High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-Read Technologies
High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-Read Technologies
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DOI：
10.1093/molbev/msz156
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发表时间：
2019-11-01
影响因子：
10.7
通讯作者：
Makova, Kateryna D.
中科院分区：
文献类型：
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作者：
Cechova, Monika;Harris, Robert S.;Makova, Kateryna D.
卫星重复序列是着丝粒和端粒的结构组成部分，在某些情况下，它们的分歧被称为驱动物种形成。由于其高度重复的性质，卫星序列在基因组组装中的研究和代表性不足。为了研究它们在类人猿中的周转率，我们研究了人类、黑猩猩、倭黑猩猩、大猩猩、苏门答腊猩猩和婆罗洲猩猩中单位大小高达50 bp的卫星重复序列，使用未组装的短和长测序读数。卫星重复序列的密度，从准确的短读段（Illumina）中识别，在大猿基因组中变化很大。这些主要由少数丰富的重复基序，经常在物种之间共享，形成两组：1）（AATGG）（n）重复（热休克反应的关键）及其衍生物;和2）亚端粒32-聚体参与端粒代谢。利用重复序列的丰富度可以将个体划分为种。然而，聚类没有再现公认的物种同源性，这表明快速重复进化。几个丰富的重复序列在男性和女性中富集;使用Y染色体组装或荧光原位杂交，我们验证了它们在Y染色体上的位置。最后，应用一种新的计算工具，我们确定了许多完全嵌入长牛津纳米孔和太平洋生物科学读取的卫星重复序列。这些重复序列的长度可达59 kb，由散布有其他相似序列的完美重复序列组成。我们的研究结果基于三种不同技术产生的测序读数，首次详细描述了类人猿卫星重复序列，并为探索其功能开辟了新的途径。
Satellite repeats are a structural component of centromeres and telomeres, and in some instances, their divergence is known to drive speciation. Due to their highly repetitive nature, satellite sequences have been understudied and underrepresented in genome assemblies. To investigate their turnover in great apes, we studied satellite repeats of unit sizes up to 50 bp in human, chimpanzee, bonobo, gorilla, and Sumatran and Bornean orangutans, using unassembled short and long sequencing reads. The density of satellite repeats, as identified from accurate short reads (Illumina), varied greatly among great ape genomes. These were dominated by a handful of abundant repeated motifs, frequently shared among species, which formed two groups: 1) the (AATGG)(n) repeat (critical for heat shock response) and its derivatives; and 2) subtelomeric 32-mers involved in telomeric metabolism. Using the densities of abundant repeats, individuals could be classified into species. However, clustering did not reproduce the accepted species phylogeny, suggesting rapid repeat evolution. Several abundant repeats were enriched in males versus females; using Y chromosome assemblies or Fluorescent In Situ Hybridization, we validated their location on the Y. Finally, applying a novel computational tool, we identified many satellite repeats completely embedded within long Oxford Nanopore and Pacific Biosciences reads. Such repeats were up to 59 kb in length and consisted of perfect repeats interspersed with other similar sequences. Our results based on sequencing reads generated with three different technologies provide the first detailed characterization of great ape satellite repeats, and open new avenues for exploring their functions.