High quality genome annotation and expression visualisation of a mupirocin-producing bacterium.
High quality genome annotation and expression visualisation of a mupirocin-producing bacterium.
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DOI：
10.1371/journal.pone.0268072
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发表时间：
2022
期刊：
影响因子：
3.7
通讯作者：
中科院分区：
文献类型：
--
作者：
假单胞菌属菌株NCIMB 10586，在荧光假单胞菌亚组中，产生聚酮化合物抗生素莫匹罗星，并且具有作为一系列有价值产品的工业生产的宿主的潜力。为了支持对其遗传学和生理学的进一步研究，我们使用了标准和非典型方法的组合来实现基因组序列和注释的质量，高于当前自动化途径的标准。将Illumina读数组装到PacBio基因组序列中创建了回顾性杂交组装，识别并修复了415个测序错误，否则这些错误将影响近5%的注释编码区。我们的注释管道结合了基于相关注释良好的基因组的自动化和严格的部分手动功能特征测试。该菌株与P. synxantha和P. libaniensis接近，并且被发现与加拿大正在开发的作为杂草害虫控制剂的菌株高度相似。由于莫匹罗星是一种次级代谢产物，其产生在指数期后期开启，因此我们在18小时生长期内进行了RNAseq分析，并开发了一种将RNAseq样品作为一组而不是成对标准化的方法。为了回顾这些数据，我们开发了一种易于解释的方法来呈现整个区域或整个基因组的表达谱。在我们的时间过程的2小时粒度下，莫匹罗星簇作为基本上均匀的块在表达上增加，尽管莫匹罗星抗性基因突出为在所有时间点表达。
Pseudomonas strain NCIMB10586, in the P. fluorescens subgroup, produces the polyketide antibiotic mupirocin, and has potential as a host for industrial production of a range of valuable products. To underpin further studies on its genetics and physiology, we have used a combination of standard and atypical approaches to achieve a quality of the genome sequence and annotation, above current standards for automated pathways. Assembly of Illumina reads to a PacBio genome sequence created a retrospectively hybrid assembly, identifying and fixing 415 sequencing errors which would otherwise affect almost 5% of annotated coding regions. Our annotation pipeline combined automation based on related well-annotated genomes and stringent, partially manual, tests for functional features. The strain was close to P. synxantha and P. libaniensis and was found to be highly similar to a strain being developed as a weed-pest control agent in Canada. Since mupirocin is a secondary metabolite whose production is switched on late in exponential phase, we carried out RNAseq analysis over an 18 h growth period and have developed a method to normalise RNAseq samples as a group, rather than pair-wise. To review such data we have developed an easily interpreted way to present the expression profiles across a region, or the whole genome at a glance. At the 2-hour granularity of our time-course, the mupirocin cluster increases in expression as an essentially uniform bloc, although the mupirocin resistance gene stands out as being expressed at all the time points.
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DOI：
10.1039/c39740000847
发表时间：
1974-01-01
影响因子：
--
作者：
CHAIN, EB;MELLOWS, G
通讯作者：
MELLOWS, G
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
16.6
作者：
通讯作者：
--
影响因子：
--
作者：
El-Sayed, AK;Hothersall, J;Thomas, CM
通讯作者：
Thomas, CM
影响因子：
14.9
作者：
Lagesen K;Hallin P;Rødland EA;Staerfeldt HH;Rognes T;Ussery DW
通讯作者：
Ussery DW