Extraordinary Moss Genome Structure and Evolution uncovered by the Physcomitrella V3 Chromosome-Scale Assembly

On behalf of the P. patens Genome Consortium I will present our work on the chromosome-scale assembly for the flagship moss, Physcomitrella patens. It comprises a total scaffold length of 473 Mbp, located on 27 pseudochromosomes of 5-30 Mbp size (containing 1.2% Ns), and 351 unassigned scaffolds (totaling 4.9 Mbp).

Approximately 57% of the genome consists of transposable elements (TEs), some of which apparently actively transposing. While at small scales gene- and TE-rich regions alternate, this is not the case on the Mbp scale, where they show an even distribution. Although cytological evidence demonstrates the chromosomes to be monocentric, no heterochromatic pericentromeres are evident - centromeres might be defined by a subclass of Copia elements. TE bodies are highly methylated with CG and CHG context more abundant than CHH, the latter being more prominent in intergenic regions; gene body methylation is generally low.

The genome evolved from a moss-typical base number of seven chromosomes via two rounds of whole genome duplications (WGDs), one chromosome loss, and several fusions and fissions. Paranome-based detection methods show that WGDs are common in mosses, but not in liverworts and hornworts. Ecotype analyses demonstrate hotspots of nucleotide diversity, including some predicted to be under purifying or positive selection.

Several hundred genes are present in colinear regions shared with 15 or more other plant genomes and were thus apparently conserved since the last common ancestor of land plants. These genes are enriched for functions related to land plant specific cell growth and tissue organization.