Jayakodi Murukarthick, Schreiber Mona, Stein Nils, Mascher Martin
Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
DNA Res. 2021 Jan 19;28(1). doi: 10.1093/dnares/dsaa030.
Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence diversity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers.
泛基因组研究旨在呈现一个物种内的全部序列多样性，为进化研究、功能基因组学以及栽培植物育种提供有用资源。高通量测序成本的降低以及序列组装算法的进步，使得创建多个参考基因组以及植物物种（具有庞大、复杂或多倍体基因组）所有形式遗传变异的目录成为可能。在本综述中，我们总结了构建泛基因组作为植物序列多样性的电子计算机表示的当前方法，并概述了将其有效用于将结构变异与表型变异相联系的相关方法。我们提出了未来的研究方向：（i）跨多个参考基因组的转录组学和表观基因组学研究，以及（ii）开发用户友好且功能丰富的泛基因组浏览器。
