Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
Genes Genomics. 2021 Oct;43(10):1133-1141. doi: 10.1007/s13258-021-01146-4. Epub 2021 Aug 18.
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.
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).
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.
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.
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.
长散布元件 1（LINE-1 或 L1）是灵长类基因组中最丰富的反转录转座子。它们大约有 520,000 个拷贝，占灵长类基因组的 17%左右。全长 L1 可以利用其酶机制移动到新的基因组位置。大猩猩是继黑猩猩之后与人类最接近的物种，人类和大猩猩在 700 万至 1200 万年前分离。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。
L1 在灵长类动物进化过程中为基因组多样性和变异做出了贡献。本研究旨在使用更新的大猩猩参考基因组（2016 年 3 月 GSMRT3/gorGor5）来鉴定大猩猩特异性 L1。
我们通过计算分析和手动检查收集了大猩猩特异性 L1 候选物。使用 L1Xplorer 来鉴定全长大猩猩特异性 L1 是否完整。此外，为了确定完整全长大猩猩特异性 L1 之间序列保守性的程度，将两个完整 L1 的两个 ORF 与 L1PA2 共识序列进行比对。
通过计算分析鉴定出 2002 个大猩猩特异性 L1 候选物。其中，我们手动检查了 1883 个大猩猩特异性 L1，其中大多数属于 L1PA2 亚家族，有 12 个是完整的 L1，可能影响大猩猩基因组中的基因组变异。有趣的是，这 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，包括 ORF1 中的 6 个突变和 ORF2 中的 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）被鉴定为大猩猩特异性非同义突变。
大猩猩特异性 L1 可能在灵长类动物进化过程中对大猩猩基因组产生了重大影响，使大猩猩基因组与其他灵长类动物的基因组不同。
