<i>De novo</i> assembly of plant complete genomes

Abstract

Plant genomes encode the mysteries of how plants cope with complex environments over long evolutionary histories. Over the past 20 years, rapidly developing technologies have allowed the decoding of hundreds of plant draft or reference genomes. The diversity, polyploidy and heterozygosity of plants make it technically challenging and time-consuming to generate high-quality plant genome assemblies. Recently invented ultra-long read sequencing technologies have achieved a milestone where several plant genomes have been gapless and assembled into telomere to telomere. Telomere-to-telomere (T2T) genome refers to a high-quality complete genome with high genomic accuracy, high continuity, and high integrity. With the release of the completed human genome and <italic>Arabidopsis thaliana</italic> genome, the era of complete T2T species genome has arrived. In this review, we summarize the history leading up to the gap free plant genomes based on emerging ultra-long read sequencing technologies. We discuss to close gaps relying on targeted genome sequencing and assembling technologies. However, there are still quite a lot of challenges in super large, polyploidy, and unstable genomes. Nevertheless, these complete genomes have already provided unprecedented information, which will certainly deepen our understanding of plant genomes and the exploration of more functional sequences. By taking advantage of the complete genomes, a series of important genes could be annotated, which will help achieve the goal of genome design in crop species.