Diversification of Secondary Metabolite Biosynthetic Gene Clusters Coincides with Lineage Divergence in Streptomyces.
Diversification of Secondary Metabolite Biosynthetic Gene Clusters Coincides with Lineage Divergence in Streptomyces.
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DOI：
10.3390/antibiotics7010012
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发表时间：
2018-02-13
期刊：
影响因子：
--
通讯作者：
Buckley DH
中科院分区：
文献类型：
--
作者：
Choudoir MJ;Pepe-Ranney C;Buckley DH
我们已经确定了链霉菌姐妹类群，共享最近的共同祖先和几乎相同的小亚基（SSU）rRNA基因序列，但居住在不同的地理范围划分的纬度和有足够的基因组差异，代表不同的物种。在这里，我们探讨了进化动力学的次级代谢产物生物合成基因簇（SMGC）的谱系分歧，这些姐妹类群。这些姐妹类群菌株包含310个不同的SMGC，属于22个不同的基因簇类。虽然这22个基因簇类别在所分析的基因组中存在广泛的保守性，但每个单独的基因组在每个类别中具有不同数量的基因簇。几乎所有菌株中共有9个SMGC是保守的，但大多数（57%）SMGC是菌株特异性的。我们发现，虽然每个个体的基因组有一个独特的SMGC组合，这种多样性显示谱系水平的模块化。总体而言，北方来源（NDR）分支比南方来源（SDR）分支具有更多的SMGC（40.7 ± 3.9和33.8 ± 3.9，平均值和S.D.，分别）。SMGC含量的这种差异对应于每个基因组预测的开放阅读框（ORF）数目的差异（7775 ± 196和7093 ± 205，平均值和S.D.，因此SMGC：ORF的比例在姐妹分类群基因组之间没有差异。我们发现，姐妹类群之间SMGC多样性的变化主要是由基因获得和缺失事件驱动的，这些变化与伴随谱系分化的基因组大小的整体变化相关。
We have identified Streptomyces sister-taxa which share a recent common ancestor and nearly identical small subunit (SSU) rRNA gene sequences, but inhabit distinct geographic ranges demarcated by latitude and have sufficient genomic divergence to represent distinct species. Here, we explore the evolutionary dynamics of secondary metabolite biosynthetic gene clusters (SMGCs) following lineage divergence of these sister-taxa. These sister-taxa strains contained 310 distinct SMGCs belonging to 22 different gene cluster classes. While there was broad conservation of these 22 gene cluster classes among the genomes analyzed, each individual genome harbored a different number of gene clusters within each class. A total of nine SMGCs were conserved across nearly all strains, but the majority (57%) of SMGCs were strain-specific. We show that while each individual genome has a unique combination of SMGCs, this diversity displays lineage-level modularity. Overall, the northern-derived (NDR) clade had more SMGCs than the southern-derived (SDR) clade (40.7 ± 3.9 and 33.8 ± 3.9, mean and S.D., respectively). This difference in SMGC content corresponded with differences in the number of predicted open reading frames (ORFs) per genome (7775 ± 196 and 7093 ± 205, mean and S.D., respectively) such that the ratio of SMGC:ORF did not differ between sister-taxa genomes. We show that changes in SMGC diversity between the sister-taxa were driven primarily by gene acquisition and deletion events, and these changes were associated with an overall change in genome size which accompanied lineage divergence.
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影响因子：
5.2
作者：
Choudoir, Mallory J.;Campbell, Ashley N.;Buckley, Daniel H.
通讯作者：
Buckley, Daniel H.
影响因子：
14.9
作者：
Blin K;Medema MH;Kazempour D;Fischbach MA;Breitling R;Takano E;Weber T
通讯作者：
Weber T
影响因子：
11
作者：
Doroghazi, James R.;Buckley, Daniel H.
通讯作者：
Buckley, Daniel H.
DOI：
10.1073/pnas.1318021111
发表时间：
2014-03-11
影响因子：
11.1
作者：
Charlop-Powers, Zachary;Owen, Jeremy G.;Brady, Sean F.
通讯作者：
Brady, Sean F.
影响因子：
3
作者：
Daily J
通讯作者：
Daily J