CAREER: De novo assembly of duplicated sequences in vertebrate genomes

职业：脊椎动物基因组中重复序列的从头组装

• 批准号: 2046753
• 负责人: Mark Chaisson
• 金额: $ 59.74万
• 依托单位: University of Southern California
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-01 至 2026-07-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2046753&HistoricalAwards=false
• 关键词: CAREER; De; novo; assembly; duplicated

Many genomes contain long, low-copy repeated sequences called segmental duplications. These arise as a result of mistakes of genome replication, and when they overlap genes or other functional DNA can have an effect on fitness of an organism and evolution of a species. Duplicated sequences have been historically difficult to study. Sequencing instruments can only read short fragments of DNA, and entire genomes must be reconstructed based on how the DNA fragments overlap, much like assembling a jigsaw puzzle. Repeated sequences longer than the length of fragment that an instrument can read cannot correctly be included in an assembly. Improvements in sequencing technology that have increased the length of fragments that may be read and algorithms for assembling genomes have enabled increased resolution of repeats, creating an opportunity to study segmental duplication in diverse species. The aim of this project is to develop computational tools to study segmental duplications in nonhuman genomes, first through constructing methods to catalog duplicated genes in multiple genomes, and next to improve methods for assembling duplicated sequences. This can help improve our understanding of how genomes have evolved through duplication, and shed light on what genes have played a role in adaptation. This project also supports the creation of a USC Summer Genome Program, where undergraduate students from the greater Southern California area participate to sequence, annotate, and publish on a genome in preparation for continuing to an advanced postgraduate degree.The initial focus of the project is to develop a method to curate duplicated genes in vertebrate genomes. This will be accomplished using a computational pipeline to detect duplicated genes that have been resolved in multiple copies in an assembly as well as identify genes that have missing copies. Genes that have missing copies are identified through excess coverage of reads mapped back to the assembly. When the missing copies of genes have paralog-specific variants, additional copies of the duplicated gene may be resolved using a more sensitive approach to assembly. A method that was previously developed to resolve missing genes that contain paralog-specific variants, SDA, will be improved to operate on new data types and address more complex duplication organizations. Finally, a combination of duplication resolution and curation will be applied to quantify gene duplication across over 100 genomes sequenced by the Vertebrate Genome Project. The results of this project will be listed under publications and resources at chaissonlab.usc.edu.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

许多基因组包含长的、低拷贝的重复序列，称为片段重复。这些是由于基因组复制错误而产生的，当它们与基因或其他功能DNA重叠时，会对生物体的适应性和物种的进化产生影响。重复序列历来难以研究。测序仪器只能读取DNA的短片段，整个基因组必须根据DNA片段的重叠方式进行重建，就像组装拼图一样。超过仪器可读取的片段长度的重复序列不能正确地包含在组装体中。测序技术的改进增加了可读取片段的长度，组装基因组的算法也提高了重复序列的分辨率，为研究不同物种的片段重复创造了机会。该项目的目的是开发计算工具来研究非人类基因组中的片段重复，首先通过构建方法来编目多个基因组中的重复基因，然后改进组装重复序列的方法。这可以帮助我们更好地理解基因组是如何通过复制进化的，并阐明哪些基因在适应中发挥了作用。该项目还支持南加州大学夏季基因组计划的创建，来自南加州地区的本科生参与基因组测序、注释和发表，为继续攻读高级研究生学位做准备。该项目的最初重点是开发一种方法来管理脊椎动物基因组中的重复基因。这将通过使用计算管道来检测在组装中以多个拷贝解析的重复基因以及识别具有缺失拷贝的基因来实现。具有缺失拷贝的基因通过映射回组装的读段的过量覆盖来鉴定。当缺失的基因拷贝具有旁系同源特异性变体时，可以使用更灵敏的组装方法来解析重复基因的额外拷贝。之前开发的用于解决包含旁系同源特异性变体的缺失基因的方法SDA将得到改进，以操作新的数据类型并解决更复杂的重复组织。最后，重复解析和策展的组合将被应用于量化脊椎动物基因组计划测序的100多个基因组中的基因重复。该项目的成果将在chaissonlab.usc.edu的出版物和资源下列出。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。