He Wenchuang, Li XiaoXia, Qian Qian, Shang Lianguang
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Yazhouwan National Laboratory, Sanya 572024, China; State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Academician Workstation, National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
Plant Commun. 2025 Feb 10;6(2):101230. doi: 10.1016/j.xplc.2024.101230. Epub 2024 Dec 24.
By integrating genomes from different accessions, pangenomes provide a more comprehensive and reference-bias-free representation of genetic information within a population compared to a single reference genome. With the rapid accumulation of genomic sequencing data and the expanding scope of plant research, plant pangenomics has gradually evolved from single-species to multi-species studies. This shift has given rise to the concept of a super-pangenome that covers all genomic sequences within a genus-level taxonomic group. By incorporating both cultivated and wild species, the super-pangenome has greatly enhanced the resolution of research in various areas such as plant genetic diversity, evolution, domestication, and molecular breeding. In this review, we present a comprehensive overview of the plant super-pangenome, emphasizing its development requirements, construction strategies, potential applications, and notable achievements. We also highlight the distinctive advantages and promising prospects of super-pangenomes while addressing current challenges and future directions.
通过整合不同种质的基因组，与单个参考基因组相比，泛基因组能更全面且无参考偏差地呈现群体内的遗传信息。随着基因组测序数据的快速积累以及植物研究范围的不断扩大，植物泛基因组学已逐渐从单物种研究发展到多物种研究。这种转变催生了超级泛基因组的概念，它涵盖了属级分类群内的所有基因组序列。通过纳入栽培种和野生种，超级泛基因组极大地提高了植物遗传多样性、进化、驯化和分子育种等各个领域的研究分辨率。在本综述中，我们全面概述了植物超级泛基因组，强调其发展要求、构建策略、潜在应用和显著成就。我们还突出了超级泛基因组的独特优势和广阔前景，同时探讨了当前面临的挑战和未来发展方向。
