypes of using long-read sequencing technology. A combination of several long-read assembly methods and short reads produced chromosomal-level assemblies for both Fish Creek (Chitose) and Goon Nure (Buffeli) isolates, including the first complete and circular apicoplast genomes generated for . Comparison with the Shintoku (Ikeda) reference sequence showed both large and small translocations in Buffeli, between chromosomes 2 and 3 and chromosomes 1 and 4, respectively. Ortholog clustering showed expansion of ABC transporter genes in Chitose and Buffeli. However, differences in several genes of unknown function, including DUF529/FAINT-domain-containing proteins, were also identified and these genes were more prevalent in Ikeda and Chitose genotypes. Phylogenetics and similarity measures were consistent with previous short-read genomic analysis. The generation of chromosomal sequences for these highly prevalent genotypes will also support future studies of population genetics and mixed genotype infections.
给东亚、大洋洲以及最近的北美地区的养牛户造成损失。一种致病基因型（池田）已被测序到染色体水平，而全球分布的千岁和布费利基因型只有草图基因组。为了进行准确的基因水平比较分析并帮助进一步了解它们的致病性，我们使用长读长测序技术对千岁和布费利基因型的分离株进行了测序。几种长读长组装方法和短读长的组合为菲什克里克（千岁）和古努雷（布费利）分离株产生了染色体水平的组装结果，包括首次为……生成的完整且环状的顶质体基因组。与新得（池田）参考序列的比较显示，布费利在2号和3号染色体之间以及1号和4号染色体之间分别存在大的和小的易位。直系同源聚类显示千岁和布费利中ABC转运蛋白基因有所扩增。然而，还鉴定出了几个功能未知基因的差异，包括含DUF529/FAINT结构域的蛋白质，这些基因在池田和千岁基因型中更为普遍。系统发育学和相似性测量结果与之前的短读长基因组分析一致。这些高度流行的……基因型染色体序列的产生也将支持未来群体遗传学和混合基因型感染的研究。
