Clade-specific gene distribution among Agrobacterium biovar 1

clade-specific sets of homologous gene clusters were determined using the ‘get_clade_specific_genes.r’ script from Pantagruel package (Lassalle et al., 2019) using the homologous gene family presence/absence matrix as input. Results are presented based on two criteria:- "bgclade_strict": where presence/absence of a gene family is deemed specific in contract to the absence/presence in other genomes of a background clade (defined to include at least 10 other genomes)- "bgclade_0.1": where absence/presence is allowed in up to 10% (rounded to the lower integer) of other genomes of a background clade, to allow the detection of genes specifically gained/lost by the ancestor of the focus clade strains but that may have independently gained/lost in close relatives; this relaxed approach often reveals large groups of contiguous clade-specific genes (Lassalle et al., 2011; Lassalle et al., 2017).

本研究借助Pantagruel软件包（Lassalle等，2019）中的`get_clade_specific_genes.r`脚本，以同源基因家族（homologous gene family）存在/缺失矩阵作为输入，鉴定得到进化枝（clade）特异性同源基因簇集合。研究结果基于两项标准呈现：
- "bgclade_strict"：当某一基因家族的存在/缺失状态，与背景进化枝（定义为至少包含10个其他基因组）中其他基因组的缺失/存在状态形成特异性对比时，即判定该基因家族为进化枝特异性；
- "bgclade_0.1"：允许在背景进化枝的最多10%（向下取整）的其他基因组中出现该基因家族的缺失/存在状态，以此实现对目标进化枝菌株祖先特异性获得/丢失的基因的检测，即便这些基因可能在近缘类群中发生了独立的获得或丢失事件；该宽松筛选策略通常可识别出大量连续分布的进化枝特异性基因（Lassalle等，2011；Lassalle等，2017）。