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Paula J. Rudall - One of the best experts on this subject based on the ideXlab platform.
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transcriptome derived evidence supports recent polyploidization and a major phylogeographic division in trithuria submersa hydatellaceae Nymphaeales
New Phytologist, 2016Co-Authors: Terry D. Macfarlane, Isabel Marques, Sean A Montgomery, Michael S Barker, John G Conran, Pilar Catalan, Loren H Rieseberg, Paula J. RudallAbstract:Relatively little is known about species-level genetic diversity in flowering plants outside the eudicots and monocots, and it is often unclear how to interpret genetic patterns in lineages with whole-genome duplications. We addressed these issues in a polyploid representative of Hydatellaceae, part of the water-lily order Nymphaeales. We examined a transcriptome of Trithuria submersa for evidence of recent whole-genome duplication, and applied transcriptome-derived microsatellite (expressed-sequence tag simple-sequence repeat (EST-SSR)) primers to survey genetic variation in populations across its range in mainland Australia. A transcriptome-based Ks plot revealed at least one recent polyploidization event, consistent with fixed heterozygous genotypes representing underlying sets of homeologous loci. A strong genetic division coincides with a trans-Nullarbor biogeographic boundary. Patterns of 'allelic' variation (no more than two variants per EST-SSR genotype) and recently published chromosomal evidence are consistent with the predicted polyploidization event and substantial homozygosity underlying fixed heterozygote SSR genotypes, which in turn reflect a selfing mating system. The Nullarbor Plain is a barrier to gene flow between two deep lineages of T. submersa that may represent cryptic species. The markers developed here should also be useful for further disentangling species relationships, and provide a first step towards future genomic studies in Trithuria.
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chromosome behavior at the base of the angiosperm radiation karyology of trithuria submersa hydatellaceae Nymphaeales
American Journal of Botany, 2014Co-Authors: Ralf G Kynast, Margaret M. Ramsay, Jaume Pellicer, Jeffrey A Joseph, Paula J. RudallAbstract: Premise of the study: Hydatellaceae are minute annual herbs with potential as a model system for studying early angiosperm evolution, but their karyology and ploidy levels are almost unknown. We investigated these aspects of Trithuria submersa , a widespread species that we show to be amenable to extended vegetative propagation. Methods: We cultivated plants of T. submersa in vitro after developing and optimizing culture conditions. We estimated genome size using fl ow cytometry, counted chromosome numbers using root-meristem squashes after Feulgen staining, and examined meiotic chromosome behavior using microsporocytes. Key results: We developed methods to reliably germinate seeds of T. submersa and to propagate them vegetatively in critical thermo- and photoperiod regimes on 1/2 Murashige–Skoog (MS) medium with vitamins and 2% sucrose solidifi ed with 0.7% agar-agar. Seedling growth requires the medium be supplemented with activated charcoal. The mean nuclear DNA content of T. submersa sporophytes is 2C = 2.74 pg (~2.68 Gbp). The sporophytic chromosome number is 2 n = 56 with a bimodal complement, which may suggest an allopolyploid origin. Some of the largest chromosomes lack a recognizable constriction, which relates to a highly unusual and irregular chromosome behavior. Microsporocytes undergo reduced and asynchronous meioses that show a modifi ed intermediate cell division with a nucleus division by fractional postreduction, indicating partially inverted microsporogenesis. Conclusions: In vitro cultivation and karyological assessment of T. submersa open new opportunities for investigating earlydivergent angiosperms. The remarkably different meiotic behavior exhibits new insights into a potentially ancestral microsporogenesis.
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reconstructing the age and historical biogeography of the ancient flowering plant family hydatellaceae Nymphaeales
BMC Evolutionary Biology, 2014Co-Authors: William J. D. Iles, Margarita V. Remizowa, Dmitry D. Sokoloff, Paula J. Rudall, Terry D. Macfarlane, Shrirang R. Yadav, Christopher M Lee, Matthew D Barrett, Russell L Barrett, Sean W. GrahamAbstract:The aquatic flowering-plant family Hydatellaceae has a classic Gondwanan distribution, as it is found in Australia, India and New Zealand. To shed light on the biogeographic history of this apparently ancient branch of angiosperm phylogeny, we dated the family in the context of other seed-plant divergences, and evaluated its biogeography using parsimony and likelihood methods. We also explicitly tested the effect of different extinction rates on biogeographic inferences. We infer that the stem lineage of Hydatellaceae originated in the Lower Cretaceous; in contrast, its crown originated much more recently, in the early Miocene, with the bulk of its diversification after the onset of the Pliocene. Biogeographic reconstructions predict a mix of dispersal and vicariance events, but considerations of geological history preclude most vicariance events, besides a split at the root of the family between southern and northern clades. High extinction rates are plausible in the family, and when these are taken into account there is greater uncertainty in biogeographic inferences. A stem origin for Hydatellaceae in the Lower Cretaceous is consistent with the initial appearance of fossils attributed to its sister clade, the water lilies. In contrast, the crown clade is young, indicating that vicariant explanations for species outside Australia are improbable. Although long-distance dispersal is likely the primary driver of biogeographic distribution in Hydatellaceae, we infer that the recent drying out of central Australia divided the family into tropical vs. subtropical/temperate clades around the beginning of the Miocene.
