Chromosome-Level Genome Assemblies of Two Hypnales (Mosses) Reveal High Intergeneric Synteny

Abstract

Mosses compose one of the three lineages of bryophytes. Today, about 13,000 species of mosses are recognized from across the globe, and at least a third of this diversity composes the Hypnales, a lineage characterized by an early rapid radiation. We sequenced and de novo assembled the genomes of two hypnalean mosses, namely Entodon seductrix and Hypnum curvifolium, based on the 10x genomics and Hi-C data. The genome assemblies of E. seductrix and H. curvifolium comprise 348.4 Mb and 262.0 Mb, respectively, estimated by k-mer analyses to represent 93.3% and 97.2% of their total genome size. Both genomes were assembled at the chromosome-level, with scaffold N50 of 30.0 Mb and 20.7 Mb, respectively. The annotated genome of E. seductrix comprises 25,801 protein-coding genes and that of H. curvifolium 29,077, estimated to represent 96.8% and 97.2%, respectively, of the total gene spaces based on BUSCO assessment. For both genomes, most contigs were anchored to the largest 11 pseudomolecules, corresponding to the 11 chromosomes of the two species, and each with a putative sex-related chromosome characterized by low gene density. The chromosomes of E. seductrix and H. curvifolium are highly syntenic, suggests limited architectural shifts occurred following the rapid radiation of the Hypnales. We compared their genomic features to the model moss Physcomitrium patens. The hypnalean moss genomes lack signatures of recent whole genome duplication (WGD). The presented high-quality moss genomes provide new resources for comparative genomics to potentially unveil the genomic evolution of derived moss lineages.

Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space

“…Furthermore, collinear blocks were also syntenic, showing virtually no movement of collinear blocks among chromosomes. This level of collinearity and synteny represents a relatively rigid genome structure that is exceptional compared to the data available for highly collinear grass and angiosperm genomes with similar depth of divergence (74–80) and is in line with findings by (26). While gene order, gene content, and chromosomal position of collinear blocks are highly conserved, their orientation appears to be dynamic.…”

“…Our analyses and the integration of previous observations suggest that moss genomes show more extensive synteny/collinearity and greater rate of gene birth/death than those of flowering plants. Therefore, our results provide further support to the hypothesis that genome dynamics of moss, bryophyte, and potentially seed-free plants differ from those of seed plants (5, 26). Our study provides a solid basis for a more extensive exploration of genome dynamics within the Funariaceae, to test for the generality of our observations.…”

“…Previous comparative analyses among moss genomes that diverged over 170-200 million years ago revealed detectable synteny among chromosomes (so-called “ancestral elements”), representing conserved blocks inherited from the common ancestor of all mosses (23, 24). Consequently, synteny and collinearity should be even more pronounced between more recently diverged species, a hypothesis virtually unexplored in seed-free plants (26). Our analysis recovered unexpectedly strong collinearity between the F. hygrometrica and P. patens genomes, despite 60 million years of divergence (37).…”

“…Very little is known about the evolution of seed-free plant genomes, in particular over shorter timescales, mainly due to the lack of high-quality genome assemblies for groups of species with shallower genetic divergence. For instance, only five pseudomolecule-scale genome assemblies are available for the most intensively sequenced clade of seed-free plants, the mosses, but these are too deeply divergent to provide information on genome dynamics on a shorter timescale (23)(24)(25)(26).…”

“…Mosses compose the most species-rich lineage of bryophytes (mosses, liverworts and hornworts) and the group with the greatest number of pseudomolecule-scale genome assemblies among seedfree plants (23)(24)(25)(26)32). Among mosses, the Funariaceae provide an appropriate model system to investigate genome evolution and dynamics in seed-free plants, as they hold the most widely used model organism of seed-free plants, the moss Physcomitrium (Physcomitrella) patens, for which a high-quality genome sequence and an ever-growing plethora of genomic resources are available (25,(33)(34)(35)(36)(37).…”