Liu Dong, Yang Jinquan, Tang Wenqiao, Zhang Xing, Royster Clay Matthew, Zhang Ming
1Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Universities, Shanghai, 201306 China.
3Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai, 201306 China.
Mob DNA. 2020 Jan 8;11:4. doi: 10.1186/s13100-019-0198-8. eCollection 2020.
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 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 . Our results reveal possible evolutionary mechanisms underlying the ecological diversity at the interface between SINE mobilization and organism defense.
短散在重复序列（SINEs）是一类非自主逆转录转座子，可从一个位点转座并整合到生物体基因组的其他位置。SINE插入可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。关于这一主题的研究主要集中在SINEs对基因的影响上。然而，鱼类的生态差异尚未用SINEs来解释。
从具有洄游型和定居型两种生态型的[具体物种未给出]中分离出新型SINEs，这两种生态型在产卵和洄游行为上存在差异。这些SINEs具有类似于tRNA基因和长散在重复序列（LINE）逆转录转座子尾部的两种结构。比较嗅觉组织转录组发现，在逆转座初始阶段，仅在洄游型鱼类中检测到完整的SINE转录本拷贝。定居型的SINE DNA拷贝数高于洄游型，而SINE插入频率在洄游型中高于定居型。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。定居型中的SINEs通过一种机制发生切除，即预测的切割位点由突变形成，导致缺口，然后微卫星通过微同源性诱导复制填充这些缺口。
值得注意的是，定居型中的SINEs经历了强烈的自然选择，导致基因组异质性并推动了[具体物种未给出]的生态多样性。我们的结果揭示了SINE转座与生物体防御之间界面处生态多样性潜在的进化机制。
