A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants

Mathews, Sarah; Clements, Mark D.; Beilstein, Mark A.

doi:10.1098/rstb.2009.0233

Cited by 53 publications

(37 citation statements)

References 105 publications

(212 reference statements)

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“…In living gymnosperms, PHYN (PHYA ortholog) is duplicated in cupressophytes (conifer families other than Pinaceae), and PHYP (PHYB ortholog) is duplicated in Pinaceae (Schmidt and Schneider-Poetsch, 2002;Mathews et al, 2010). In Pinus sylvestris, the PHYO (PHYC ortholog) lineage appears to be greatly expanded to include a large number of apparent pseudogenes (García-Gil, 2008).…”

Section: Phylogenetic Surveysmentioning

confidence: 99%

“…Outgroups for rooting the tree are the PHY sequences from M. caldariorum and M. scalaris. Seed plant species relationships are discussed by Mathews et al (2010). Amino acid alignment is provided as Supplemental Data Set 1 online.…”

Section: Conservation Of Phya and Phyb Functionmentioning

confidence: 99%

“…However, in a recently inferred tree, support for the seed plant phytochrome node is low ( Figure 2). This tree was inferred from full-length phytochrome amino acid sequences available in GenBank, with the addition of newly sequenced full-length or nearly-full-length sequences to better represent gymnosperms and basal nodes in the angiosperm tree (see Supplemental Data Set 1 online; Mathews et al, 2010). Resolution of this node is sensitive to taxon sampling, and fulllength sequences from ferns, especially from lineages that diverge early in their history, as well as from lycopods and Equisetum, are needed to further understand phytochrome phylogeny among tracheophytes.…”

Section: Phylogenetic Surveysmentioning

confidence: 99%

“…The optimal maximum likelihood tree and bootstrap percentages (numbers above branches, except for the PHYO/C node, where it is below the branch) were inferred from analyses of full-length or nearly-full-length amino acid sequences using RAxML 7.0.4 (Stamatakis, 2006), a phytochrome-specific amino acid transition matrix (Mathews et al, 2010); the thorough (designated with the f -i switch) bootstrap option was used. Outgroups for rooting the tree are the PHY sequences from M. caldariorum and M. scalaris.…”

Section: Conservation Of Phya and Phyb Functionmentioning

confidence: 99%

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Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

Mathews

2010

The Plant Cell

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107

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A synthesis of insights from functional and evolutionary studies reveals how the phytochrome photoreceptor system has evolved to impart both stability and flexibility. Phytochromes in seed plants diverged into three major forms, phyA, phyB, and phyC, very early in the history of seed plants. Two additional forms, phyE and phyD, are restricted to flowering plants and Brassicaceae, respectively. While phyC, D, and E are absent from at least some taxa, phyA and phyB are present in all sampled seed plants and are the principal mediators of red/far-red-induced responses. Conversely, phyC-E apparently function in concert with phyB and, where present, expand the repertoire of phyB activities. Despite major advances, aspects of the structural-functional models for these photoreceptors remain elusive. Comparative sequence analyses expand the array of locus-specific mutant alleles for analysis by revealing historic mutations that occurred during gene lineage splitting and divergence. With insights from crystallographic data, a subset of these mutants can be chosen for functional studies to test their importance and determine the molecular mechanism by which they might impact light perception and signaling. In

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Section: Phylogenetic Surveysmentioning

confidence: 99%

Section: Conservation Of Phya and Phyb Functionmentioning

confidence: 99%

Section: Phylogenetic Surveysmentioning

confidence: 99%

Section: Conservation Of Phya and Phyb Functionmentioning

confidence: 99%

See 2 more Smart Citations

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

Mathews

2010

The Plant Cell

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107

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“…For the phytochrome phylogeny, we used the protein alignment following the analytical strategy of Mathews et al (63). Using ProtTest (64), JTT + F was found to be the best empirical substitution model under the Akaike Information Criterion.…”

Section: Methodsmentioning

confidence: 99%

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Villarreal

Kelly

et al. 2014

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

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147

148

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Significance Despite being one of the oldest groups of land plants, the majority of living ferns resulted from a relatively recent diversification following the rise of angiosperms. To exploit fully the new habitats created by angiosperm-dominated ecosystems, ferns had to evolve novel adaptive strategies to cope with the low-light conditions exerted by the angiosperm canopy. Neochrome, an unconventional photoreceptor that allows ferns to “see the light” better, was likely part of the solution. Surprisingly, we discovered that fern neochrome was derived from a bryophyte lineage via horizontal gene transfer (HGT). This finding not only provides the first evidence that a plant-to-plant HGT can have a profound evolutionary impact but also has implications for the evolution of photosensory systems in plants.

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Phylogeny and Evolution of Vascular Plants

Qiu

2018

Encyclopedia of Life Sciences

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Vascular plants play a major role in global carbon cycling and are of fundamental importance to life on earth. Over the last half‐century, phylogenetic studies of morphological and molecular data have brought tremendous progress in our understanding of origin, phylogeny and evolution of these plants. It is clear that they evolved from a bryophytic ancestor, which likely resembles hornworts in the modern earth flora. Among all living vascular plants, lycophytes represent the first diverging lineage. Ferns and other free‐sporing vascular plants make up a clade called monilophytes, which are sister to seed plants. Extant gymnosperms form a monophyletic group in most molecular studies, but this result may need further investigation as morphological support is lacking. Among living angiosperms, Amborella , Nymphaeales and Austrobaileyales have been unequivocally demonstrated to represent the oldest lineages, a result that will facilitate solving Darwin's abominable mystery – the origin of angiosperms. Key Concepts Origin of vascular plants: Current phylogenetic and fossil evidence tends to support bryophytes as a paraphyletic group and thus vascular plants originated from a bryophytic ancestor. Phylogeny and evolution of life cycle in land plants: The bryophytic origin of vascular plants supports antithetic theory: The multicellular diploid sporophyte generation in land plants was an interpolation of a new structure derived from delay of meiosis in the life cycle, and continuously increased as plants evolved, eventually outweighing the haploid gametophyte generation. Relationships among early vascular plants: The long‐standing issue of how several relictual vascular plant lineages are related to each other have been finally resolved, with lycophytes representing the oldest living member of vascular plants and Equisetum being sister to a group composed of Psilotaceae and eusporangiate and leptosporangiate ferns. Monilophytes and origin of seed plants: Among extant free‐sporing vascular plants, Equisetum , Psilotaceae and ferns together make up a monophyletic group called monilophytes, which is sister to seed plants. The first angiosperms: Among all living angiosperms, Amborella , a shrub from New Caledonia, and Nymphaeales represent the basalmost lineages and they could offer some clues to what the first angiosperms looked like. Phylogenomics and phylogeny: The colossal amount of information that is being unearthed from genomes is enabling a new quantum leap in phylogenetics and evolutionary biology, but the data need to be carefully and rigorously analysed so that the results are not simply trees with high statistical support, and instead can withstand repeated falsification tests.

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A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants

Cited by 53 publications

References 105 publications

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Phylogeny and Evolution of Vascular Plants

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