Department of Computer Science, Kuwait University, Kuwait City, State of Kuwait, Kuwait.
Department of Computer Science, Virginia Tech, Blacksburg, VA, United States of America.
PLoS One. 2024 May 2;19(5):e0301172. doi: 10.1371/journal.pone.0301172. eCollection 2024.
Horizontal gene transfer (HGT) is a powerful evolutionary force that considerably shapes the structure of prokaryotic genomes and is associated with genomic islands (GIs). A GI is a DNA segment composed of transferred genes that can be found within a prokaryotic genome, obtained through HGT. Much research has focused on detecting GIs in genomes, but here we pursue a new course, which is identifying possible preferred locations of GIs in the prokaryotic genome. Here, we identify the locations of the GIs within prokaryotic genomes to examine patterns in those locations. Prokaryotic GIs were analyzed according to the genome structure that they are located in, whether it be a circular or a linear genome. The analytical investigations employed are: (1) studying the GI locations in relation to the origin of replication (oriC); (2) exploring the distances between GIs; and (3) determining the distribution of GIs across the genomes. For each of the investigations, the analysis was performed on all of the GIs in the data set. Moreover, to void bias caused by the distribution of the genomes represented, the GIs in one genome from each species and the GIs of the most frequent species are also analyzed. Overall, the results showed that there are preferred sites for the GIs in the genome. In the linear genomes, these sites are usually located in the oriC region and terminus region, while in the circular genomes, they are located solely in the terminus region. These results also showed that the distance distribution between the GIs is almost exponential, which proves that GIs have preferred sites within genomes. The oriC and termniuns are preferred sites for the GIs and a possible natural explanation for this could be connected to the content of the oriC region. Moreover, the content of the GIs in terms of its protein families was studied and the results demonstrated that the majority of frequent protein families are close to identical in each section.
水平基因转移（HGT）是一种强大的进化力量，它极大地影响了原核基因组的结构，并与基因组岛（GI）有关。GI 是由通过 HGT 获得的转移基因组成的 DNA 片段，可以在原核基因组中找到。许多研究都集中在检测基因组中的 GI 上，但在这里，我们寻求了一个新的方向，即确定 GI 在原核基因组中的可能首选位置。在这里，我们确定了原核基因组中 GI 的位置，以检查这些位置的模式。根据 GI 所在的基因组结构，即圆形或线性基因组，对原核 GI 进行了分析。采用的分析研究包括：（1）研究 GI 与复制起点（oriC）的位置关系；（2）探索 GI 之间的距离；（3）确定 GI 在基因组中的分布。对于每一项研究，都对数据集的所有 GI 进行了分析。此外，为了避免由所代表的基因组分布引起的偏差，还对每个物种的一个基因组中的 GI 以及最常见的物种的 GI 进行了分析。总的来说，研究结果表明，基因组中有 GI 的首选位置。在线性基因组中，这些位置通常位于 oriC 区域和末端区域，而在圆形基因组中，它们仅位于末端区域。这些结果还表明，GI 之间的距离分布几乎是指数的，这证明了 GI 在基因组中有首选位置。oriC 和 terminus 是 GI 的首选位置，这种情况的一个可能的自然解释可能与 oriC 区域的内容有关。此外，还研究了 GI 中蛋白质家族的内容，结果表明，每个部分的大多数常见蛋白质家族都非常相似。
