A Functional Phylogenomic View of the Seed Plants

Lee, Ernest K.; Cibrián-Jaramillo, Angélica; Kolokotronis, Sergios‐Orestis; Katari, Manpreet S.; Stamatakis, Alexandros; Ott, Michael; Chiu, Joanna C.; Little, Damon P.; Stevenson, Dennis Wm.; McCombie, W. Richard; Martienssen, Robert A.; Coruzzi, Gloria M.; DeSalle, Rob

doi:10.1371/journal.pgen.1002411

Cited by 137 publications

(134 citation statements)

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“…Although most genes involved in DNA methylation are conserved across angiosperm species, these genes have not been extensively studied in gymnosperms, and the existence of Pol V in gymnosperms has been controversial (13). Previous studies showed that many subunits of RNA POLYMERASE IV (Pol IV) were conserved across land plants.…”

Section: Resultsmentioning

confidence: 99%

DNA methylome of the 20-gigabase Norway spruce genome

Ausín

Feng

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

101

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DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.NA methylation is the most studied stable and heritable epigenetic modification of eukaryotes, and plays important roles in transcriptional regulation and silencing of repetitive elements and transposons (1). In plants, DNA methylation occurs in three contexts, CG, CHG (H is A, T, or C), and CHH (2-4). In Arabidopsis, forward genetic screens have uncovered many components that are required for DNA methylation. For example, the maintenance of CG, CHG, and a subset of CHH DNA methylation is mediated by METHYLTRANSFERASE 1 (MET1), CHRO-MOMETHYLASE (CMT) 3, and CMT2, respectively, whereas the de novo establishment of DNA methylation in all three contexts and the maintenance of the rest of the CHH methylation is mediated by the RNA-directed DNA methylation (RdDM) pathway that employs DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) (5).Genome-wide methylome studies have been performed in many plant species, such as Arabidopsis, tomato, poplar, soybean, rice, and cassava (2, 3, 6-11). These studies uncovered conserved DNA methylation patterns in genic regions and transposable element regions across plant genomes. However, the DNA methylation landscapes of gymnosperm species that have large genome sizes and high repeat content are relatively understudied. Takuno et al. have demonstrated that genic CHG methylation was correlated with genome size by studying gene body methylation in selected gymnosperm species (12). However, genome-wide high coverage single-base resolution DNA methylation maps of any gymnosperm are still lacking. It is known that transposable elements (TEs) are the main targets of DNA methylation. However, the roles of DNA methylation in TE-abundant gymnosperm species, for example Norway spruce (Picea abies), whose TEs comprise more than 70% of the genome, have not been studied in detail. Using next generation sequencing technology, the genome o...

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Section: Resultsmentioning

confidence: 99%

DNA methylome of the 20-gigabase Norway spruce genome

Ausín

Feng

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

101

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“…Gnetales-sister (Lee et al 2011) Angiosperms Eudi + Mag (Lee et al 2011) Eudi + Mag/Chl (Burleigh et al 2009) Mono + Eudi (Soltis et al 2011) A…”

Section: Relationships Among Streptophytic Algal Lineages and Land Plmentioning

confidence: 99%

“…Increasingly, analyses of nuclear genes assembled from publicly available genome or transcriptome databases are being used to assess previously recalcitrant relationships within the green tree of life (27,29,35,(51)(52)(53).…”

mentioning

confidence: 99%

Phylotranscriptomic analysis of the origin and early diversification of land plants

Wickett

Mirarab

Nguyen

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

1,162

1,173

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Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximumlikelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.land plants | Streptophyta | phylogeny | phylogenomics | transcriptome T he origin of embryophytes (land plants) in the Ordovician period roughly 480 Mya (1-4) marks one of the most important events in the evolution of life on Earth. The early evolution of embryophytes in terrestrial environments was facilitated by numerous innovations, including parental protection for the developing embryo, sperm and egg production in multicellular protective structures, and an alternation of phases (often referred to as generations) in which a diploid sporophytic life history stage gives rise to a multicellular haploid gametophytic phase. With Significance Early branching events in the diversification of land plants and closely related algal lineages remain fundamental and unresolved questions in plant evolutionary biology. Accurate reconstructions of these relationships are critical for testing hypotheses of character evolution: for example, the origins of the embryo, vascular tissue, seeds, and flowers. We investigated relationships among streptophyte algae and land plants using the largest set of nuclear genes that has been applied to this problem to date. Hypothesized relationships were rigorously tested through a series of analyses to assess systematic er...

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“…Reports on sRNA studies in gymnosperm seeds have been lacking so far, but previous work on conifer sRNAs have reached different and contradicting conclusions regarding the presence of 24-nt sRNAs, typically associated with hetsiRNAs, in the sRNA transcriptome of the conifers clade Morin et al 2008;Lee et al 2011;Chávez-Montes et al 2014;Wan et al 2012;Zhang et al 2012bZhang et al , 2013bNystedt et al 2013;Niu et al 2015). In somatic embryo-derived material from the conifer Japanese larch (Larix leptolepis) the presence of significant amounts of 24-nt sRNAs has been reported (Zhang et al 2012b(Zhang et al , 2013b, but it would be interesting to check for the presence of these sRNAs in conifer seeds.…”

Section: Abundance Of Small Rnas In Seed Tissuesmentioning

confidence: 99%