<scp>DNA</scp> methylation in <i>Marchantia polymorpha</i>

Aguilar-Cruz, Adolfo; Grimanelli, Daniel; Haseloff, Jim; Arteaga-Vázquez, Mario

doi:10.1111/nph.15818

Cited by 12 publications

(7 citation statements)

References 45 publications

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“…Altogether, our data suggest that gene body methylated genes have partially different characteristics in P. patens and M. polymorpha. We propose that this is not due to a functionally divergent methylation machinery because M. polymorpha and P. patens share a common set of orthologous genes involved in DNA methylation (Bowman et al , ; Ikeda et al , ; Schmid et al , ; Aguilar‐Cruz et al , ). We rather speculate that the genomic distribution and characteristics of genes prone to gene body methylation may differ between the two species, which could be a consequence of their divergent mating systems and/or large‐scale genomic organization.…”

Section: Discussionmentioning

confidence: 99%

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

et al. 2019

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Summary Marchantia polymorpha has recently become a prime model for cellular, evo‐devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule‐scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high‐density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map‐based cloning, feasible.

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Section: Discussionmentioning

confidence: 99%

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

et al. 2019

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“…Control of gene expression through DNA methylation is a fundamental epigenetic mechanism involved in the defense against invading nucleic acids and in the regulation of developmental pathways ( Feng et al, 2010 ). The M. polymorpha genome encodes core members of the major sRNA mediated epigenetic pathway operating in plants—termed the RNA-dependent DNA methylation (RdDM) pathway—( Matzke and Mosher, 2014 ), including 24-nt siRNAs and two plant-specific RNA polymerases involved in gene silencing, Nuclear RNA polymerase D (POLIV) and the Nuclear RNA polymerases E (POLVa and POLVb) ( Huang et al, 2015 ; Bowman et al, 2017 ; Aguilar-Cruz et al, 2019 ). DNA methylation has been proven important for silencing of transposable elements and for the perpetuation of cell identity during the gametophytic phase of M. polymorpha ( Ikeda et al, 2018 ).…”

Section: Vignettes Of Recent Research Highlights Of the Post-genomic Agementioning

confidence: 99%

The renaissance and enlightenment ofMarchantiaas a model system

et al. 2022

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The liverwort Marchantia polymorpha has been utilized as a model for biological studies since the 18th century. In the past few decades there has been a Renaissance in its utilization in genomic and genetic approaches to investigating physiological, developmental, and evolutionary aspects of land plant biology. The reasons for its adoption are similar to those of other genetic models, e.g. simple cultivation, ready access via its worldwide distribution, ease of crossing, facile genetics, and more recently, efficient transformation, genome editing, and genomic resources. The haploid gametophyte dominant life cycle of M. polymorpha is conducive to forward genetic approaches. The lack of ancient whole-genome duplications within liverworts facilitates reverse genetic approaches, and possibly related to this genomic stability, liverworts possess sex chromosomes that evolved in the ancestral liverwort. As a representative of one of the three bryophyte lineages, its phylogenetic position allows comparative approaches to provide insights into ancestral land plants. Given the karyotype and genome stability within liverworts, the resources developed for M. polymorpha have facilitated the development of related species as models for biological processes lacking in M. polymorpha.

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“…Phylogenetic analyses have identified genes encoding Pol IV and Pol V subunits in species throughout the terrestrial plant lineage (Embryophyta), suggesting that Pol IV-RdDM evolved in a common ancestor of land plants (Figure 3a) [28,[107][108][109]. Supporting this hypothesis, the analysis of Pol IV subunit mutations has revealed Pol IV-dependent siRNA biogenesis and de novo DNA methylation in the moss Physcomitrella patens [110] and in diverse angiosperms, including tomato (Solanum lycopersicum) [111], rice (Oryza sativa) [112][113][114], maize (Zea mays) [104,[115][116][117], Brassica rapa [118] and Capsella rubella [119].…”

Section: Diverse Biological Functions Of Pol IV and Rna-directed Dna mentioning

confidence: 99%

Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants

2020

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Multisubunit RNA polymerase (Pol) complexes are the core machinery for gene expression in eukaryotes. The enzymes Pol I, Pol II and Pol III transcribe distinct subsets of nuclear genes. This family of nuclear RNA polymerases expanded in terrestrial plants by the duplication of Pol II subunit genes. Two Pol II-related enzymes, Pol IV and Pol V, are highly specialized in the production of regulatory, non-coding RNAs. Pol IV and Pol V are the central players of RNA-directed DNA methylation (RdDM), an RNA interference pathway that represses transposable elements (TEs) and selected genes. Genetic and biochemical analyses of Pol IV/V subunits are now revealing how these enzymes evolved from ancestral Pol II to sustain non-coding RNA biogenesis in silent chromatin. Intriguingly, Pol IV-RdDM regulates genes that influence flowering time, reproductive development, stress responses and plant–pathogen interactions. Pol IV target genes vary among closely related taxa, indicating that these regulatory circuits are often species-specific. Data from crops like maize, rice, tomato and Brassica rapa suggest that dynamic repositioning of TEs, accompanied by Pol IV targeting to TE-proximal genes, leads to the reprogramming of plant gene expression over short evolutionary timescales.

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DNA methylation in Marchantia polymorpha

Cited by 12 publications

References 45 publications

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

The renaissance and enlightenment ofMarchantiaas a model system

Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants

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