USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.
Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
Genetics. 2024 May 7;227(1). doi: 10.1093/genetics/iyae036.
Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.
泛基因组包含了一个分支内的一组基因组中发现的全部遗传序列，对于研究物种多样性来说比单一参考基因组更有用。对于像玉米这样具有特别多样化和复杂基因组的物种来说尤其如此。呈现泛基因组数据、分析和可视化是具有挑战性的，特别是对于一个多样化的物种来说，但当泛基因组数据与广泛的基因模型和基因数据（包括经典的基因信息、标记、插入、表达和蛋白质组数据以及蛋白质结构）相关联时，情况更是如此，这就是 MaizeGDB 的情况。在这里，我们描述了 MaizeGDB 的扩展，包括在一个泛基因数据中心中包含玉米泛基因组的基因子集，该数据中心以 MaizeGDB 托管的玉米基因组以及 Pan-Andropoganeae 项目中的外群类蜀黍基因组为特色。新的数据中心提供了各种浏览和可视化工具，包括序列比对可视化、基因树和其他工具，以探索由 Pandagma 流水线计算的玉米中的泛基因。这些数据结合在一起，将帮助玉米研究人员研究玉米的复杂性和多样性，并利用比较功能来验证选定基因模型的泛基因关系。
