Standage Daniel S, Lai Tim, Brendel Volker P
Department of Biology, Indiana University, Bloomington, IN 47405, USA.
Department of Mathematics, Indiana University, Bloomington, IN 47405, USA.
NAR Genom Bioinform. 2022 Feb 22;4(1):lqac013. doi: 10.1093/nargab/lqac013. eCollection 2022 Mar.
We introduce a new framework for genome analyses based on parsing an annotated genome assembly into distinct interval loci (iLoci), available as open-source software as part of the AEGeAn Toolkit (https://github.com/BrendelGroup/AEGeAn). We demonstrate that iLoci provide an alternative coordinate system that is robust to changes in assembly and annotation versions and facilitates granular quality control of genome data. We discuss how statistics computed on iLoci reflect various characteristics of genome content and organization and illustrate how these statistics can be used to establish a baseline for assessment of the completeness and accuracy of the data. We also introduce a well-defined measure of relative genome compactness and compute other iLocus statistics that reveal genome-wide characteristics of gene arrangements in the whole genome context. Given the fast pace of assembly/annotation updates, our AEGeAn Toolkit fills a niche in computational genomics based on deriving persistent and species-specific genome statistics. Gene structure model-centric iLoci provide a precisely defined coordinate system that can be used to store assembly/annotation updates that reflect either stable or changed assessments. Large-scale application of the approach revealed species- and clade-specific genome organization in precisely defined computational terms, promising intriguing forays into the forces of shaping genome structure as more and more genome assemblies are being deposited.
我们引入了一种新的基因组分析框架，该框架基于将带注释的基因组组装解析为不同的区间位点（iLoci），作为AEGeAn工具包（https://github.com/BrendelGroup/AEGeAn）的一部分以开源软件形式提供。我们证明，iLoci提供了一种替代坐标系，该坐标系对组装和注释版本的变化具有鲁棒性，并有助于对基因组数据进行精细的质量控制。我们讨论了在iLoci上计算的统计数据如何反映基因组内容和组织的各种特征，并说明了如何使用这些统计数据来建立评估数据完整性和准确性的基线。我们还引入了一种定义明确的相对基因组紧凑度度量，并计算了其他iLocus统计数据，这些数据揭示了全基因组背景下基因排列的全基因组特征。鉴于组装/注释更新的快速步伐，我们的AEGeAn工具包基于推导持久且特定于物种的基因组统计数据，填补了计算基因组学的一个空白。以基因结构模型为中心的iLoci提供了一个精确定义的坐标系，可用于存储反映稳定或变化评估的组装/注释更新。该方法的大规模应用以精确的计算术语揭示了特定物种和进化枝的基因组组织，随着越来越多的基因组组装被存入，有望对塑造基因组结构的力量进行有趣的探索。
