ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data.
ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data.
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DOI：
10.1186/s12864-015-1860-2
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发表时间：
2015-09-03
期刊：
影响因子：
4.4
通讯作者：
Holt KE
中科院分区：
文献类型：
--
作者：
Hawkey J;Hamidian M;Wick RR;Edwards DJ;Billman-Jacobe H;Hall RM;Holt KE
插入序列（IS）是常见于细菌基因组中的小的转座因子。确定IS在细菌基因组中的位置可用于多种目的，包括流行病学追踪和预测抗生素耐药性。然而，IS通常以多个拷贝存在于单个基因组中，这使得基因组组装和IS插入位点的鉴定复杂化。在这里，我们提出了ISMapper，一个基于映射的工具，用于识别细菌基因组中IS插入的位点和方向，直接从配对末端短读数据。ISMapper使用三种类型的短读段数据进行验证：（i）来自各种物种的模拟读段，（ii）来自5种分离株的Illumina读段，其完成的基因组序列可用于比较，以及（iii）来自7种鲍氏不动杆菌分离株的Illumina读段，其预测的IS位置使用PCR进行测试。共20个基因组，包括13个物种和32个不同的IS，用于验证。ISMapper在模拟读段的分析中正确识别了97%的已知IS插入，在真实的Illumina读段中正确识别了98%。对较低深度的真实的Illumina读段进行二次采样表明ISMapper能够正确检测平均基因组范围读段深度> 20 x的插入，尽管需要读段深度> 50 x以获得由来自读段的证据高度支持的置信判定。ISMapper在A.通过PCR确认鲍曼不动杆菌基因组。在每个A. ISMapper成功鉴定了ampC β-内酰胺酶上游的IS插入，这可以解释对第三代头孢菌素的表型耐药性。ISMapper的实用性进一步通过分析138个公开的结核分枝杆菌基因组中的全基因组IS 6110插入来证明，揭示了谱系特异性插入和多个插入热点。ISMapper提供了一种快速而强大的方法，用于直接从短读段数据中识别IS插入位点，在广泛的细菌中表现出高度的准确性。
Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copies in a single genome, which complicates genome assembly and the identification of IS insertion sites. Here we present ISMapper, a mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes, directly from paired-end short read data. ISMapper was validated using three types of short read data: (i) simulated reads from a variety of species, (ii) Illumina reads from 5 isolates for which finished genome sequences were available for comparison, and (iii) Illumina reads from 7 Acinetobacter baumannii isolates for which predicted IS locations were tested using PCR. A total of 20 genomes, including 13 species and 32 distinct IS, were used for validation. ISMapper correctly identified 97 % of known IS insertions in the analysis of simulated reads, and 98 % in real Illumina reads. Subsampling of real Illumina reads to lower depths indicated ISMapper was able to correctly detect insertions for average genome-wide read depths >20x, although read depths >50x were required to obtain confident calls that were highly-supported by evidence from reads. All ISAba1 insertions identified by ISMapper in the A. baumannii genomes were confirmed by PCR. In each A. baumannii genome, ISMapper successfully identified an IS insertion upstream of the ampC beta-lactamase that could explain phenotypic resistance to third-generation cephalosporins. The utility of ISMapper was further demonstrated by profiling genome-wide IS6110 insertions in 138 publicly available Mycobacterium tuberculosis genomes, revealing lineage-specific insertions and multiple insertion hotspots. ISMapper provides a rapid and robust method for identifying IS insertion sites directly from short read data, with a high degree of accuracy demonstrated across a wide range of bacteria.