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Generic exemplars of the Physcomitrium-Entosthodon complex. A, Physcomitrium pyriforme with long exerted capsules and differentiated operculum. B, Aphanorrhegma serratum with immersed capsules and median dehiscence line. C, Physcomitridium readeri with immersed, indehiscent capsules. D, Physcomitrella magdalenae with immersed capsules lacking any differentiated dehiscence mechanism. E, Physcomitrellopsis africana with an immersed capsule and a vestigial, nonfunctional operculum, and a large and strongly papillose calyptra. F, Physcomitrella patens with immersed capsules lacking any differentiated dehiscence mechanism.
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Selection on spore dispersal mechanisms in mosses is thought to shape the transformation of the sporophyte. The majority of extant mosses develop a sporangium that dehisces through the loss of an operculum, and regulates spore release through the movement of articulate teeth, the peristome, lining the capsule mouth. Such complexity was acquired by...
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... focused on resolving the affinities of five species belonging to four genera diagnosed by their highly reduced sporophytes (Figs. 1B-1F), and potentially scattered within clades of the E-P complex, whose species typically have long exserted sporangia (Fig. 1A). Aphanorrhegma serratum (Wilson & Hook.) Sull. (Fig. 1B) was segregated from Physcomitrium (Sullivant, 1848) and is characterized by immersed capsules, dehiscing along an equatorial line, rather than by the loss ...
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... focused on resolving the affinities of five species belonging to four genera diagnosed by their highly reduced sporophytes (Figs. 1B-1F), and potentially scattered within clades of the E-P complex, whose species typically have long exserted sporangia (Fig. 1A). Aphanorrhegma serratum (Wilson & Hook.) Sull. (Fig. 1B) was segregated from Physcomitrium (Sullivant, 1848) and is characterized by immersed capsules, dehiscing along an equatorial line, rather than by the loss of an operculum. The genus had been expanded to include species otherwise treated in Physcomitrella (Lindberg, 1864;Kindberg, ...
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... focused on resolving the affinities of five species belonging to four genera diagnosed by their highly reduced sporophytes (Figs. 1B-1F), and potentially scattered within clades of the E-P complex, whose species typically have long exserted sporangia (Fig. 1A). Aphanorrhegma serratum (Wilson & Hook.) Sull. (Fig. 1B) was segregated from Physcomitrium (Sullivant, 1848) and is characterized by immersed capsules, dehiscing along an equatorial line, rather than by the loss of an operculum. The genus had been expanded to include species otherwise treated in Physcomitrella (Lindberg, 1864;Kindberg, 1897;Ochyra & Pócs, 1985) or Physcomitrium (Lindberg, ...
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... 1864; Kindberg, 1889), but such concepts are not widely accepted and the genus is currently circumscribed with a single species ( Crosby et al., 1999). Physcomitrella is characterized by capsules that are immersed and cleistocarpous (i.e., lacking any dehiscence mechanism at all). Beside the type species, P. patens (Hedw.) Bruch & Schimp. (Fig. 1F), the genus has been circumscribed with two other species (Crum & Anderson, 1955; or infraspecific taxa (Tan, 1979). McDaniel et al. (2010) raised the possibility that these taxa may, in fact, not share a unique common ancestor, prompting Hooper et al. (2010) to segregate and recognize one as Ephemerella readeri Müll. Hal., a name that ...
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... taxa (Tan, 1979). McDaniel et al. (2010) raised the possibility that these taxa may, in fact, not share a unique common ancestor, prompting Hooper et al. (2010) to segregate and recognize one as Ephemerella readeri Müll. Hal., a name that is illegitimate and was replaced by Physcomitridium readeri (Müll. Hal.) G. Roth (Goffinet & Buck, 2011) (Fig. 1C). The African Physcomitrella magdalenae De Sloover (Fig. 1D), although not sister to P. patens, was not formally moved to another genus pending resolution of generic circumscriptions ( Liu et al., 2012;Medina et al., 2015). Fife (1982a) described a third species, P. bartletii Fife, but subsequently accommodated it in its own genus ...
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... that these taxa may, in fact, not share a unique common ancestor, prompting Hooper et al. (2010) to segregate and recognize one as Ephemerella readeri Müll. Hal., a name that is illegitimate and was replaced by Physcomitridium readeri (Müll. Hal.) G. Roth (Goffinet & Buck, 2011) (Fig. 1C). The African Physcomitrella magdalenae De Sloover (Fig. 1D), although not sister to P. patens, was not formally moved to another genus pending resolution of generic circumscriptions ( Liu et al., 2012;Medina et al., 2015). Fife (1982a) described a third species, P. bartletii Fife, but subsequently accommodated it in its own genus Bryobeck- ettia (Fife, 1985). Finally, Physcomitrellopsis ...
