Mageeney Catherine M, Trubl Gareth, Williams Kelly P
Systems Biology Department, Sandia National Laboratories, Livermore, CA, United States.
Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
Front Bioinform. 2022 Apr 11;2:866850. doi: 10.3389/fbinf.2022.866850. eCollection 2022.
The mobilome of a microbe, i.e., its set of mobile elements, has major effects on its ecology, and is important to delineate properly in each genome. This becomes more challenging for incomplete genomes, and even more so for metagenome-assembled genomes (MAGs), where misbinning of scaffolds and other losses can occur. Genomic islands (GIs), which integrate into the host chromosome, are a major component of the mobilome. Our GI-detection software TIGER, unique in its precise mapping of GI termini, was applied to 74,561 genomes from 2,473 microbial species, each species containing at least one MAG and one isolate genome. A species-normalized deficit of ∼1.6 GIs/genome was measured for MAGs relative to isolates. To test whether this undercount was due to the higher fragmentation of MAG genomes, TIGER was updated to enable detection of split GIs whose termini are on separate scaffolds or that wrap around the origin of a circular replicon. This doubled GI yields, and the new split GIs matched the quality of single-scaffold GIs, except that highly fragmented GIs may lack central portions. Cross-scaffold search is an important upgrade to GI detection as fragmented genomes increasingly dominate public databases. TIGER2 better captures MAG microdiversity, recovering niche-defining GIs and supporting microbiome research aims such as virus-host linking and ecological assessment.
微生物的移动基因组，即其移动元件集合，对其生态具有重大影响，并且在每个基因组中准确界定都很重要。对于不完整的基因组来说，这变得更具挑战性，对于宏基因组组装基因组（MAG）而言更是如此，在MAG中可能会发生支架错误分箱和其他信息丢失。整合到宿主染色体中的基因组岛（GI）是移动基因组的主要组成部分。我们的GI检测软件TIGER在GI末端的精确映射方面独具特色，已应用于来自2473种微生物的74561个基因组，每种微生物至少包含一个MAG和一个分离株基因组。相对于分离株，MAG的物种标准化GI缺失量约为1.6个GI/基因组。为了测试这种计数不足是否是由于MAG基因组的更高碎片化程度所致，TIGER进行了更新，以能够检测末端位于不同支架上或环绕环状复制子起点的分裂GI。这使GI产量增加了一倍，并且新的分裂GI与单支架GI的质量相当，只是高度碎片化的GI可能缺少中心部分。随着碎片化基因组在公共数据库中越来越占主导地位，跨支架搜索是GI检测的一项重要升级。TIGER2能更好地捕捉MAG的微观多样性，找回定义生态位的GI，并支持微生物组研究目标，如病毒-宿主关联和生态评估。
