The Physcomitrella patens chromosome‐scale assembly reveals moss genome structure and evolution

Abstract

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.

Physcomitrella patens Reute mCherry as a tool for efficient crossing within and between ecotypes

“…) and Kaskaskia (Ka; Lang et al . ). Vx displays a single nucleotide polymorphism (SNP) rate five to ten times higher than either Ka or Re, as compared to Gd (Table S1; Lang et al .…”

“…Vx displays a single nucleotide polymorphism (SNP) rate five to ten times higher than either Ka or Re, as compared to Gd (Table S1; Lang et al . ). Vx is also the only other ecotype besides Gd to have been used so far in the context of forward genetics studies.…”

“…) and reassembly (Lang et al . ) had led to the establishment of a solid genome platform for evolutionary, functional and biotechnological approaches. Most of the sequence data and publications are based on the ecotype Gransden (Gd), based on a plant isolated in Gransden Wood, Huntingdonshire, UK, in 1962, by H.L.K.…”

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

“…However, the current assembly contains 2957 unordered scaffolds, which precludes chromosome‐scale genome structure comparisons with P. patens . For example, in contrast with vascular plant genomes sequenced to date, the P. patens genome showed an even distribution of genes, repeat density, and recombination rate along the chromosomes (Lang et al , ). It is currently unclear whether this is a unique feature of the P. patens genome or it is shared with other bryophyte groups, such as the liverworts.…”

Efficient and modular CRISPR‐Cas9 vector system for Physcomitrella patens

“…As expansion of gene families is common in Physcomitrella patens (Lang et al, ; Zimmer et al, ), multiple family members can be targeted in a single transformation, eliminating repetitive and prolonged procedures. We have demonstrated the ability of our vector system to perform multiplex editing by targeting six different genomic sites in a single transformation using two expression vectors.…”