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... sister to P. patens, was not formally moved to another genus pending resolution of generic circumscriptions ( Liu et al., 2012;Medina et al., 2015). Fife (1982a) described a third species, P. bartletii Fife, but subsequently accommodated it in its own genus Bryobeck- ettia (Fife, 1985). Finally, Physcomitrellopsis africana Broth. & Wager ex Dixon (Fig. 1E), a narrow endemic species of South Africa (Magill, 1987) is diagnosed by an immersed capsule with a vestigial, nonfunctional operculum, and a large and strongly papillose calyptra. Dixon (in Gupta, 1933) included a second species, P. indica, but it was subsequently transferred to Physcomitrium ( Gangulee, 1969) and the genus ...
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... for which no data were obtained (Bryobartramia schelpei), eliminating 14 samples that bore signatures of strong heterozygosity, and discarding 161 loci for which two or more paralogs were identified in two or more taxa, we assembled a primary matrix of 70 accessions and 648 loci (Table S1). For the retained samples the recovery rate was high ( Fig. S1) with an average percentage of recovery (as measured by the number of amino acids recovered for a locus divided by the length of the targeted Physcomitrella coding region) of 90% with a range of 64%-99% and median of 91% (Table S2). The average number of loci with a recovery of at least 75% per sample is 564 (or 87%) ranging between ...
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... trees of exons only (Figs. S8, S9) or of supercontigs (Figs. S10, S11) rooted on the Physcomitrellopsis clade are concordant with the one obtained by the supermatrix analysis (Figs. S6, S7), with the E. attenuatus clade sister to the Physcomitrium s. lat. clade in the vast majority of gene trees (Figs. 2A, S12, S13). The inclusion of flanking regions increased the concordance among genes trees at all but ...
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... trees of exons only (Figs. S8, S9) or of supercontigs (Figs. S10, S11) rooted on the Physcomitrellopsis clade are concordant with the one obtained by the supermatrix analysis (Figs. S6, S7), with the E. attenuatus clade sister to the Physcomitrium s. lat. clade in the vast majority of gene trees (Figs. 2A, S12, S13). The inclusion of flanking regions increased the concordance among genes trees at all but three nodes (Figs. 2A, S12 vs. S13; Table S6), namely nodes 14 and 17 (see Fig. S14) in the E. attenuatus clade and 41 in P. pyriforme clade (Table S6). The number of concordant gene trees increased on average by 107 (median 83; Table ...
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... rooted on the Physcomitrellopsis clade are concordant with the one obtained by the supermatrix analysis (Figs. S6, S7), with the E. attenuatus clade sister to the Physcomitrium s. lat. clade in the vast majority of gene trees (Figs. 2A, S12, S13). The inclusion of flanking regions increased the concordance among genes trees at all but three nodes (Figs. 2A, S12 vs. S13; Table S6), namely nodes 14 and 17 (see Fig. S14) in the E. attenuatus clade and 41 in P. pyriforme clade (Table S6). The number of concordant gene trees increased on average by 107 (median 83; Table ...
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... one obtained by the supermatrix analysis (Figs. S6, S7), with the E. attenuatus clade sister to the Physcomitrium s. lat. clade in the vast majority of gene trees (Figs. 2A, S12, S13). The inclusion of flanking regions increased the concordance among genes trees at all but three nodes (Figs. 2A, S12 vs. S13; Table S6), namely nodes 14 and 17 (see Fig. S14) in the E. attenuatus clade and 41 in P. pyriforme clade (Table S6). The number of concordant gene trees increased on average by 107 (median 83; Table ...
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... monophyly of the E. attenuatus clade is supported by only a minority of exon trees (i.e., 43 in Fig. S12, or Fig. 2A) or supercontig trees (i.e., 103 in Fig. S13 or Fig. 2B). The early splits within this clade, that is., the relationships of E. lindigii, are incongruent in the exon and supercontig ASTRAL trees, with in each case the topology only supported by a minority of trees (Fig. 2). By contrast, the monophyly of the Physcomitrium clade, while ...
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... monophyly of the E. attenuatus clade is supported by only a minority of exon trees (i.e., 43 in Fig. S12, or Fig. 2A) or supercontig trees (i.e., 103 in Fig. S13 or Fig. 2B). The early splits within this clade, that is., the relationships of E. lindigii, are incongruent in the exon and supercontig ASTRAL trees, with in each case the topology only supported by a minority of trees (Fig. 2). By contrast, the monophyly of the Physcomitrium clade, while only supported by a minority of exon trees (i.e., 193, ...
