Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin.
Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin.
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DOI：
10.1186/1471-2164-15-970
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发表时间：
2014-11-15
期刊：
影响因子：
4.4
通讯作者：
Buckley DH
中科院分区：
文献类型：
--
作者：
Doroghazi JR;Buckley DH
链霉菌是广泛分布的细菌，有助于陆地碳循环，并产生大多数临床有用的抗生素。虽然种间的基因组多样性已被调查链霉菌，信息是缺乏种内的基因组多样性。草地链霉菌具有很高的同源重组率，但这种基因交换对基因组进化和天然产物基因簇进化的影响仍然没有得到表征。我们报告了四个S的基因组序列。将其与黄灰链霉菌IAF-45-CD（=ATCC 33331）的全基因组进行比较，该菌株最近被重新分类为S.草地尽管地理起源不同，但基因组高度相似，85.9%的基因存在于核心基因组中，并且保留了所有天然产物基因簇。天然产物包括碳青霉烯和β-内酰胺酶抑制剂基因簇的新型组合。虽然高的种内重组率消除了整个基因组的系统发育信号，但种内重组在两个基因组区域中受到抑制。第一个区域以插入/缺失多态性为中心，第二个区域以杂合NRPS-PKS基因为中心。最后，两个基因家族占核心基因组中分歧基因的25%以上。第一个包括bldB的同源物（孢子发育和抗生素生产所需），而第二个包括具有螺旋-转角-螺旋基序（hpb）的未表征蛋白质的同源物。来自这些家族的基因与分布在基因组中的15对基因共存。这些基因有证据表明，共同进化的共同定位对，支持以前的断言，这些基因的功能可能类似于一个毒素-抗毒素系统。S. Pratensis基因组高度相似，具有异常水平的重组，其消除了物种菌株之间的系统发育信号。这个物种有一个大的核心基因组和可变的末端区域，比种间比较中发现的要小。这些菌株之间没有地理差异，但有证据表明，局部连锁不平衡影响两个基因组区域。我们还显示了进一步的观察证据，DUF 397-HTH（bldB和hpb）是一种新的毒素-抗毒素对。
Streptomyces are widespread bacteria that contribute to the terrestrial carbon cycle and produce the majority of clinically useful antibiotics. While interspecific genomic diversity has been investigated among Streptomyces, information is lacking on intraspecific genomic diversity. Streptomyces pratensis has high rates of homologous recombination but the impact of such gene exchange on genome evolution and the evolution of natural product gene clusters remains uncharacterized. We report draft genome sequences of four S. pratensis strains and compare to the complete genome of Streptomyces flavogriseus IAF-45-CD (=ATCC 33331), a strain recently reclassified to S. pratensis. Despite disparate geographic origins, the genomes are highly similar with 85.9% of genes present in the core genome and conservation of all natural product gene clusters. Natural products include a novel combination of carbapenem and beta-lactamase inhibitor gene clusters. While high intraspecies recombination rates abolish the phylogenetic signal across the genome, intraspecies recombination is suppressed in two genomic regions. The first region is centered on an insertion/deletion polymorphism and the second on a hybrid NRPS-PKS gene. Finally, two gene families accounted for over 25% of the divergent genes in the core genome. The first includes homologs of bldB (required for spore development and antibiotic production) while the second includes homologs of an uncharacterized protein with a helix-turn-helix motif (hpb). Genes from these families co-occur with fifteen pairs spread across the genome. These genes have evidence for co-evolution of co-localized pairs, supporting previous assertions that these genes may function akin to a toxin-antitoxin system. S. pratensis genomes are highly similar with exceptional levels of recombination which erase phylogenetic signal among strains of the species. This species has a large core genome and variable terminal regions that are smaller than those found in interspecies comparisons. There is no geographic differentiation between these strains, but there is evidence for local linkage disequilibrium affecting two genomic regions. We have also shown further observational evidence that the DUF397-HTH (bldB and hpb) are a novel toxin-antitoxin pair.
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
3.2
作者：
Eccleston, M;Ali, RA;Nodwell, J
通讯作者：
Nodwell, J
影响因子：
11
作者：
Doroghazi, James R.;Buckley, Daniel H.
通讯作者：
Buckley, Daniel H.
影响因子：
2.8
作者：
ISHAQUE, M;KLUEPFEL, D
通讯作者：
KLUEPFEL, D
影响因子：
3.3
作者：
Doroghazi JR;Buckley DH
通讯作者：
Buckley DH