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embryo and seedling morphology in trithuria lanterna hydatellaceae Nymphaeales new data for infrafamilial systematics and a novel type of syncotyly
Botanical Journal of the Linnean Society, 2014Co-Authors: Dmitry D. Sokoloff, Margaret M. Ramsay, Margarita V. Remizowa, Terry D. Macfarlane, John G Conran, Paula J. RudallAbstract:The monogeneric early-divergent angiosperm family Hydatellaceae (Trithuria) was formerly placed in the monocots and shows several features that are at least superficially monocot-like. Seedlings of Hydatellaceae are unusually diverse and have been interpreted as either dicotylar or monocotylar. We provide the first detailed developmental description of seedlings of Trithuria lanterna (including the first data on mature embryos of tropical Hydatellaceae) as a basis for the general discussion of seedling diversity in Hydatellaceae. Seedlings at various stages after germination were studied using serial sections and scanning electron microscopy. The embryo is dicotylar. It lacks pronounced asymmetry and lacks a plumule before seed germination. In the majority of seedlings, the cotyledons are free and appear attached to the seedling axis at different levels. In other seedlings, the cotyledons are united via a non-haustorial leaf-like organ; this alternative condition represents a novel type of syncotyly for seed plants and a second type of syncotyly recorded for Hydatellaceae. Seedling morphology is determined by strong one-sided growth of the hypocotyl, which is an unusual way of overcoming the basic seed plant spatial constraint at germination. The direction of one-sided growth is independent of cotyledon orientation and could be environmentally determined. Seedlings provide synapomorphies for the two major clades of Trithuria, which can be regarded as subgenera. Although no direct homology is inferred, the exceptional degree of morphological variation in Hydatellaceae seedlings, including the variable occurrence of several superficially monocot-like features, leads us to hypothesize that the stem group of monocots could have exhibited an analogous degree of variation in cotyledon morphology. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 551–573.
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impact of spatial constraints during seed germination on the evolution of angiosperm cotyledons a case study from tropical hydatellaceae Nymphaeales
American Journal of Botany, 2013Co-Authors: Dmitry D. Sokoloff, Margaret M. Ramsay, Margarita V. Remizowa, Anton S. Beer, Terry D. Macfarlane, Shrirang R. Yadav, Paula J. RudallAbstract:UNLABELLED PREMISE OF THE STUDY A bipolar embryo with cotyledons is a characteristic feature that appeared early in the evolution of seed plants. Cotyledon number is an important character in angiosperm classification. We explore the links between functional aspects of seed germination and the number and location of the cotyledons, using as a model the early-divergent angiosperm family Hydatellaceae, in which seedlings are superficially monocot-like. • METHODS Seedlings of two species of tropical Hydatellaceae were studied using light and scanning electron microscopy. • KEY RESULTS Seedlings of Trithuria cowieana bear two free cotyledons. Each cotyledon possesses a green, filiform, vascularized blade that resembles subsequent leaves, and a basal, nonvascularized, haustorial outgrowth that remains in close contact with the endosperm. Seedlings of Trithuria konkanensis have two free cotyledonary haustoria inserted close to each other and a leaf blade probably belonging to one of the cotyledons. The cotyledonary node elongates between the haustoria and the leaf blade to form a mesocotyl. • CONCLUSIONS To date, the absence or presence of a cotyledonary tube represents the only known qualitative morphological difference between the two major clades of Hydatellaceae. Cotyledons with a haustorium and leaf blade are unusual at the scale of seed plants and probably evolved due to homeosis. The mesocotyl of T. konkanensis resembles that of grasses and sedges. Seedling diversity in Hydatellaceae and other seed plants is linked with the principal physical and spatial constraint of their embryo structure, with the primary root and shoot apical meristems located at opposite poles, and haustorial cotyledon tips.