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... or Fig. 2B). The early splits within this clade, that is., the relationships of E. lindigii, are incongruent in the exon and supercontig ASTRAL trees, with in each case the topology only supported by a minority of trees (Fig. 2). By contrast, the monophyly of the Physcomitrium clade, while only supported by a minority of exon trees (i.e., 193, Fig. S12 or Fig. 2A left pie chart), is supported by a majority of supercontig trees (i.e., 417; Fig. S13; Fig. 2A, right pie chart). Virtually all nodes within this clade are supported by a vast majority of supercontig trees ( Fig. 2A). If the threshold of gene tree bootstrap support prior to species tree inferences is increased to 70% (Fig. ...
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... incongruent in the exon and supercontig ASTRAL trees, with in each case the topology only supported by a minority of trees (Fig. 2). By contrast, the monophyly of the Physcomitrium clade, while only supported by a minority of exon trees (i.e., 193, Fig. S12 or Fig. 2A left pie chart), is supported by a majority of supercontig trees (i.e., 417; Fig. S13; Fig. 2A, right pie chart). Virtually all nodes within this clade are supported by a vast majority of supercontig trees ( Fig. 2A). If the threshold of gene tree bootstrap support prior to species tree inferences is increased to 70% (Fig. S15), concordance among exon trees decreased on average by 52 trees but concordance among exons ...
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... 193, Fig. S12 or Fig. 2A left pie chart), is supported by a majority of supercontig trees (i.e., 417; Fig. S13; Fig. 2A, right pie chart). Virtually all nodes within this clade are supported by a vast majority of supercontig trees ( Fig. 2A). If the threshold of gene tree bootstrap support prior to species tree inferences is increased to 70% (Fig. S15), concordance among exon trees decreased on average by 52 trees but concordance among exons for the primary conflicting topology decreased even more, by 94 trees (Table S6). The same pattern applied to increasing the threshold for the supercontig trees (Fig. S16), although the loss of concordance was less (i.e., 26 and 50, Table S6), ...
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... of gene tree bootstrap support prior to species tree inferences is increased to 70% (Fig. S15), concordance among exon trees decreased on average by 52 trees but concordance among exons for the primary conflicting topology decreased even more, by 94 trees (Table S6). The same pattern applied to increasing the threshold for the supercontig trees (Fig. S16), although the loss of concordance was less (i.e., 26 and 50, Table S6), and still stronger with regard to the number of conflicting supercontig trees composing the second best alternative (Figs. S13 vs. S16). At this threshold, a single node (node 14 in Fig. S14) saw its support decrease when inferring relationships from supercontigs ...
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... S6). The same pattern applied to increasing the threshold for the supercontig trees (Fig. S16), although the loss of concordance was less (i.e., 26 and 50, Table S6), and still stronger with regard to the number of conflicting supercontig trees composing the second best alternative (Figs. S13 vs. S16). At this threshold, a single node (node 14 in Fig. S14) saw its support decrease when inferring relationships from supercontigs versus exons (Table S6), and on average the number of the most concordant supercontig trees was 135 trees larger than that for the set of most concordant exons trees (Table ...
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... sphaericum and Aphanorrhegma. Physcomitridium readeri is resolved in an isolated position, sister to the P. japonicum to P. pyriforme clade. Support is always maximal based on concatenated data (Figs. S2, S6, S7), and gene tree support rises from a small plurality to a large majority, when inferences are drawn from supercontigs versus exons only (Figs. 2A, S12, S13; Table ...
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... targeting of nuclear loci was not only highly effective, in terms of yield (Fig. S1) but also in terms of consistency and reliability. Sequences retrieved from replicate exemplars for Chamaebryum pottioides, Entosthodon attenuatus, E. clavatus, E. obtusus, Physcomitrella patens or Physcomitrium japonicum were consistent, with inferences resolving these species as monophyletic (Fig. 2). By contrast, Funaria ...
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... close affinity of Aphanorrhegma serratum to species of Physcomitrium was proposed as early as 1851 when Müller treated it as a Physcomitrium (Müller, 1851), and later when Mitten (1869) treated Aphanorrhegma as a section of Physcomitrium. Aphanorrhegma is similar to Physcomitrium immersum, also an Eastern North American endemic (McIntosh, 2007), but differs in the distinct median dehiscence line. ...
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... was erected by Brotherus and Wager (in Dixon, 1922) to accommodate a new South African species, which was similar to Physcomitrella but differed by the distinct seta and rostrate calyptra (Fig. 1E). Dixon (in Gupta, 1933) proposed a second species, which Gangulee (1969) transferred to Physcomitrium. Gupta (1933 had doubted that Physcomitrellopsis was sufficiently distinct from Physcomitrella, but refrained from synonymizing the generic names and Fife (1985) retained the monospecific genus. The species is robustly nested within a ...
