Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.
PLoS One. 2013;8(3):e59427. doi: 10.1371/journal.pone.0059427. Epub 2013 Mar 15.
Salmonella serovars Enteritidis and Gallinarum are closely related, but their host ranges are very different: the former is host-promiscuous and the latter can infect poultry only. Comparison of their genomic sequences reveals that Gallinarum has undergone much more extensive degradation than Enteritidis. This phenomenon has also been observed in other host restricted Salmonella serovars, such as Typhi and Paratyphi A. The serovar Gallinarum can be further split into two biovars: Gallinarum and Pullorum, which take poultry as their common host but cause distinct diseases, with the former eliciting typhoid and the latter being a dysentery agent. Genomic comparison of the two pathogens, with a focus on pseudogenes, would provide insights into the evolutionary processes that might have facilitated the formation of host-restricted Salmonella pathogens.
METHODOLOGIES/PRINCIPAL FINDINGS: We sequenced the complete genome of Pullorum strains and made comparison with Gallinarum and other Salmonella lineages. The gene contents of Gallinarum and Pullorum were highly similar, but their pseudogene compositions differed considerably. About one fourth of pseudogenes had the same inactivation mutations in Gallinarum and Pullorum but these genes remained intact in Enteritidis, suggesting that the ancestral Gallinarum may have already been restricted to poultry. On the other hand, the remaining pseudogenes were either in the same genes but with different inactivation sites or unique to Gallinarum or Pullorum, reflecting unnecessary functions in infecting poultry.
Our results support the hypothesis that the divergence between Gallinarum and Pullorum was initiated and facilitated by host restriction. Formation of pseudogenes instead of gene deletion is the major form of genomic degradation. Given the short divergence history of Gallinarum and Pullorum, the effect of host restriction on genomic degradation is huge and rapid, and such effect seems to be continuing to work. The pseudogenes may reflect the unnecessary functions for Salmonella within the poultry host.
肠炎沙门氏菌血清型肠炎亚种和鸡白痢亚种密切相关，但它们的宿主范围却非常不同：前者宿主范围广泛，后者只能感染家禽。比较它们的基因组序列表明，鸡白痢亚种比肠炎亚种经历了更多的广泛退化。这种现象也在其他宿主受限的沙门氏菌血清型中观察到，如伤寒和甲型副伤寒。血清型鸡白痢亚种可进一步分为两个生物型：鸡白痢和鸡伤寒，它们以家禽为共同宿主，但引起不同的疾病，前者引起伤寒，后者是痢疾的病原体。对这两种病原体的基因组比较，重点是假基因，将提供有关可能促进宿主受限沙门氏菌病原体形成的进化过程的见解。
方法/主要发现：我们对鸡白痢菌株进行了全基因组测序，并与鸡白痢亚种和其他沙门氏菌谱系进行了比较。鸡白痢和鸡白痢亚种的基因含量高度相似，但它们的假基因组成差异很大。大约四分之一的假基因在鸡白痢和鸡白痢亚种中具有相同的失活突变，但这些基因在肠炎亚种中保持完整，这表明鸡白痢亚种的祖先可能已经局限于家禽。另一方面，其余的假基因要么在相同的基因中但具有不同的失活位点，要么是鸡白痢或鸡伤寒特有的，反映了在感染家禽中的不必要功能。
我们的结果支持这样的假设，即鸡白痢亚种和鸡白痢亚种的分化是由宿主限制引发和促进的。假基因的形成而不是基因缺失是基因组退化的主要形式。鉴于鸡白痢亚种和鸡白痢亚种的短分化历史，宿主限制对基因组退化的影响是巨大而迅速的，而且这种影响似乎还在继续。这些假基因可能反映了沙门氏菌在家禽宿主中的不必要功能。
