Evolution of Genome Organization

基因组组织的进化

• 批准号: 217222-2013
• 负责人: ElMabrouk, Nadia
• 金额: $ 2.62万
• 依托单位: Université de Montréal
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2015
• 资助国家: 加拿大
• 起止时间: 2015-01-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=570121
• 关键词: Evolution; Genome; Organization

This is a computational biology program aiming to improve our understanding of genome evolution. The abundance of sequenced and annotated genomes present in public repositories has revealed a tremendous diversity of structures in terms of sequence, gene organization and karyotype, which is the footprint of the various mechanisms taking place during evolution: single nucleotide substitutions are at the origin of sequence diversity, duplications and other content-modifying operations are at the origin of gene family diversity and rearrangements are at the origin of gene order diversity. Each of these types of footprints has been used separately to address different questions. Sequence similarity is the main criterion used to cluster genes into families and to construct phylogenetic trees. Content-modifying operations are used to infer the orthology/paralogy relation between gene copies, which has important implications towards the annotation and functional specificity of genes. As for the diversity of gene order, it is used in comparative genomics to infer ancestral features and study the rearrangements (inversions, transpositions, translocations, fusions, fissions) taking place during evolution. In this program we seek to integrate the three types of footprints in a unified methodology for the Inference of Ancestral Genomes. This is one of the main goals of comparative genomics essential not only from an evolutionary perspective, but also for important implications of the mechanisms taking place during evolution on the genetic and physiological specificities of species, with far-reaching applications to drug discovery and personal medicine. Most existing methods for inferring ancestral genomes stand exclusively on gene order information, ignoring all available phylogenetic information on gene families, which is a serious limitation towards their applicability to genomes with multiple gene copies. The most direct benefit of an integrative method accounting for gene trees will be to avoid a drastic filtering of datasets, allowing an increase of precision of the predicted ancestral features.

这是一项旨在提高我们对基因组进化的理解的计算生物学计划。公共存储库中存在的测序和注释基因组的丰度揭示了在序列，基因组织和核型方面的结构多样性，这是进化过程中发生的各种机制的足迹：单核苷酸替代方案是序列的多样性，重复构建的序列和其他构建作品的起源，其起源是序列的起源，其起源是有效的，其起源是有成立的，有成立的成分，是有成立的，有成立的成分。基因顺序多样性。 这些类型的足迹中的每一种已被单独使用来解决不同的问题。序列相似性是用于将基因聚集到家族并构建系统发育树的主要标准。内容改造操作用于推断基因副本之间的正畸形/旁观关系，这对基因的注释和功能特异性具有重要意义。 至于基因顺序的多样性，它用于比较基因组学来推断祖先特征并研究进化过程中发生的重排（反转，转置，易位，融合，融合，裂缝）。 在此计划中，我们试图将三种类型的足迹整合到祖先基因组推理的统一方法中。这是比较基因组学的主要目标之一，不仅是从进化的角度来看，而且对于在进化过程中对物种的遗传和生理特异性进行的机制的重要含义，以及对药物发现和个人医学的广泛应用。推断祖先基因组的大多数现有方法仅基于基因顺序信息，忽略了有关基因家族的所有可用系统发育信息，这是对它们对具有多个基因拷贝基因组的适用性的严重限制。对基因树的综合方法的最直接好处是避免对数据集进行严重的过滤，从而提高预测祖先特征的精度。