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... ASTRAL-III for all samples. Support values indicate multilocus bootstrap (MLBS) values from 100 replicates; each replicate had a single topology chosen from RAxML gene tree bootstrap pseudoreplicates. Branch lengths are in coalescent units (2*N generations), which have been shown to be directly proportional to the amount of gene tree discordance. Fig. S10. Species phylogeny for the Physcomitrium-Entosthodon complex inferred from 648 RAxML supercontig (exon plus flanking non-coding sequence) gene trees (each locus treated as a single partition) using the summary coalescent method ASTRAL-III. Support values indicate local posterior probability (LPP). Branch lengths are in coalescent units ...
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... plus flanking non-coding sequence) gene trees (each locus treated as a single partition) using the summary coalescent method ASTRAL-III. Support values indicate local posterior probability (LPP). Branch lengths are in coalescent units (2*N generations), which have been shown to be directly proportional to the amount of gene tree discordance. Fig. S11. Species phylogeny for the Physcomitrium-Entosthodon complex inferred from 648 RAxML nucleotide supercontig (coding plus flanking non-coding sequence) gene trees using the summary coalescent method ASTRAL-III, and assuming a single partition per locus and a GTRCAT approximation model. Support values indicate multilocus bootstrap (MLBS) ...
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... GTRCAT approximation model. Support values indicate multilocus bootstrap (MLBS) values from 100 replicates; each replicate had a single topology chosen from RAxML gene tree bootstrap pseudoreplicates. Branch lengths are in coalescent units (2*N generations), which have been shown to be directly proportional to the amount of gene tree discordance. Fig. S12. Bipartition analysis for discordant gene trees in the Physcomitrium-Entosthodon complex. On each branch, the number above the branch indicates the number of nucleotide coding sequence gene trees concordant with the ASTRAL-III topology; the number below the branch is the number of gene trees discordant with at least 33% bootstrap ...
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... the number of gene trees discordant with at least 33% bootstrap support. The pie charts also show this information as percentages of the 648 nuclear protein coding loci: concordant gene trees (blue), discordant trees with the second most common rearrangement (green), all other discordant trees (red), and uninformative trees for that node (gray). Fig. S13. Bipartition analysis for discordant gene trees in the Physcomitrium-Entosthodon complex. On each branch, the number above the branch indicates the number of supercontig (coding plus flanking non-coding sequence) gene trees concordant with the ASTRAL-III topology; the number below the branch is the number of gene trees discordant with ...
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... the number of gene trees discordant with at least 33% bootstrap support. The pie charts also show this information as percentages of the 648 nuclear protein coding loci: concordant gene trees (blue), discordant trees with the second most common rearrangement (green), all other discordant trees (red), and uninformative trees for that node (gray). Fig. S14. Tree with node numbers used in Table S6. Fig. S15. Bipartition analysis for discordant gene trees in the Physcomitrium-Entosthodon complex. On each branch, the number above the branch indicates the number of nucleotide coding sequence gene trees concordant with the ASTRAL-III topology; the number below the branch is the number of gene ...
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... 33% bootstrap support. The pie charts also show this information as percentages of the 648 nuclear protein coding loci: concordant gene trees (blue), discordant trees with the second most common rearrangement (green), all other discordant trees (red), and uninformative trees for that node (gray). Fig. S14. Tree with node numbers used in Table S6. Fig. S15. Bipartition analysis for discordant gene trees in the Physcomitrium-Entosthodon complex. On each branch, the number above the branch indicates the number of nucleotide coding sequence gene trees concordant with the ASTRAL-III topology; the number below the branch is the number of gene trees discordant with at least 70% bootstrap ...
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... the number of gene trees discordant with at least 70% bootstrap support. The pie charts also show this information as percentages of the 648 nuclear protein coding loci: concordant gene trees (blue), discordant trees with the second most common rearrangement (green), all other discordant trees (red), and uninformative trees for that node (gray). Fig. S16. Bipartition analysis for discordant gene trees in the Physcomitrium-Entosthodon complex. On each branch, the number above the branch indicates the number of supercontig (coding plus flanking non-coding sequence) gene trees concordant with the ASTRAL-III topology; the number below the branch is the number of gene trees discordant with ...
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... across all taxa (i.e., matrix) for the exons and supercontigs, the average, standard deviation and range in size across all exons and supercontigs, and the loci for which flanking regions were recovered (i.e., all). Table S6. Contrast of support recovered from exons only versus exons and their flanking regions for each node within the E-P complex (Fig. S14 for node number on tree) using a 33% or 70% bootstrap threshold. Data S1. Nucleotide alignments, gene trees, and bipartition analyses for the complete (all Funariaceae) and reduced (E-P complex) datasets, as well as the baits used for the targeted enrichment. available from the Dryad Digital Repository: ...
