CAREER: De novo assembly of duplicated sequences in vertebrate genomes

许多基因组包含被称为片段复制的长而低拷贝的重复序列。这些是由于基因组复制错误而产生的，当它们重叠时，基因或其他功能DNA可能会对有机体的适合性和物种的进化产生影响。从历史上看，重复序列一直很难研究。测序仪器只能读取较短的DNA片段，必须根据DNA片段的重叠情况重建整个基因组，就像组装拼图游戏一样。长于仪器可以读取的片段长度的重复序列不能正确地包括在组件中。测序技术的改进增加了可读取的片段长度，以及组装基因组的算法，使重复序列的分辨率得以提高，为研究不同物种中的片段复制创造了机会。这个项目的目的是开发计算工具来研究非人类基因组中的节段性复制，首先通过构建方法来对多个基因组中的重复基因进行分类，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。该项目还支持创建南加州大学夏季基因组计划，来自大南加州地区的本科生参与对基因组进行排序、注释和发表，为继续攻读研究生学位做准备。该项目最初的重点是开发一种方法来管理脊椎动物基因组中的复制基因。这将使用计算流水线来检测已在组装中的多个副本中分解的重复基因，以及识别缺失副本的基因。有缺失拷贝的基因通过过度覆盖映射回组装的读数来识别。当缺失的基因拷贝具有平行对数特有的变异时，复制基因的额外拷贝可能会使用更灵敏的组装方法来解决。以前开发的一种用于解决包含Paralog特定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，复制解析和精选的组合将被用于量化脊椎动物基因组计划测序的100多个基因组的基因复制。该项目的结果将在chaissonLab.usc.edu.的出版物和资源中列出。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.