Comparative Genomics in the Enterobacteriaceae

描述（由申请人提供）：可用基因组序列的数量 肠杆菌科细菌的数量达到了一个临界点， 比较基因组学可以推动假说和实验。在这个项目中，我们 已经根据它们的致病性和它们的 分类位置这些序列将帮助我们理解这些和其他 通过定义它们在基因上的差异和相似性， 内容(1)序列分析表明，S.甲型副伤寒（SPA）， 已经抽样到97%的覆盖率，将完成和注释。spa是 伤寒的第二大流行原因，和沙门氏菌一样。伤寒 (STY)仅限于人类。也许伤寒正在经历基因组退化 与其最近适应一个狭窄的主机范围;我们将确定 如果甲型副伤寒也在经历类似的降解肺炎克雷伯氏菌是一种 主要的机会致病菌我们已经对这个基因组进行了8倍覆盖的测序; 它将被关闭，完成和注释。(2)高性价比的四重 将对四个基因组进行采样（97%的覆盖率）： S.肠道副伤寒B（SP B），这是第三个最普遍的原因， 伤寒沙门氏菌（S. enterica Arizonae（SAR）， 关系密切的S。经常引起人类疾病的肠道菌; 科氏柠檬酸杆菌（CKO）和阴沟肠杆菌（ECL），两者均为 机会致病菌代表未测序的属内或邻近 去急诊大肠杆菌/沙门氏菌/克雷伯氏菌分支。基于Web的分析工具， 考虑到样本的不完整性，将使用这些样本来呈现这些 与其他相关基因组相比。最后，（3）我们放大了， 排列了S中几乎每个CDS的完整开放阅读框架。enterica 亚种1，鼠伤寒血清型LT2。这一资源将得到补充， 新的推定CDS，在STM中未发现，因为这些序列可从 STY、SPA、SPB等血清型。肠因此，我们将开发一个 阵列，可用于各种沙门氏菌，测序和 未测序的，用于分析表达和基因组内容。

DESCRIPTION (provided by applicant): The number of available genome sequences from the bacterial family Enterobacteriaceae is reaching a threshold where comparative genomics can drive hypotheses and experiments. In this project we have selected genomes for sequencing based on their pathogenicity and their taxonomic position. These sequences will help us understand these and other related pathogens by defining their differences and similarities in gene content. (1) The genome sequences of S. enterica serovar Paratyphi A (SPA), already sampled to 97 percent coverage, will be completed and annotated. SPA is the second most prevalent cause of typhoid and, like S. enterica serovar Typhi (STY), is restricted to humans. Typhi is undergoing genome degradation, perhaps associated with its recent adaptation to a narrow host range; we will determine if Paratyphi A is undergoing similar degradation. Klebsiella pneumoniae is a major opportunistic pathogen. We have sequenced this genome to 8-fold coverage; it will be closed, finished and annotated. (2) Cost-effective four-fold sampling (97 percent coverage) will be performed for four genomes: a biotype of S. enterica Paratyphi B (SPB), which is the third most prevalent cause of typhoid and is host-adapted to man; S. enterica Arizonae (SAR), the most distantly related S. enterica that regularly causes disease in humans; Citrobacter koseri (CKO) and Enterobacter cloacae (ECL) both of which are opportunistic pathogens representing the unsequenced genera within or adjacent to the E. coli/Salmonella/Klebsiella clade. Web-based analysis tools that take into account the incomplete nature of the samples will be used to present these data in comparison to other related genomes. Finally, (3) we have amplified and arrayed the complete open reading frames of nearly every CDS in S. enterica subspecies 1, serovar Typhimurium LT2. This resource will be supplemented with new putative CDSs, not found in STM, as these sequences become available from STY, SPA, SPB, and other serovars of S. enterica. Thus, we will develop an array that can be used in a wide variety of Salmonella, both sequenced and unsequenced, for analysis of expression and of genome content.