Citations
... The diversification of moss lineages may have resulted in species differing in their vegetative bodies but sharing a highly conserved sporophytic architecture (e.g., Sphagnum; Crum, 2001), or in congeneric taxa exhibiting distinct morphologies in both generations (e.g., Lewinskya F. Lara & al. in the Orthotrichaceae;Draper & al., 2021), or in taxa sharing a rather stenotypic vegetative body but differing in their morphologically divergent sporophytes (e.g., Physcomitrium (Brid.) Brid. in the Funariaceae; Liu & al., 2012;Medina & al., 2019). ...
... sensu Tan (1979) arose from within a lineage (i.e., Physcomitrium) with long exserted and dehiscent sporophytes. Further evidence against sporophytic trait-based generic concepts within the Physcomitrium-Entosthodon complex was gained from analyses of all organellar protein encoding genes (Medina & al., 2018) and hundreds of putative single-copy nuclear genes (Medina & al., 2019). These phylogenetic hypotheses suggest that transformations of the sporophyte are evolutionarily much more labile than previously assumed, a hypothesis congruent with sporophytic development perhaps being controlled by shifts in temporal expression of just a few genes (Kirbis & al., 2020). ...
... So far only one species with an immersed capsule appears to be of hybrid origin, namely P. immersum Sull. (Medina & al., 2019;Patel & al., in press). ...
Traits of the spore‐bearing generation have historically provided the basis for systematic concepts across the phylogenetic spectrum and depth of mosses. Whether taxa characterized by a simple sporophytic architecture are closely related or emerged from independent reduction is often ambiguous. Phylogenomic inferences in the Funariaceae, which hold the model taxon Physcomitrium patens , revealed that several such shifts in sporophyte complexity occurred, and mostly within the Entosthodon‐Physcomitrium complex. Here, we report the rediscovery of the monospecific, Himalayan endemic genera Brachymeniopsis and Clavitheca , after nearly 100 years and 40 years since their respective descriptions. The genera are characterized by, among other traits, their short sporophytes lacking the sporangial peristome teeth controlling spore dispersal. Phylogenomic inferences reveal that Brachymeniopsis gymnostoma arose within the clade of Entosthodon s.str., a genus with typically long‐exserted capsules. We therefore propose to transfer B. gymnostoma to the genus Entosthodon , as E. gymnostomus comb. nov . Furthermore, Clavitheca poeltii , the sole species of the genus, is morphologically highly similar to E. gymnostomus , and should also be transferred to Entosthodon , but is retained as a distinct taxon, E. poeltii comb. nov . , until additional populations allow for testing the robustness of the observed divergence in costa and seta length between the Nepalese and Chinese populations.
... The moss Physcomitrium patens (P. patens) is a useful material for observing cellular growth due to its simple organ structures, such as phyllids (hereafter, leaves) with a single cell layer (Kofuji & Hasebe, 2014;Medina et al., 2019;Lin et al., 2021). Our analysis of the deletion mutant of the ABCB14 ortholog in P. patens revealed that mutant leaf cells lost regular anisotropic expansion, resulting in shrunken leaves. ...
Anisotropic cell expansion is crucial for the morphogenesis of land plants, as cell migration is restricted by the rigid cell wall. The anisotropy of cell expansion is regulated by mechanisms acting on the deposition or modification of cell wall polysaccharides. Besides the polysaccharide components in the cell wall, a layer of hydrophobic cuticle covers the outer cell wall and is subjected to tensile stress that mechanically restricts cell expansion. However, the molecular machinery that deposits cuticle materials in the appropriate spatiotemporal manner to accommodate cell and tissue expansion remains elusive.
Here, we report that PpABCB14, an ATP‐binding cassette transporter in the moss Physcomitrium patens, regulates the anisotropy of cell expansion. PpABCB14 localized to expanding regions of leaf cells. Deletion of PpABCB14 resulted in impaired anisotropic cell expansion.
Unexpectedly, the cuticle proper was reduced in the mutants, and the cuticular lipid components decreased. Moreover, induced PpABCB14 expression resulted in deformed leaf cells with increased cuticle lipid accumulation on the cell surface.
Taken together, PpABCB14 regulates the anisotropy of cell expansion via cuticle deposition, revealing a regulatory mechanism for cell expansion in addition to the mechanisms acting on cell wall polysaccharides.
... In this study we aim (1) first to confirm the allopolyploidy of three species of the Funariaceae using 50 nuclear genes: Entosthodon hungaricus, Physcomitrium eurystomum, and Physcomitrium collenchymatum, and investigate new evidence of allopolyploidy in Physcomitrium immersum, Physcomitrium sphaericum, and Physcomitrium pyriforme. All species except P. collenchymatum were sampled for target capture sequencing in Medina et al. (2019) but excluded from phylogenetic analysis as they showed heterozygosity congruent with a potential allopolyploid origin. The ploidy and evolutionary origins of P. collenchymatum are additionally considered here to address previously conflicting reports of allopolypoidy associated with the P. collenchymatum phenotype. ...
