The First 50 Plant Genomes

F IFTY-FIVE plant genomes have been published to date representing 49 diferent species (Table 1 includes PubMed IDs for complete reference). What have we learned from the irst wave of plant genomes? It has been said that plant genome papers (and genome papers in general) are dry and lack “biology” and that the days of high impact plant genome papers are drawing to a close unless they explore signiicant biology. However, with each new genome, earlier observations are reined and plant genome papers continue to reveal novel aspects of genome biology. For example, the tomato and banana genome papers reined current thinking on the whole genome duplications (WGD) that shaped dicot and monocot genome evolution (D’Hont et al., 2012; Tomato Genome Consortium, 2012). hese observations were enabled not only by high quality genome assemblies but also by a greater number of genomes available for comparisons. In addition, the initial round of plant genomes enabled the irst generation of functional genomics that helped to deine the roles of hundreds of genes, provided unprecedented access to sequence-based markers for breeding, and provided glimpses into plant evolutionary history. More genomes, representing the diverse array of species in Viridiplantae are still required to gain a full understanding of plant genome structure, evolution, and complexity. It All Started with a Wild Mustard Plant Since the publication in 2000 of the model Arabidopsis thaliana genome in the journal Nature, the number of genomes has steadily increased, peaking in 2012 with 13 publications (Fig. 1A). At this current trajectory there should be hundreds of plant genome publications over the next several years. Genome papers have been quite formulaic with a description of the assembly, gene numbers, repeats, WGDs, over and under-represented gene families, and inally, some aspect of novel biology, usually with a focus on transcription factors. Genomes have been published in 12 diferent journals with 38 of the 55 (69%) published genomes appearing in Nature journals (Nature, Nature Genetics, Nature Biotech, and Nature Communications); Science is second with six published genomes. As we see from the most recent publication of the Capsella rubella genome paper, the genome paper is shiting from a formulaic approach to a focus on how the genome elucidates novel biological aspects, such as the evolution of seling to an outcrossing mating system (Slotte et al., 2013). he trend toward biology is quite positive and necessitated by demands for publication in high impact journals. However, the plant community is just at the beginning of exploring the diversity of plant genomes, and the rigor of the genome paper model with the associated in-depth exploration of genome features provides an essential foundation for the plant research community. One of the forces driving the rapid increase in fully sequenced plant genomes is the exponential decrease in cost and speed of genome sequencing fueled by high throughput DNA sequencing (Schatz et al., 2012). More than half of the published genomes have been sequenced entirely or partly using Sanger technology (Table 1), which provides long Published in The Plant Genome 6 doi: 10.3835/plantgenome2013.03.0001in © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication