Plant pan-genomics: recent advances, new challenges, and roads ahead

Pan-genomics can encompass most of the genetic diversity of a species or population and has proved to be a powerful tool for studying genomic evolution and the origin and domestication of species, and for providing information for plant improvement. Plant genomics has greatly progressed because of improvements in sequencing technologies and the rapid reduction of sequencing costs. Nevertheless, pangenomics still presents many challenges, including computationally intensive assembly methods, high costs with large numbers of samples, ineffective integration of big data, and difficulty in applying it to downstream multi-omics analysis and breeding research. In this review, we summarize the definition and recent achievements of plant pan-genomics, computational technologies used for pan-genome construction, and the applications of pan-genomes in plant genomics and molecular breeding. We also discuss challenges and perspectives for future pan-genomics studies and provide a detailed pipeline for sample selection, genome assembly and annotation, structural variation identification, and construction and application of graph-based pan-genomes. The aim is to provide important guidance for plant pan-genome research and a better understanding of the genetic basis of genome evolution, crop domestication, and phenotypic diversity for future studies. Copyright (C) 2022, The Authors. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press.

Automated summary

Pan-genomics is a powerful tool for studying genetic diversity, genomic evolution, and species domestication, as well as providing information for plant improvement. However, challenges such as computational complexity, high costs, and data integration remain. This review summarizes the definition and recent achievements of plant pan-genomics and discusses challenges and perspectives for future studies.