... The ploidy and evolutionary origins of P. collenchymatum are additionally considered here to address previously conflicting reports of allopolypoidy associated with the P. collenchymatum phenotype. McDaniel et al. (2010), Beike et al. (2014), and Ostendorf et al. (2021), each using the same nuclear dataset, report, based on a single identical population, that P. collenchymatum is an allopolyploid whereas Medina et al. (2018Medina et al. ( , 2019 treated other populations with this phenotype as haploid. Our second aim (2) is to infer evolutionary origins for component subgenomes and in doing so (3) highlight the utility and drawbacks of Homologizer as an approach to subgenome phasing and in identifying maternal and paternal progenitors of hybrid species. ...
... This four-digit identifier is consistent among vouchers, DNA extractions, and sequence data submitted to NCBI's GenBank. Medina et al. (2019) did not include in their nuclear target capture phylogeny 14 samples present in the organellar plastome phylogeny (Medina et al., 2018) though the data were published (https:// www.ncbi.nlm.nih.gov/bioproject/PRJNA674709). These 14 samples were initially flagged as allopolyploid due to (i) high numbers of paralog warnings during sequence assembly with HybPiper 1.3.1 (Johnson et al., 2016), and (ii) high mean heterozygosity across all loci (>10 bp/locus) in gametophyte tissue estimated by mapping reads to a Physcomitrium patens reference sequence. ...
Allopolyploids represent a new frontier in species discovery among embryophytes. Within mosses, allopolyploid discovery is challenged by low morphological complexity. The rapid expansion of sequencing approaches in addition to computational developments to identifying genome merger and whole-genome duplication using variation among nuclear loci representing homeologs has allowed for increased allopolyploid discovery among mosses. Here, we test a novel approach to phasing homeologs within loci and phasing loci across subgenomes, or subgenome assignment, called Homologizer, in the family Funariaceae. We confirm the intergeneric hybrid nature of Entosthodon hungaricus, and the allopolyploid origin of Physcomitrium eurystomum and of one population of P. collenchymatum. We also reveal that hybridization gave rise to P. immersum, as well as to yet unrecognized lineages sharing the phenotype of P. Pyriforme, and P. sphaericum. Our findings demonstrate the utility of our approach when working with polyploid genomes, and its value in identifying progenitor species using target capture data.
... which is expected to increase P. patens datasets in PEATmoss and provide expression data from Anthoceros agrestis and Marchantia polymorpha in the next years. P. patens, recently renamed to Physcomitrium patens [2,3], has been for a long time the main reference for bryophyte species because it was the only species with a complete reproducible life cycle in the lab, a good set of optimized molecular tools and a genome reference. Consequently, most of the expression experiments for bryophytes were done in P. patens. ...
PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data from multiple gene annotation versions. This atlas includes more than 100 experiments of P. patens, is expanding to host Anthoceros agrestis and Marchantia polymorpha, and aims to host data from more species in the future. PEATmoss has multiple visualization methods and tools for data downloading and is connected to the Physcomitrium patens Gene Model Lookup DB (PpGML DB), which links P. patens genes to annotations and resources from several databases and contains tools for gene version lookup and sequence and annotation extraction. Among the new features available in PEATmoss are dataset privacy control, multispecies menu, interactive color scale, co-expression network visualization, and replicate data downloading.Key wordsBryophytesGene expressionRNA-seq
Physcomitrium patens
BioinformaticsMicroarraysAnnotations
Marchantia polymorpha
... The bryophyte Physcomitrium patens (formerly Physcomitrella patens; Medina et al., 2019), which diverged from angiosperms approximately 0.5 billion years ago, has features of ancestral land plants and has been key to our understanding of land plant evolution (Rensing et al., 2020). This plant comprises a two-dimensional (2D) spreading mat of basal assimilatory filaments (chloronemata) and foraging filaments (caulonemata) that comprise foodconducting cells necessary for resource acquisition in dry habitats (reviewed in Ligrone et al., 2012). ...