Rebecca A Povilus - One of the best experts on this subject based on the ideXlab platform.
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transcriptomes across fertilization and seed development in the water lily nymphaea thermarum Nymphaeales reveal dynamic expression of dna and histone methylation modifiers
bioRxiv, 2021Co-Authors: Rebecca A Povilus, W E FriedmanAbstract:Studies of gene expression during seed development have been performed for a growing collection of species from a phylogenetically broad sampling of flowering plants (angiosperms). However, attention has mostly been focused on crop species or a small number of model systems. Information on gene expression during seed development is minimal for those angiosperm lineages whose origins predate the divergence of monocots and eudicots. In order to provide a new perspective on the early evolution of seed development in flowering plants, we sequenced transcriptomes of whole ovules and seeds from three key stages of reproductive development in the waterlily Nymphaea thermarum, an experimentally-tractable member of the Nymphaeales. We first explore general patterns of gene expression, beginning with mature ovules and continuing through fertilization into early- and mid-seed development. We then examine the expression of genes associated with DNA and histone methylation - processes known to be essential for development in distantly-related and structurally-divergent monocots and eudicots. Around 60% of transcripts putatively homologous to DNA and histone methylation modifiers are differentially expressed during seed development in N. thermarum, suggesting that the importance of dynamic epigenetic patterning during seed development dates to the earliest phases of angiosperm evolution. However, genes involved in establishing, maintaining, and removing methylation marks associated with genetic imprinting show a mix of conserved and unique expression patterns between N. thermarum and other flowering plants. Our data suggests that the regulation of imprinting has likely changed throughout angiosperm evolution, and furthermore identifies genes that merit further characterization in any angiosperm system.
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water lily nymphaea thermarum genome reveals variable genomic signatures of ancient vascular cambium losses
Proceedings of the National Academy of Sciences of the United States of America, 2020Co-Authors: Rebecca A Povilus, Jeffrey M Dacosta, Prasad R V Satyaki, Morgan Moeglein, Johan Jaenisch, Christopher J Grassa, Zhenxiang Xi, Sarah MathewsAbstract:For more than 225 million y, all seed plants were woody trees, shrubs, or vines. Shortly after the origin of angiosperms ∼140 million y ago (MYA), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium, the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem, which are produced by apical meristems and retained in nearly all seed plants. Here, we sequenced and assembled a draft genome of the water lily Nymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compared it to genomes from other cambium-bearing and cambium-less lineages (e.g., monocots and Nelumbo). This revealed lineage-specific patterns of gene loss and divergence. Nymphaea is characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss of REVOLUTA, which influences cambial activity in other angiosperms. We also found the Nymphaea and monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids. Nelumbo displays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent loss of vascular cambium reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent events of trait loss. Our results shed light on the evolution of herbaceousness—one of the key biological innovations associated with the earliest phases of angiosperm evolution.
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water lily nymphaea thermarum draft genome reveals variable genomic signatures of ancient vascular cambium losses
bioRxiv, 2019Co-Authors: Rebecca A Povilus, Jeffrey M Dacosta, Prasad R V Satyaki, Morgan Moeglein, Johan Jaenisch, Christopher J Grassa, Sarah Mathews, Zhenxiang Xi, Mary Gehring, Charles C DavisAbstract:For more than 225 million years, all seed plants were woody trees, shrubs, or vines (1,2,3,4). Shortly after the origin of angiosperms ~135 million years ago (MYA) (5), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium (6), the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem (7,8,9), which are produced by apical meristems and retained in nearly all seed plants. Here we sequence and assemble a draft genome of the water lily Nymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compare it to genomes from other cambium-bearing and cambium-less lineages (like monocots and Nelumbo). This reveals lineage-specific patterns of gene loss and divergence. Nymphaea is characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss of REVOLUTA, which influences cambial activity in other angiosperms. We also find the Nymphaea and monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids. Nelumbo displays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent vascular cambium loss reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent trait loss events. Our results shed light on the evolution of herbaceousness,which is one of the key biological innovations associated with the earliest phases of angiosperm evolution.
