Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains.
Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains.
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DOI：
10.1186/gb-2007-8-6-r103
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发表时间：
2007
期刊：
影响因子：
12.3
通讯作者：
Ehrlich GD
中科院分区：
文献类型：
--
作者：
Hogg JS;Hu FZ;Janto B;Boissy R;Hayes J;Keefe R;Post JC;Ehrlich GD
对9个非分型流感嗜血杆菌临床分离株的基因组进行了测序，并与参考菌株进行了比较，从而可以对这种生物的核心和超基因组进行表征和建模。分布基因组假说(DGH)假设慢性细菌病原体利用多克隆感染和基因特征的重新分类来确保面对适应性宿主防御时的持久性。基于多个菌株文库的随机测序的研究表明，自由生活的细菌物种拥有一个比任何单一细菌的基因组都大得多的超基因组。我们获得了9个非分型流感嗜血杆菌(NTHi)临床分离株的高度基因组覆盖范围，使测序的NTHi基因组数量达到13个。聚类法确定了2,786个基因，其中1,461个是所有菌株共有的，其余的1,328个基因都在一个菌株子集中发现；每个菌株的聚类数从1,686到1,878不等。每对菌株之间的基因差异在96到585之间。对每个NTHi毒株和RD毒株的比较显示，每个基因组的插入在107到158之间，缺失在100到213之间。平均插入和缺失大小分别为1,356和1,020个碱基对，平均最大插入和缺失分别为26,977和37,299个碱基对。菌株之间的这种相对大量的小重排与已知的这种天然活性病原体的转化机制是一致的。发展了一个有限的超基因组模型来解释基因在菌株之间的分布。该模型预测，NTHi超基因组包含4,425至6,052个基因，稀有基因数量的不确定性最大，这些稀有基因在菌株中的频率为<；0.1；总的来说，这些结果支持DGH。
The genomes of 9 non-typeable H. influenzae clinical isolates were sequenced and compared with a reference strain, allowing the characterisation and modelling of the core-and supra genomes of this organism. The distributed genome hypothesis (DGH) posits that chronic bacterial pathogens utilize polyclonal infection and reassortment of genic characters to ensure persistence in the face of adaptive host defenses. Studies based on random sequencing of multiple strain libraries suggested that free-living bacterial species possess a supragenome that is much larger than the genome of any single bacterium. We derived high depth genomic coverage of nine nontypeable Haemophilus influenzae (NTHi) clinical isolates, bringing to 13 the number of sequenced NTHi genomes. Clustering identified 2,786 genes, of which 1,461 were common to all strains, with each of the remaining 1,328 found in a subset of strains; the number of clusters ranged from 1,686 to 1,878 per strain. Genic differences of between 96 and 585 were identified per strain pair. Comparisons of each of the NTHi strains with the Rd strain revealed between 107 and 158 insertions and 100 and 213 deletions per genome. The mean insertion and deletion sizes were 1,356 and 1,020 base-pairs, respectively, with mean maximum insertions and deletions of 26,977 and 37,299 base-pairs. This relatively large number of small rearrangements among strains is in keeping with what is known about the transformation mechanisms in this naturally competent pathogen. A finite supragenome model was developed to explain the distribution of genes among strains. The model predicts that the NTHi supragenome contains between 4,425 and 6,052 genes with most uncertainty regarding the number of rare genes, those that have a frequency of <0.1 among strains; collectively, these results support the DGH.
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影响因子：
3.1
作者：
BARENKAMP, SJ;LEININGER, E
通讯作者：
LEININGER, E
影响因子：
56.9
作者：
FLEISCHMANN, RD;ADAMS, MD;VENTER, JC
通讯作者：
VENTER, JC
11 个碱基对序列决定了嗜血杆菌转化过程中 DNA 吸收的特异性
影响因子：
3.5
作者：
DANNER, DB;DEICH, RA;SMITH, HO
通讯作者：
SMITH, HO
影响因子：
3.1
作者：
Fuller, JD;Bast, DJ;de Azavedo, JCS
通讯作者：
de Azavedo, JCS
影响因子：
14.9
作者：
Delcher, AL;Kasif, S;Salzberg, SL
通讯作者：
Salzberg, SL