The plant-specific TOPLESS (TPL) family of transcriptional corepressors is integral to multiple angiosperm developmental processes. Despite this, we know little about TPL function in other plants. To address this gap, we investigated the roles TPL plays in the bryophyte Physcomitrium patens, which diverged from angiosperms approximately 0.5 billion years ago. Although complete loss of PpTPL function is lethal, transgenic lines with reduced PpTPL activity revealed that PpTPLs are essential for two fundamental developmental switches in this plant: the transitions from basal photosynthetic filaments (chloronemata) to specialised foraging filaments (caulonemata) and from 2-dimensional to 3-dimensional growth. Using a transcriptomics approach, we integrate PpTPL into the regulatory network governing 3D growth and propose that PpTPLs represent another important class of regulators that are essential for the 2D to 3D developmental switch. Transcriptomics also revealed a previously unknown role for PpTPL in the regulation of flavonoids. Intriguingly, 3D growth and formation of caulonemata were crucial innovations that facilitated the colonization of land by plants; a major transformative event in the history of life on Earth. We conclude that TPL, which existed before the land plants, was co-opted into new developmental pathways, enabling phytoterrestrialisation and the evolution of land plants.
... Brid. [11,12], or Ditrichum Timm ex Hampe [8], although the larger pleurocarpous mosses, such as in the traditionally delimited Hygrohypnum or Hypnum, have also been shown to be prone to the homoplasic retention of distinct morphological features in unrelated lineages [7,[13][14][15]. ...
... Plants 2023,12, 1360 ...
The recent molecular phylogenetic study of the families Aongstroemiaceae and Di-cranellaceae, which resolved the genera Aongstroemia and Dicranella as polyphyletic, indicated the need for changes in their circumscription and provided new morphological evidence to support the formal description of newly recognized lineages. Following up on these results, the present study adds another molecular marker, the highly informative trnK-psbA region, to a subset of previously analyzed taxa and presents molecular data from newly analyzed austral representatives of Di-cranella and collections of Dicranella-like plants from North Asia. The molecular data are linked with morphological traits, particularly the leaf shape, tuber morphology, and capsule and peristome characters. Based on this multi-proxy evidence, we propose three new families (Dicranellopsida-ceae, Rhizogemmaceae, and Ruficaulaceae) and six new genera (Bryopalisotia, Calcidicranella, Di-cranellopsis, Protoaongstroemia, Rhizogemma, and Ruficaulis) to accommodate the described species according to the revealed phylogenetic affinities. Additionally, we amend the circumscriptions of the families Aongstroemiaceae and Dicranellaceae, as well as the genera Aongstroemia and Di-cranella. In addition to the monotypic Protoaongstroemia that contains the newly described di-cranelloid plant with a 2-3-layered distal leaf portion from Pacific Russia, P. sachalinensis, Dicranella thermalis is described for a D. heteromalla-like plant from the same region. Fourteen new combinations , including one new status change, are proposed.
... P. patens is the first bryophyte whose genome was sequenced (Rensing et al. 2008;Medina et al. 2019). In 2002, the transcriptome of P. patens was represented by roughly 175,000 expressed sequence tags (ESTs) (Rensing et al. 2002a, b). ...
Model organisms are commonly employed in research as convenient tools for studying diverse biological processes. Plant research relied on several non-model plants until the Arabidopsis thaliana was developed as powerful model for identifying genes and determining their functions. To study the genetics of unique processes in different species, few other model photosynthetic organisms have recently been established, including Synechocystis sp. PCC 6803, Anabaena sp. PCC 7120, Chlamydomonas reinhardatii, Oryza sativa, Zea mays, Triticum dicoccoides, Populus trichocarpa, and Picea abies. However, when it comes to answering different biological problems, each of the current model plants has its own set of advantages and disadvantages, and many questions about land plant adaptation strategies at the level of morpho-physiology, development, and stress mitigation could not be adequately answered using these models. Furthermore, the high occurrence of embryo lethal mutations rendered studying the molecular basis of 3-dimensional (3-D) growth and gametogenesis unfeasible. Since bryophytes have a low cellular complexity and a dominant haploid gametophytic phase, they could be useful models not only for avoiding the aforementioned drawbacks, but also for functional genomics research and understanding the chronology of land plant evolution. These distinguishing characteristics and the advancement of sequencing technology have led to the development of some bryophytes as modern model plants, including Physcomitrium patens, Marchantia polymorpha, Anthoceros agrestis. Here, we review at how bryophytes became model plants, and how they have been able to answer crucial plant biology-related concerns like stress tolerance and evolutionary developmental (evo-devo) biology that other model plants have not been able to.
... Physcomitrella patens) 25 (Gransden ecotype) was obtained from the International Moss Stock Center at the University of Freiburg (http:// www. moss-stock-center. ...
