Twenty years of plant genome sequencing: achievements and challenges

Over the past 20 years the sequences of over 1000 plant genomes have been published, representing 788 different species with a high level of diversity. Long-read sequencing with novel scaffolding strategies has further revolutionized genome sequencing, enabling access to more chromosome-scale assemblies of plant species with increasing genome complexity and size. Citation trees for the first genome papers for Arabidopsis and rice illustrate substantial developments in plant genomics and a plant genome-enabled renaissance in all disciplines of plant biology over the past 20 years. Constructing near-complete genomes, assembling complex genomes, and building reference pan-genomes are some of the most challenges in future sequencing of plant genomes. Publication of the complete genome sequence of Arabidopsis thaliana, the first plant reference genome, in December 2000 heralded the beginning of the plant genome era. Over the past 20 years reference genomes have been generated for hundreds of plant species, spanning non-vascular to flowering plants. Releasing these plant genomes has dramatically advanced studies in all disciplines of plant biology. Importantly, multiple reference-level genomes have been generated for the major crops and their progenitors, enabling the creation of pan-genomes and exploration of domestication history and natural variations that can be adopted by modern crop breeding. We summarize the progress of plant genome sequencing and the challenges of sequencing more complex plant genomes and generating pan-genomes. Publication of the complete genome sequence of Arabidopsis thaliana, the first plant reference genome, in December 2000 heralded the beginning of the plant genome era. Over the past 20 years reference genomes have been generated for hundreds of plant species, spanning non-vascular to flowering plants. Releasing these plant genomes has dramatically advanced studies in all disciplines of plant biology. Importantly, multiple reference-level genomes have been generated for the major crops and their progenitors, enabling the creation of pan-genomes and exploration of domestication history and natural variations that can be adopted by modern crop breeding. We summarize the progress of plant genome sequencing and the challenges of sequencing more complex plant genomes and generating pan-genomes. roots that grow from the aboveground parts of a plant. polyploids in which all sets of chromosomes originate from a single parent with a homogenous genome. an informal group consisting of three divisions of non-vascular land plants (embryophytes): liverworts, hornworts, and mosses. complex green algae that form a sister group to the Chlorophyta and from which the Embryophyta emerged. sister clade of the streptophytes/charophytes that include about 4300 species. species that have male and female reproductive structures on separate plants. a group of vascular plants (plants with xylem and phloem) that reproduce via spores and have neither seeds nor flowers. reducing the complexity of genome by generating haploid or selfing to reach homozygosity. also known as 'fern allies', a clade of vascular plants similar to ferns but with unique leaves called microphylls. When broadly circumscribed, the lycophytes represent a line of evolution distinct from that leading to all other vascular plants. the state of having pistils and stamens on separate flowers of the same plant. a condition in which cells of an organism contain two pairs or more of homologous chromosomes. Polyploidy is especially common in plants. green plants, a clade of eukaryotic organisms that comprise green algae and land plants.