Evolution of the Populus Genome: From a Reference to Holo- to Meta- to Pan-Genomes

We pragmatically treat plant genomes, as viewed through web portals and genome browsers, as static. Yet we intuitively know that somatic mutations create nucleotide substitutions as well larger rearrangements, insertions and deletions. And, at the population level, natural selection is operating on genomic variation to fine-tune genotypes to their local environment. These types of variation in a species’ communal or holo-genome are generally not reflected in our computational representation found on various data bases. This is true of Populus as well, one of the first plant genomes to be published (circa 2006), and a genome that is now in its 4^th updated version. From version 1.0 to version 4.0, N50 and L50 metrics have improved substantially, 80% of the gaps have been filled, gene annotations have deeper RNAseq support, gene counts have varied but remain in the 43K range, and roughly 80 Mb of the 450 Mb genome have been finished. When the first Populus genome was assembled, we reported the assembly of over 20 fungal contigs and 40 bacterial contigs, and reported at that time that these were potentially endophytes of Populus trichocarpa. Since then we have been able to demonstrate that there are thousands of fungal, bacterial and archaea endophytic associates in the Populus metagenome. Many of which have been isolated and reintroduced to axenic Populus genotypes, with a subsequent impact of plant growth and development. In a comparative manner, among all available sequenced plant genomes, we have also been able to identify and validate species-specific orphan gene evolution. Moreover, as more and more Populus genotypes have been sequenced, assembled and annotated, we have gained a better understanding of the Populus pan genome. In a resequenced pool of 1000 diverse representatives of the species Populus trichocarpa we have preliminary indications that there may be as much a 50% increase in gene content at the population level compared to the reference genome, Nisqually-1. Finally, in sequencing individual lateral branches of several P. trichocarpa genotypes, and comparing those sequences to the reference genome we have been able to obtain estimates of the rate of accumulated somatic mutations, where individual vegetative lineages separated by hundreds of years contain thousands of sequence variants. All of the above noted observations and insights on the Populus reference genome, hologenome, metagenome and pan genome will be presented in the context of a species’ potential in an agronomic, industrial or environmental applications.