Background

Long interspersed element-1 (LINE-1 or L1) is the most abundant retrotransposons in the primate genome. They have approximately 520,000 copies and make up ~ 17% of the primate genome. Full-length L1s can mobilize to a new genomic location using their enzymatic machinery. Gorilla is the second closest species to humans after the chimpanzee, and human-gorilla split 7–12 million years ago. The gorilla genome provides an opportunity to explore primate origins and evolution.

Objective

L1s have contributed to genome diversity and variations during primate evolution. This study aimed to identify gorilla-specific L1s using a more recent version of the gorilla reference genome (Mar. 2016 GSMRT3/gorGor5).

Methods

We collected gorilla-specific L1 candidates through computational analysis and manual inspection. L1Xplorer was used to identify whether full-length gorilla-specific L1s were intact. In addition, to determine the level of sequence conservation between intact fulllength gorilla-specific L1s, two ORFs of intact L1s were aligned with the L1PA2 consensus sequence.

Results

2002 gorilla-specific L1 candidates were identified through computational analysis. Among them, we manually inspected 1,883 gorilla-specific L1s, among which most of them belong to the L1PA2 subfamily and 12 were intact L1s that could influence genomic variations in the gorilla genome. Interestingly, the 12 intact full-length gorilla-specific L1s have 14 highly conserved nonsynonymous mutations, including 6 mutations and 8 mutations in ORF1 and ORF2, respectively. In comparison to the intact full-length chimpanzee-specific L1s and human-specific hot-L1s, two of these in ORF1 (L256F and E293G) were shown as gorilla-specific nonsynonymous mutations.

Conclusion

The gorilla-specific L1s may have had significantly affected the gorilla genome to compose a genome different form that of other primates during primate evolution.

中文翻译：

---

大猩猩特异性 LINE-1 反转录转座子的综合分析

背景

长散在元素 1（LINE-1 或 L1）是灵长类动物基因组中最丰富的反转录转座子。它们有大约 520,000 个拷贝，约占灵长类动物基因组的 17%。全长 L1 可以使用它们的酶促机器移动到新的基因组位置。大猩猩是继黑猩猩之后距离人类第二近的物种，人类与大猩猩在 7 至 1200 万年前分裂。大猩猩基因组为探索灵长类动物的起源和进化提供了机会。

客观的

L1 在灵长类动物进化过程中对基因组多样性和变异做出了贡献。本研究旨在使用更新版本的大猩猩参考基因组（2016 年 3 月 GSMRT3/gorGor5）来识别大猩猩特异性 L1。

方法

我们通过计算分析和人工检查收集了特定于大猩猩的 L1 候选者。L1Xplorer 用于识别全长大猩猩特异性 L1 是否完整。此外，为了确定完整的全长大猩猩特异性 L1 之间的序列保守水平，将完整 L1 的两个 ORF 与 L1PA2 共有序列对齐。

结果

通过计算分析确定了 2002 个特定于大猩猩的 L1 候选者。其中，我们手动检查了 1883 个大猩猩特异性 L1，其中大部分属于 L1PA2 亚科，12 个是完整的 L1，可以影响大猩猩基因组的基因组变异。有趣的是，12 个完整的全长大猩猩特异性 L1 有 14 个高度保守的非同义突变，其中 ORF1 和 ORF2 分别有 6 个突变和 8 个突变。与完整的全长黑猩猩特异性 L1 和人类特异性热 L1 相比，ORF1 中的两个（L256F 和 E293G）显示为大猩猩特异性非同义突变。

结论

在灵长类动物进化过程中，特定于大猩猩的 L1 可能已经显着影响了大猩猩基因组，从而构成了与其他灵长类动物不同的基因组。