Group II (gII) introns are mobile retroelements that can spread to new DNA sites through retrotransposition, which can be influenced by a variety of host factors. To determine if these host factors bear any relationship to the genomic location of gII introns, we developed a bioinformatic pipeline wherein we focused on the genomic neighborhoods of bacterial gII introns within their native contexts and sought to determine global relationships between introns and their surrounding genes. We found that, although gII introns inhabit diverse regions, these neighborhoods are often functionally enriched for genes that could promote gII intron retention or proliferation. On one hand, we observe that gII introns are frequently found hiding in mobile elements or after transcription terminators. On the other hand, gII introns are enriched in locations in which they could hijack host functions for their movement, potentially timing expression of the intron with genes that produce favorable conditions for retrotransposition. Thus, we propose that gII intron distributions have been shaped by relationships with their surrounding genomic neighbors.

中文翻译：

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II类细菌内含子基因组区域反映了生存策略：隐藏和劫持。

II组（gII）内含子是可通过逆转座传播到新的DNA位点的移动逆转录元件，这可能受到多种宿主因素的影响。为了确定这些宿主因素是否与gII内含子的基因组位置有任何关系，我们开发了一条生物信息学流水线，其中我们专注于细菌gII内含子在其天然环境中的基因组邻域，并试图确定内含子与其周围基因之间的全局关系。我们发现，尽管gII内含子居住在不同的区域，但这些邻域通常在功能上丰富了可能促进gII内含子保留或增殖的基因。一方面，我们观察到，经常发现gII内含子隐藏在移动元件中或转录终止子之后。另一方面，gII内含子丰富了它们可以劫持宿主功能进行移动的位置，可能通过产生有利于逆转座条件的基因来定时内含子的表达。因此，我们建议gII内含子的分布已经通过与其周围的基因组邻居的关系而形成。