Miao Zepu, Yue Jia-Xing
State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
Genome Res. 2025 Feb 14;35(2):296-310. doi: 10.1101/gr.279461.124.
With the increasing availability of high-quality genome assemblies, pangenome graphs emerged as a new paradigm in the genomic field for identifying, encoding, and presenting genomic variation at both the population and species level. However, it remains challenging to truly dissect and interpret pangenome graphs via biologically informative visualization. To facilitate better exploration and understanding of pangenome graphs toward novel biological insights, here we present a web-based interactive visualization and interpretation framework for linear reference-projected pangenome graphs (VRPG). VRPG provides efficient and intuitive support for exploring and annotating pangenome graphs along a linear-genome-based coordinate system (e.g., that of a primary linear reference genome). Moreover, VRPG offers many unique features such as in-graph path highlighting for graph-constituent input assemblies, copy number characterization for graph-embedding nodes, and graph-based mapping for query sequences, all of which are highly valuable for researchers working with pangenome graphs. Additionally, VRPG enables side-by-side visualization between the graph-based pangenome representation and the conventional primary linear reference genome-based feature annotations, therefore seamlessly bridging the graph and linear genomic contexts. To further demonstrate its functionality and scalability, we applied VRPG to the cutting-edge yeast and human reference pangenome graphs derived from hundreds of high-quality genome assemblies via a dedicated web portal and examined their local genome diversity in the graph contexts.
随着高质量基因组组装的可得性不断提高，泛基因组图谱作为基因组领域的一种新范式出现，用于在群体和物种水平上识别、编码和呈现基因组变异。然而，通过具有生物学信息的可视化来真正剖析和解释泛基因组图谱仍然具有挑战性。为了促进对泛基因组图谱的更好探索和理解，以获得新的生物学见解，我们在此展示了一个基于网络的交互式可视化和解释框架，用于线性参考投影泛基因组图谱（VRPG）。VRPG为沿着基于线性基因组的坐标系（例如，主要线性参考基因组的坐标系）探索和注释泛基因组图谱提供了高效且直观的支持。此外，VRPG还提供了许多独特的功能，例如对构成图谱的输入组装进行图谱内路径高亮显示、对嵌入图谱的节点进行拷贝数特征分析以及对查询序列进行基于图谱的映射，所有这些功能对于研究泛基因组图谱的研究人员都具有很高的价值。此外，VRPG能够在基于图谱的泛基因组表示和传统的基于主要线性参考基因组的特征注释之间进行并排可视化，从而无缝地连接图谱和线性基因组背景。为了进一步展示其功能和可扩展性，我们通过一个专用的网络门户将VRPG应用于从数百个高质量基因组组装中获得的前沿酵母和人类参考泛基因组图谱，并在图谱背景下检查了它们的局部基因组多样性。