Regulation of cell division is crucial for the development of multicellular organisms, and in plants, this is in part regulated by the D-type cyclins (CYCD) and cyclin-dependent kinase A (CDKA) complex. Cell division regulation in Physcomitrium differs from other plants, by having cell division checks at both the G1 to S and G2 to M transition, controlled by the CYCD1/CDKA2 and CYCD2/CDKA1 complexes, respectively. This led us to hypothesize that upregulation of cell division could be archived in Bryophytes, without the devastating phenotypes observed in Arabidopsis. Overexpressing lines of PpCYCD1, PpCYCD2, PpCDKA1, or PpCDKA2 under Ubiquitin promotor control provided transcriptomic and phenotypical data that confirmed their involvement in the G1 to S or G2 to M transition control. Interestingly, combinatorial overexpression of all four genes produced plants with dominant PpCDKA2 and PpCYCD1 phenotypes and led to plants with twice as large gametophores. No detrimental phenotypes were observed in this line and two of the major carbon sinks in plants, the cell wall and starch, were unaffected by the increased growth rate. These results show that the cell cycle characteristics of P. patens can be manipulated by the ectopic expression of cell cycle regulators.
... Genome-scale data including plastid and nuclear genome data have significantly increased the number of informative characters for phylogenetic analyses and have been successfully utilized for reconstructing phylogenies of many plant groups recently Xiang et al., 2017;Kleinkopf et al., 2019;Leebens-Mack et al., 2019;Li et al., 2019;Medina et al., 2019;Ma et al., 2021). The chloroplast genome sequences, easily obtainable from genome skimming (Jansen & Ruhlman, 2012), have become a popular source of data for reconstructing the phylogenetic relationships of many groups at different levels in the past ten years (Bock et al., 2014;Panero et al., 2014;Zhang et al., 2015Zhang et al., , 2016Wen et al., 2018;Liu et al., 2019;Valcárcel & Wen, 2019;Wang et al., 2020;Li et al., 2021;. ...
Genome-scale data have significantly increased the number of informative characters for phylogenetic analyses and recent studies have also revealed widespread phylogenomic discordance in many plant lineages. Aralia sect. Aralia is a small plant lineage (14 spp.) of the ginseng family Araliaceae with a disjunct distribution between eastern Asia (11 spp.) and North America (3 spp.). We herein employ sequences of hundreds of nuclear loci and the complete plastomes using targeted sequence capture and genome skimming to reconstruct the phylogenetic and biogeographic history of this section. We detected substantial conflicts among nuclear genes, yet different analytical strategies generated largely congruent topologies from the nuclear data. Significant cytonuclear discordance was detected, especially concerning the positions of the three North American species. The phylogenomic results support two intercontinental disjunctions: (1) Aralia californica of western North America is sister to the eastern Asian clade consisting of A. cordata and A. continentalis in the nuclear tree, and (2) the eastern North American A. racemosa forms a clade with A. bicrenata from southwestern North America, and the North American A. racemosa - A. bicrenata clade is then sister to the eastern Asian clade consisting of A. glabra (Japan), A. fargesii (C China), and A. apioides and A. atropurpurea (the Hengduan Mountains). Aralia cordata is supported to be disjunctly distributed in Japan, Taiwan, the Ulleung island of Korea, and in Central, Southwest and South China, and Aralia continentalis is redefined with a narrower distribution in Northeast China, eastern Russia and peninsular Korea.
... A similar pattern long characterized the Funariales, with three genera holding nearly 95% of species and 15 genera exhibiting "unique" combinations of morphological traits harboring a single, or perhaps four, species (Fife 1982(Fife , 1985Ochyra 1990;Werner et al. 2007;Goffinet & Buck 2011;Ignatov et al. 2015). Within the Funariaceae, such systematic concepts, based primarily on the degree of modification of the sporophyte only, were recently rejected (Liu et al. 2012;Medina et al. 2018Medina et al. , 2019, highlighting that the perceived morphological distance may be a poor indicator of phylogenetic relatedness. Testing the phylogenetic isolation of monospecific genera from their speciose relatives, especially based on inferences from molecular characters, may often be delayed by the lack of recent and well-preserved collections to extract and sequence specific loci. ...
Florschuetziella scaberrima (Broth.) Vitt, previously known only from the type material collected in 1915 from Yunnan, China, was rediscovered nearly a century later in 2005. The species is morphologically indistinguishable from the Mexican endemic F. steerei Vitt, but given the paucity of material the two are provisionally retained as distinct, allopatric species. Both species exhibit traits reminiscent of Leratia neocaledonica Broth. & Paris, a species endemic to New Caledonia. A shared ancestry with the other species currently accommodated in Leratia Broth. & Paris, i.e., L. exigua (Sull.) Goffinet and L. obtusifolia (Hook.) Goffinet, and the phylogenetically nested position of Florschuetziella Vitt within Leratia supports the merger of the two generic names, and hence the transfer of species of Florschuetziella, prompting the proposed new combinations Leratia steerei (Vitt) Goffinet, S.He & Shevock and Leratia scaberrima (Broth.) Goffinet, S.He & Shevock.
