Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA.
USDA-ARS, Plant Science Research Unit, St. Paul, MN, 55108, USA.
BMC Genomics. 2024 Oct 31;25(1):1022. doi: 10.1186/s12864-024-10931-w.
The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire genome of numerous individuals of a single species at a reasonable cost. Pangenomes have been constructed for many major diploid crops, including rice, maize, soybean, sorghum, pearl millet, peas, sunflower, grapes, and mustards. However, pangenomes for polyploid species are relatively scarce and are available in only few crops including wheat, cotton, rapeseed, and potatoes.
In this review, we explore the various methods used in crop pangenome development, discussing the challenges and implications of these techniques based on insights from published pangenome studies. We offer a systematic guide and discuss the tools available for constructing a pangenome and conducting downstream analyses. Alfalfa, a highly heterozygous, cross pollinated and autotetraploid forage crop species, is used as an example to discuss the concerns and challenges offered by polyploid crop species. We conducted a comparative analysis using linear and graph-based methods by constructing an alfalfa graph pangenome using three publicly available genome assemblies. To illustrate the intricacies captured by pangenome graphs for a complex crop genome, we used five different gene sequences and aligned them against the three graph-based pangenomes. The comparison of the three graph pangenome methods reveals notable variations in the genomic variation captured by each pipeline.
Pangenome resources are proving invaluable by offering insights into core and dispensable genes, novel gene discovery, and genome-wide patterns of variation. Developing user-friendly online portals for linear pangenome visualization has made these resources accessible to the broader scientific and breeding community. However, challenges remain with graph-based pangenomes including compatibility with other tools, extraction of sequence for regions of interest, and visualization of genetic variation captured in pangenome graphs. These issues necessitate further refinement of tools and pipelines to effectively address the complexities of polyploid, highly heterozygous, and cross-pollinated species.
泛基因组学的概念和结构变异的重要性在植物基因组学界得到了认可。由于测序和计算技术的进步，以合理的成本对单个物种的许多个体进行全基因组测序已经成为可能。包括水稻、玉米、大豆、高粱、珍珠粟、豌豆、向日葵、葡萄和芥菜在内的许多主要的二倍体作物都已经构建了泛基因组。然而，多倍体物种的泛基因组相对较少，只有少数作物有，包括小麦、棉花、油菜和土豆。
在这篇综述中，我们探讨了作物泛基因组开发中使用的各种方法，根据已发表的泛基因组研究的见解，讨论了这些技术的挑战和影响。我们提供了一个系统的指导，并讨论了构建泛基因组和进行下游分析的可用工具。苜蓿是一种高度杂合的、异花授粉的、自交四倍体的饲料作物，我们以它为例讨论了多倍体作物物种带来的关注和挑战。我们使用三种公开的基因组组装，通过构建苜蓿图泛基因组，使用线性和基于图的方法进行了比较分析。为了说明复杂作物基因组中泛基因组图捕捉到的复杂性，我们使用了五个不同的基因序列，并将它们与三种基于图的泛基因组进行比对。三种图泛基因组方法的比较显示了每个管道捕捉到的基因组变异的显著差异。
泛基因组资源通过提供核心和非必需基因、新基因发现以及全基因组变异模式的见解，变得非常有价值。开发用于线性泛基因组可视化的用户友好型在线门户，使这些资源更容易被更广泛的科学和育种界使用。然而，基于图的泛基因组仍然存在挑战，包括与其他工具的兼容性、感兴趣区域序列的提取以及泛基因组图中捕获的遗传变异的可视化。这些问题需要进一步改进工具和管道，以有效地解决多倍体、高度杂合和异花授粉物种的复杂性。
