Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.
Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.
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从全基因组shot弹枪序列数据中的灵长类感中心DNA的组织和演变。
DOI：
10.1371/journal.pcbi.0030181
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发表时间：
2007-09
影响因子：
4.3
通讯作者：
Eichler, Evan E.
中科院分区：
文献类型：
--
作者：
Alkan, Can;Ventura, Mario;Archidiacono, Nicoletta;Rocchi, Mariano;Sahinalp, S. Cenk;Eichler, Evan E.
灵长类着丝粒的主要DNA成分是α卫星DNA。作为灵长类动物基因组测序项目的一部分，多达2%-5%的序列由这种材料组成，由于其高度重复的性质，这种材料被片段化或未组装成已发表的基因组序列的一部分。在这里，我们开发的计算方法，以快速恢复和分类α-卫星序列从以前未表征的全基因组鸟枪序列数据。我们提出了一种算法来计算预测潜在的高阶阵列结构的双端序列数据的基础上，然后实验验证其组织和分布的实验分析。使用来自人类，黑猩猩和猕猴基因组的全基因组鸟枪数据，我们研究了这些序列的系统发育关系，并为它们在过去2500万年的进化和突变模型提供了进一步的支持。我们的研究结果证实了在旧大陆猴和猿进化谱系中着丝粒卫星的扩散和进化的根本差异。着丝粒DNA已被描述为基因组测序的最后前沿;由于其重复的复杂性，这些区域通常在全基因组鸟枪序列组装过程中组装不良。本文开发了一种计算算法，系统地提取数据的灵长类动物着丝粒DNA结构和组织的，不包括作为标准的基因组序列组装的一部分的序列的0.5%。使用这种计算方法，我们确定和重建已发表的人类高阶α卫星阵列，并发现新的家庭在人类，黑猩猩，和旧世界的猴子。实验验证证实了这种计算方法的实用性，以了解其他非人类灵长类动物的着丝粒组织。对不同灵长类动物基因组的进化分析支持猿和旧大陆猴谱系之间着丝粒DNA结构和组织的根本差异。从随机鸟枪测序数据中提取有意义的生物数据的能力有助于填补灵长类动物基因组大规模测序的重要空白，并对其他基因组测序项目产生影响。
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution. Centromeric DNA has been described as the last frontier of genomic sequencing; such regions are typically poorly assembled during the whole-genome shotgun sequence assembly process due to their repetitive complexity. This paper develops a computational algorithm to systematically extract data regarding primate centromeric DNA structure and organization from that ∼5% of sequence that is not included as part of standard genome sequence assemblies. Using this computational approach, we identify and reconstruct published human higher-order alpha satellite arrays and discover new families in human, chimpanzee, and Old World monkeys. Experimental validation confirms the utility of this computational approach to understanding the centromere organization of other nonhuman primates. An evolutionary analysis in diverse primate genomes supports fundamental differences in the structure and organization of centromere DNA between ape and Old World monkey lineages. The ability to extract meaningful biological data from random shotgun sequence data helps to fill an important void in large-scale sequencing of primate genomes, with implications for other genome sequencing projects.
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影响因子：
4.4
作者：
ALEXANDROV, IA;MASHKOVA, TD;YUROV, YB
通讯作者：
YUROV, YB
影响因子：
4.4
作者：
MAHTANI, MM;WILLARD, HF
通讯作者：
WILLARD, HF
影响因子：
5.8
作者：
Paar, V;Pavin, N;Zinic, SD
通讯作者：
Zinic, SD
DOI：
10.1073/pnas.89.8.3310
发表时间：
1992-04-15
影响因子：
11.1
作者：
JORGENSEN, AL;LAURSEN, HB;BAK, AL
通讯作者：
BAK, AL
影响因子：
1.6
作者：
MUSICH, PR;BROWN, FL;MAIO, JJ
通讯作者：
MAIO, JJ