SINEs are a type of nonautonomous retrotransposon that can transpose from one site to be integrated elsewhere in an organism genome. SINE insertion can give rise to genetic variants and regulate gene expression, allowing organisms to acquire new adaptive capacity. Studies on this subject have focused on the impacts of SINEs on genes. However, ecological disparities in fish have not yet been explained by SINEs. New SINEs were isolated from Coilia nasus, which has two ecotypes—migratory and resident—that differ in their spawning and migration behaviors. The SINEs possess two structures that resemble a tRNA gene and a LINE retrotransposon tail. Comparison of olfactory tissue transcriptomes, intact SINE transcript copies were detected in only the migratory fish at the initial retrotransposition stage. The SINE DNA copy numbers were higher in the resident type than in the migratory type, while the frequency of SINE insertion was higher in the migratory type than in the resident type. Furthermore, SINE insertions can lead to new repeats of short DNA fragments in the genome, along with target site duplications. SINEs in the resident type have undergone excision via a mechanism in which predicted cleavage sites are formed by mutations, resulting in gaps that are then filled by microsatellites via microhomology-induced replication. Notably, SINEs in the resident type have undergone strong natural selection, causing genomic heteroplasmy and driving ecological diversity of C. nasus. Our results reveal possible evolutionary mechanisms underlying the ecological diversity at the interface between SINE mobilization and organism defense.

中文翻译：

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SINE 反转录转座子变异驱动 Coilia nasus 自然种群的生态差异

SINE 是一种非自主反转录转座子，可以从一个位点转座以整合到生物体基因组的其他位置。SINE 插入可以产生遗传变异并调节基因表达，使生物体获得新的适应能力。关于这个主题的研究集中在 SINE 对基因的影响上。然而，SINEs 尚未解释鱼类的生态差异。新的 SINEs 是从 Coilia nasus 中分离出来的，它有两种生态型——迁徙型和常驻型——它们的产卵和迁徙行为不同。SINE 具有两种结构，类似于 tRNA 基因和 LINE 反转录转座子尾。嗅觉组织转录组的比较，完整的 SINE 转录本拷贝仅在最初的逆行转座阶段的洄游鱼中检测到。常驻型的SINE DNA拷贝数高于迁徙型，而迁徙型的SINE插入频率高于常驻型。此外，SINE 插入可导致基因组中短 DNA 片段的新重复以及靶位点重复。常驻型 SINE 通过一种机制被切除，其中预测的切割位点由突变形成，导致间隙由微卫星通过微同源诱导的复制填充。值得注意的是，居民类型的 SINEs 经历了强烈的自然选择，导致基因组异质性并推动了 C. nasus 的生态多样性。我们的研究结果揭示了 SINE 动员和生物体防御之间生态多样性的潜在进化机制。