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Alu家族在4种旧世界猴基因组中的特征
Characteristics of Alu Family in Four Old World Monkey Genomes
张雪艳, 余浩洋, 孙天琳, 邱实, 蔡延森, 李静*
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DOI:10.11984/j.issn.1000-7083.20190159
作者单位:四川大学生命科学学院, 生物资源与生态环境教育部重点实验室, 四川省濒危野生动物保护生物学重点实验室, 成都 610065
中文关键字:旧世界猴;转座子;Alu家族;多态性Alu位点;物种特有的Alu位点
英文关键字:Old World monkey; transposable element; Alu family; polymorphic Alu locus; species-specific Alu locus
中文摘要:为了揭示转座子对旧世界猴基因组多样性和进化的影响,基于Repbase数据库和RepeatMasker比较了4种旧世界猴——东非狒狒Papio anubis、猕猴Macaca mulatta、绿猴Chlorocebus sabaeus和长鼻猴Nasalis larvatus基因组中转座子的特征,重点关注Alu家族的组成、插入/缺失多态性Alu位点和物种特有Alu插入。结果显示,4个基因组中短散在重复序列拷贝数最丰富,平均分歧率最小,其中灵长目Primates特有的Alu逆转座子的拷贝数超过了100万个(长鼻猴除外)。4个基因组中转座子的基本组成和分布与它们的进化关系相吻合,东非狒狒和猕猴的转座子特征相似,二者与绿猴、长鼻猴有较大差异。通过基因组的两两比较,鉴定了大量在4个基因组间具有插入/缺失多态性的Alu位点,以及7 882个各物种特有的Alu位点,95%以上的物种特有位点都属于AluY家族。研究结果揭示了Alu的转座活动对于旧世界猴动物基因组的进化及多样性具有重要影响。
英文摘要:In order to clarify the influence of transposable elements (TEs) on the genomic diversity and evolution of Old World monkeys, this study provided TEs annotation for the 4 Old World monkey species:olive baboon (Papio anubis), rhesus macaque (Macaca mulatta), green monkey (Chlorocebus sabaeus) and proboscis monkey (Nasalis larvatus) based on Repbase database. The types and divergence rates of TEs in the 4 species were analyzed by focusing on the primate-specific Alu families, the insertion/deletion polymorphic Alu loci, and the species-specific Alu (SSA) loci. The results showed that the Alu transposons had more than a million copies (except N. larvatus). The composition and distribution of TEs in the 4 genomes were consistent with their evolutionary relationship. TEs characteristics of P. anubis were similar with M. mulatta, but different from C. sabaeus and N. larvatus. A large number of insertion/deletion polymorphic Alu loci were identified in the 4 genomes by comparative-genomic analysis. We further identified 7 882 SSA loci, and more than 95% of them were belonging to the AluY family. The SSA of the 3 Cercopithecinae species were mainly composed of the AluYRa1 subfamily, while in the N. larvatus were mainly composed of the Alu YRa2 subfamily. The study revealed that the transposition activity of the Alu family might play a significant role in the evolution and the genomic diversity of the Old World monkey.
2019,38(6): 638-645 收稿日期:2019-05-07
分类号:Q959.848;Q349+.55
基金项目:国家自然科学基金项目(31530068;31770415)
作者简介:张雪艳,女,硕士研究生,研究方向:濒危动物保护,E-mail:516004671@qq.com
*通信作者:李静,E-mail:ljtjf@126.com
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