Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life.
Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life.
复制标题
DOI：
10.1371/journal.pone.0002018
复制
发表时间：
2008
期刊：
影响因子：
3.7
通讯作者：
Sobral, Bruno S.
中科院分区：
文献类型：
--
作者：
Gillespie, Joseph J.;Williams, Kelly;Shukla, Maulik;Snyder, Eric E.;Nordberg, Eric K.;Ceraul, Shane M.;Dharmanolla, Chitti;Rainey, Daphne;Soneja, Jeetendra;Shallom, Joshua M.;Vishnubhat, Nataraj Dongre;Wattam, Rebecca;Purkayastha, Anjan;Czar, Michael;Crasta, Oswald;Setubal, Joao C.;Azad, Abdu F.;Sobral, Bruno S.
立克次体的完整基因组序列正在迅速增加，立克次体是一种专有细胞内α蛋白的细菌，可导致各种人类疾病，包括流行性斑疹伤寒和落基山斑点热。从系统发育的角度来看，开放阅读框(ORF)的同源群(OGs)的建立将把核心立克次体基因和其他群体特异性基因(1类OG或C1OG)与那些不分青红皂白地分布在整个立克次体树上的基因(2OG或C2OG)区分开来。我们提出了1823个代表性(无基因复制)和259个非代表性(至少一个基因复制)立克次体OG。虽然在预测的ORF中高度还原(∼1.2MB)立克次体基因组的范围从872年到1512年，但确定了752OGs的核心，描述了立克次体的基本基因。不出所料，这一核心缺乏许多代谢基因，反映了对宿主资源的生长和生存的依赖。此外，我们通过确定定义AG(祖先组)、TG(斑疹伤寒组)、TRG(过渡组)和SFG(斑点热组)立克次体的OG来支持我们最近对立克次体的重新分类。还预测了与昆虫相关的物种、与扁虱相关的物种和含有质粒的物种的OGS。通过将所有OGs叠加到稳健的系统发育估计上，我们区分了C1OGs和C2OGs，后者描述的基因要么是从保守的C1OGs退化的，要么是横向获得的。最后，对不具代表性的OG的仔细检查揭示了高水平的分裂基因与基因复制，这两种现象都混淆了基因正交学分配。有趣的是，不具代表性的OGs以及由几个基因家族组成的OGs主要属于C2OG分布，这些基因家族通常涉及微生物致病和/或获得毒力因子。总而言之，我们通过稳健的系统发育估计确定了来自10个立克次体基因组的14354个预测ORF的相对保守性和分布。这些数据可在Patric(路径系统资源整合中心)获得，为解开与立克次体发病机制相关的错综复杂的问题提供了新的信息，扩大了潜在诊断、疫苗和治疗靶点的范围。
Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular α-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In light of phylogeny, the establishment of orthologous groups (OGs) of open reading frames (ORFs) will distinguish the core rickettsial genes and other group specific genes (class 1 OGs or C1OGs) from those distributed indiscriminately throughout the rickettsial tree (class 2 OG or C2OGs). We present 1823 representative (no gene duplications) and 259 non-representative (at least one gene duplication) rickettsial OGs. While the highly reductive (∼1.2 MB) Rickettsia genomes range in predicted ORFs from 872 to 1512, a core of 752 OGs was identified, depicting the essential Rickettsia genes. Unsurprisingly, this core lacks many metabolic genes, reflecting the dependence on host resources for growth and survival. Additionally, we bolster our recent reclassification of Rickettsia by identifying OGs that define the AG (ancestral group), TG (typhus group), TRG (transitional group), and SFG (spotted fever group) rickettsiae. OGs for insect-associated species, tick-associated species and species that harbor plasmids were also predicted. Through superimposition of all OGs over robust phylogeny estimation, we discern between C1OGs and C2OGs, the latter depicting genes either decaying from the conserved C1OGs or acquired laterally. Finally, scrutiny of non-representative OGs revealed high levels of split genes versus gene duplications, with both phenomena confounding gene orthology assignment. Interestingly, non-representative OGs, as well as OGs comprised of several gene families typically involved in microbial pathogenicity and/or the acquisition of virulence factors, fall predominantly within C2OG distributions. Collectively, we determined the relative conservation and distribution of 14354 predicted ORFs from 10 rickettsial genomes across robust phylogeny estimation. The data, available at PATRIC (PathoSystems Resource Integration Center), provide novel information for unwinding the intricacies associated with Rickettsia pathogenesis, expanding the range of potential diagnostic, vaccine and therapeutic targets.
登录
查看更多内容
影响因子：
4.4
作者：
Baldridge, Gerald D.;Burkhardt, Nicole Y.;Munderloh, Ulrike G.
通讯作者：
Munderloh, Ulrike G.
影响因子：
4.5
作者：
Blanc, Guillaume;Ogata, Hiroyuki;Robert, Catherine;Audic, Stephane;Suhre, Karsten;Vestris, Guy;Claverie, Jean-Michel;Raoult, Didier
通讯作者：
Raoult, Didier
影响因子：
12.3
作者：
Anantharaman V;Aravind L
通讯作者：
Aravind L
DOI：
10.1099/00207713-51-2-339
发表时间：
2001-03-01
影响因子：
2.8
作者：
Bouyer, DH;Stenos, J;Walker, DH
通讯作者：
Walker, DH
影响因子：
7
作者：
Blanc, Guillaume;Ogata, Hiroyuki;Raoult, Didier
通讯作者：
Raoult, Didier