Paired-end sequence mapping detects extensive genomic rearrangement and translocation during divergence of Francisella tularensis subsp tularensis and Francisella tularensis subsp holarctica populations
Paired-end sequence mapping detects extensive genomic rearrangement and translocation during divergence of Francisella tularensis subsp tularensis and Francisella tularensis subsp holarctica populations
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DOI：
10.1128/jb.00437-06
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发表时间：
2006-08-01
影响因子：
3.2
通讯作者：
Benson, Andrew K.
中科院分区：
文献类型：
--
作者：
Dempsey, Michael P.;Nietfeldt, Joseph;Benson, Andrew K.
图拉氏方丝酵母亚种的比较基因组杂交。Tularensis和F.tularensis亚种。冬虫夏草种群的基因组内容是高度保守的，图拉氏华山菌亚种的基因相对较少。其他亚种中不存在图拉氏针叶蝉基因组。以确定全球种群之间的基因组组织是否不同。Tularensis和F.tularensis亚种。Holarctica，我们使用配对末端序列映射(PESM)来识别基因组中共性断裂的区域。PESM方法比较了野生型参考图拉氏菌亚种文库的配对末端测序读数之间的物理距离。根据图拉氏福氏杆菌两个不同基因组序列的图谱坐标，预测了两个读数之间的长度。在该亚种中共有17个不同的连续区。Holarctica基因组(CRholarctica)在图拉氏针叶蝉亚种中是不连续的。图拉尔人基因组。在17个不同的CRholarctica中，有6个被定位为相邻对。Tularensis基因组序列，但易位于F.tularensis亚种。Holarctica，暗示它们的排列是图拉夫酵母亚种的祖先。Tularens，并衍生于F.tularensis亚种。霍拉迪卡。新增加的88个图拉氏菌亚种中CRholarctica的PCR分析Tularensis和F.tularensis亚种。Holarctica分离物显示CRholarctica的排列高度保守，特别是在F.tularensis亚种中。Holarctica)，与图拉氏针叶蝉亚种全球种群的假设一致。冬虫夏草最近经历了一次周期性的选择事件，或者它们是从最近的克隆扩张中出现的。2个独有的图拉夫酵母亚种。还观察到了类似图拉氏菌的菌株，它们可能来自进化中间产物，可能代表了一个新的分类单位。
Comparative genome hybridization of the Francisella tularensis subsp. tularensis and F. tularensis subsp. holarctica populations have shown that genome content is highly conserved, with relatively few genes in the F. tularensis subsp. tularensis genome being absent in other F. tularensis subspecies. To determine if organization of the genome differs between global populations of F. tularensis subsp. tularensis and F. tularensis subsp. holarctica, we have used paired-end sequence mapping (PESM) to identify regions of the genome where synteny is broken. The PESM approach compares the physical distances between paired-end sequencing reads of a library of a wild-type reference F. tularensis subsp. holarctica strain to the predicted lengths between the reads based on map coordinates of two different F. tularensis genome sequences. A total of 17 different continuous regions were identified in the F. tularensis subsp. holarctica genome (CRholarctica) which are noncontiguous in the F. tularensis subsp. tularensis genome. Six of the 17 different CRholarctica are positioned as adjacent pairs in the F. tularensis subsp. tularensis genome sequence but are translocated in F. tularensis subsp. holarctica, implying that their arrangements are ancestral in F. tularensis subsp. tularensis and derived in F. tularensis subsp. holarctica. PCR analysis of the CRholarctica in 88 additional F. tularensis subsp. tularensis and F. tularensis subsp. holarctica isolates showed that the arrangements of the CRholarctica are highly conserved, particularly in F. tularensis subsp. holarctica, consistent with the hypothesis that global populations of F. tularensis subsp. holarctica have recently experienced a periodic selection event or they have emerged from a recent clonal expansion. Two unique F. tularensis subsp. tularensis-like strains were also observed which likely are derived from evolutionary intermediates and may represent a new taxonomic unit.