BACKGROUND Retrotransposons are the major determinants of genome sizes and they have shaped both genes and genomes in mammalian organisms, but their overall activity, diversity, and evolution dynamics, particularly their impact on protein coding and lncRNA genes in pigs remain largely unknown. RESULTS In the present study, we performed de novo detection of retrotransposons in pigs by using multiple pipelines, four distinct families of pig-specific L1 s classified into 51 distinct subfamilies and representing four evolution models and three expansion waves of pig-specific SINEs represented by three distinct families were identified. ERVs were classified into 18 families and found two most "modern" subfamilies in the pig genome. The transposition activity of pig L1 was verified by experiment, the sense and antisense promoter activities of young L1 5'UTRs and ERV LTRs and expression profiles of young retrotransposons in multiple tissues and cell lines were also validated. Furthermore, retrotransposons had an extensive impact on lncRNA and protein coding genes at both the genomic and transcriptomic levels. Most protein coding and lncRNA (> 80%) genes contained retrotransposon insertions, and about half of protein coding genes (44.30%) and one-fourth (24.13%) of lncRNA genes contained the youngest retrotransposon insertions. Nearly half of protein coding genes (43.78%) could generate chimeric transcripts with retrotransposons. Significant distribution bias of retrotransposon composition, location, and orientation in lncRNA and protein coding genes, and their transcripts, were observed. CONCLUSIONS In the current study, we characterized the classification and evolution profile of retrotransposons in pigs, experimentally proved the transposition activity of the young pig L1 subfamily, characterized the sense and antisense expression profiles and promoter activities of young retrotransposons, and investigated their impact on lncRNA and protein coding genes by defining the mobilome landscapes at the genomic and transcriptomic levels. These findings help provide a better understanding of retrotransposon evolution in mammal and their impact on the genome and transcriptome.

中文翻译：

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逆转录转座子进化及其对猪lncRNA和蛋白质编码基因的影响。

背景逆转录转座子是基因组大小的主要决定因素，它们塑造了哺乳动物生物体中的基因和基因组，但它们的整体活性、多样性和进化动态，特别是它们对猪中蛋白质编码和lncRNA基因的影响仍然很大程度上未知。结果在本研究中，我们通过使用多个管道对猪中的反转录转座子进行了从头检测，猪特异性L1的四个不同家族被分为51个不同的亚科，代表了猪特异性SINE的四种进化模型和三个扩展波，如下所示：确定了三个不同的家庭。ERV被分为18个科，并在猪基因组中发现了两个最“现代”的亚科。通过实验验证了猪L1的转座活性，验证了Young L1 5'UTR和ERV LTR的正义和反义启动子活性以及Young反转录转座子在多个组织和细胞系中的表达谱。此外，逆转录转座子在基因组和转录组水平上对 lncRNA 和蛋白质编码基因产生广泛影响。大多数蛋白质编码和lncRNA（> 80%）基因含有逆转录转座子插入，大约一半的蛋白质编码基因（44.30%）和四分之一（24.13%）的lncRNA基因含有最年轻的逆转录转座子插入。近一半的蛋白质编码基因（43.78%）可以与逆转录转座子产生嵌合转录本。观察到 lncRNA 和蛋白质编码基因及其转录本中逆转录转座子的组成、位置和方向存在显着的分布偏差。结论在本研究中，我们表征了猪逆转录转座子的分类和进化谱，实验证明了幼猪L1亚科的转座活性，表征了幼龄逆转录转座子的正义和反义表达谱以及启动子活性，并研究了它们对lncRNA的影响通过在基因组和转录组水平上定义移动组景观来识别和蛋白质编码基因。这些发现有助于更好地了解哺乳动物的逆转录转座子进化及其对基因组和转录组的影响。