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floral biology and ovule and seed ontogeny of nymphaea thermarum a water lily at the brink of extinction with potential as a model system for basal angiosperms
Annals of Botany, 2015Co-Authors: Rebecca A Povilus, Juan M Losada, William E. FriedmanAbstract:BACKGROUND AND AIMS: Nymphaea thermarum is a member of the Nymphaeales, of one of the most ancient lineages of flowering plants. This species was only recently described and then declared extinct in the wild, so little is known about its reproductive biology. In general, the complete ontogeny of ovules and seeds is not well documented among species of Nymphaea and has never been studied in the subgenus Brachyceras, the clade to which N. thermarum belongs. METHODS: Flowers and fruits were processed for brightfield, epifluorescence and confocal microscopy. Flower morphology, with emphasis on the timing of male and female functions, was correlated with key developmental stages of the ovule and the female gametophyte. Development of the seed tissues and dynamics of polysaccharide reserves in the endosperm, perisperm and embryo were examined. KEY RESULTS: Pollen release in N. thermarum starts before the flower opens. Cell walls of the micropylar nucellus show layering of callose and cellulose in a manner reminiscent of transfer cell wall patterning. Endosperm development is ab initio cellular, with micropylar and chalazal domains that embark on distinct developmental trajectories. The surrounding maternal perisperm occupies the majority of seed volume and accumulates starch centrifugally. In mature seeds, a minute but fully developed embryo is surrounded by a single, persistent layer of endosperm. CONCLUSIONS: Early male and female function indicate that N. thermarum is predisposed towards self-pollination, a phenomenon that is likely to have evolved multiple times within Nymphaea. While formation of distinct micropylar and chalazal developmental domains in the endosperm, along with a copious perisperm, characterize the seeds of most members of the Nymphaeales, seed ontogenies vary between and among the constituent families. Floral biology, life history traits and small genome size make N. thermarum uniquely promising as an early-diverging angiosperm model system for genetic and molecular studies.
Dmitry D. Sokoloff - One of the best experts on this subject based on the ideXlab platform.
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developmental flower and rhizome morphology in nuphar Nymphaeales an interplay of chaos and stability
Frontiers in Cell and Developmental Biology, 2020Co-Authors: Elena S El, Margarita V. Remizowa, Dmitry D. SokoloffAbstract:European species of Nuphar are amongthe most accessible members of the basal angiosperm grade, but detailed studies using scanning electron microscopy are lacking. We provide such data and discuss them in the evolutionary context. Dorsiventral monopodial rhizomes of Nuphar bear foliage leaves and non-axillary reproductive units (RUs) arranged in a Fibonacci spiral. The direction of the phyllotaxis spiral is established in seedlings apparently environmentally and maintained through all rhizome branching events. The RUs can be located on dorsal, ventral or lateral side of the rhizome. There is no seasonality in timing of their initiation. The RUs usually form pairs in positions N and N + 2 along the ontogenetic spiral. New rhizomes appear on lateral sides of the mother rhizome. A lateral rhizome is subtended by a foliage leaf (N) and is accompanied by a RU in the position N + 2. We hypothesize a two-step process of regulation of RU/branch initiation, with the second step possibly involving environmental factors such as gravitropism. Each RU has a short stalk, 1-2 scale-like phyllomes and a long-pedicellate flower. We support a theory that the flower is lateral to the RU axis. The five sepals initiate successively and form two whorls as 3 + 2. The sepal arrangement is not 'intermediate' between whorled and spiral. Mechanisms of phyllotaxis establishment differ between flowers and lateral rhizomes. Petal, stamen and carpel numbers are not precisely fixed. Petals are smaller than sepals and form a whorl. They appear first in the sectors of the outer whorl sepals. The stamen arrangement is whorled to chaotic. The merism of the androecium tends to be the same as in the corolla. Flowers with odd numbers of stamen orthostichies are found. These are interpreted as having a non-integer merism of the androecium (e.g., 14.5). Carpels form a whorl in N. lutea and normally alternate with inner whorl stamens. Sterile second whorl carpel(s) are found in some flowers of N. pumila.
