Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes
Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes
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DOI：
10.3389/fmicb.2020.01486
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发表时间：
2020-07-03
影响因子：
5.2
通讯作者：
Baba, Tomoya
中科院分区：
文献类型：
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作者：
Abe, Takashi;Akazawa, Yu;Baba, Tomoya
水平基因转移(HGT)已被广泛认为在微生物的环境适应中发挥关键作用；然而，通过HGT获得的微生物基因组中基因的数量和来源仍然未知，因为检测到的HGT事件的频率通常被低估，特别是在缺乏关于供体序列的信息的情况下。作为依赖于序列比对的基于系统发育的方法的替代，我们开发了一种基于无监督神经网络的无比对聚类方法-批处理学习自组织映射(BLSOM)，其中序列片段仅基于没有分类信息的寡核苷酸相似性进行聚类，以在整个基因组中检测HGT候选及其起源。通过绘制由几乎所有原核基因组构建的大规模BLSOM上的微生物基因组序列，可以识别HGT候选者，并全面确定其来源，即使是表现出高度新颖性的微生物基因组也是如此。通过聚焦于两种类型的甲蛋白细菌，特别是来自南极湖泊的耐冷鞘氨醇单胞菌菌株，我们使用BLSOM检测到HGT候选菌株，并发现与大陆菌株相比，这两种南极菌株基因组中属于β蛋白细菌的HGT候选菌株比例更高。此外，在两个南极菌株中发现的HGT候选菌株之间存在起源差异。尽管它们的起源是高度多样化的，但与细胞壁或膜生物发生相关的基因功能在HGT候选者中是共享的。此外，氨基酸频率分析表明，南极菌株的看家基因和一些HGT候选基因表现出与其他大陆菌株不同的特征。在南极品系中，Lys、Ser、Thr和Val呈上升趋势，而Ala、Arg、Glu和Leu呈下降趋势。我们的发现有力地表明，微生物的低温适应过程可能在每一种南极菌株中作为一种独立的进化策略而收敛地出现。因此，BLSOM分析不仅可以作为一种强大的工具来检测HGT候选者及其在整个基因组中的起源，而且还可以为微生物的环境适应提供新的视角。
Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network "Batch-Learning Self-Organizing Map (BLSOM)" in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types ofAlphaproteobacteria, specifically psychrotolerantSphingomonasstrains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging toBetaproteobacteriain the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.