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reconstructing the age and historical biogeography of the ancient flowering plant family hydatellaceae Nymphaeales
BMC Evolutionary Biology, 2014Co-Authors: William J. D. Iles, Margarita V. Remizowa, Dmitry D. Sokoloff, Paula J. Rudall, Terry D. Macfarlane, Shrirang R. Yadav, Christopher M Lee, Matthew D Barrett, Russell L Barrett, Sean W. GrahamAbstract:The aquatic flowering-plant family Hydatellaceae has a classic Gondwanan distribution, as it is found in Australia, India and New Zealand. To shed light on the biogeographic history of this apparently ancient branch of angiosperm phylogeny, we dated the family in the context of other seed-plant divergences, and evaluated its biogeography using parsimony and likelihood methods. We also explicitly tested the effect of different extinction rates on biogeographic inferences. We infer that the stem lineage of Hydatellaceae originated in the Lower Cretaceous; in contrast, its crown originated much more recently, in the early Miocene, with the bulk of its diversification after the onset of the Pliocene. Biogeographic reconstructions predict a mix of dispersal and vicariance events, but considerations of geological history preclude most vicariance events, besides a split at the root of the family between southern and northern clades. High extinction rates are plausible in the family, and when these are taken into account there is greater uncertainty in biogeographic inferences. A stem origin for Hydatellaceae in the Lower Cretaceous is consistent with the initial appearance of fossils attributed to its sister clade, the water lilies. In contrast, the crown clade is young, indicating that vicariant explanations for species outside Australia are improbable. Although long-distance dispersal is likely the primary driver of biogeographic distribution in Hydatellaceae, we infer that the recent drying out of central Australia divided the family into tropical vs. subtropical/temperate clades around the beginning of the Miocene.
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embryo and seedling morphology in trithuria lanterna hydatellaceae Nymphaeales new data for infrafamilial systematics and a novel type of syncotyly
Botanical Journal of the Linnean Society, 2014Co-Authors: Dmitry D. Sokoloff, Margaret M. Ramsay, Margarita V. Remizowa, Terry D. Macfarlane, John G Conran, Paula J. RudallAbstract:The monogeneric early-divergent angiosperm family Hydatellaceae (Trithuria) was formerly placed in the monocots and shows several features that are at least superficially monocot-like. Seedlings of Hydatellaceae are unusually diverse and have been interpreted as either dicotylar or monocotylar. We provide the first detailed developmental description of seedlings of Trithuria lanterna (including the first data on mature embryos of tropical Hydatellaceae) as a basis for the general discussion of seedling diversity in Hydatellaceae. Seedlings at various stages after germination were studied using serial sections and scanning electron microscopy. The embryo is dicotylar. It lacks pronounced asymmetry and lacks a plumule before seed germination. In the majority of seedlings, the cotyledons are free and appear attached to the seedling axis at different levels. In other seedlings, the cotyledons are united via a non-haustorial leaf-like organ; this alternative condition represents a novel type of syncotyly for seed plants and a second type of syncotyly recorded for Hydatellaceae. Seedling morphology is determined by strong one-sided growth of the hypocotyl, which is an unusual way of overcoming the basic seed plant spatial constraint at germination. The direction of one-sided growth is independent of cotyledon orientation and could be environmentally determined. Seedlings provide synapomorphies for the two major clades of Trithuria, which can be regarded as subgenera. Although no direct homology is inferred, the exceptional degree of morphological variation in Hydatellaceae seedlings, including the variable occurrence of several superficially monocot-like features, leads us to hypothesize that the stem group of monocots could have exhibited an analogous degree of variation in cotyledon morphology. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 551–573.
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impact of spatial constraints during seed germination on the evolution of angiosperm cotyledons a case study from tropical hydatellaceae Nymphaeales
American Journal of Botany, 2013Co-Authors: Dmitry D. Sokoloff, Margaret M. Ramsay, Margarita V. Remizowa, Anton S. Beer, Terry D. Macfarlane, Shrirang R. Yadav, Paula J. RudallAbstract:UNLABELLED PREMISE OF THE STUDY A bipolar embryo with cotyledons is a characteristic feature that appeared early in the evolution of seed plants. Cotyledon number is an important character in angiosperm classification. We explore the links between functional aspects of seed germination and the number and location of the cotyledons, using as a model the early-divergent angiosperm family Hydatellaceae, in which seedlings are superficially monocot-like. • METHODS Seedlings of two species of tropical Hydatellaceae were studied using light and scanning electron microscopy. • KEY RESULTS Seedlings of Trithuria cowieana bear two free cotyledons. Each cotyledon possesses a green, filiform, vascularized blade that resembles subsequent leaves, and a basal, nonvascularized, haustorial outgrowth that remains in close contact with the endosperm. Seedlings of Trithuria konkanensis have two free cotyledonary haustoria inserted close to each other and a leaf blade probably belonging to one of the cotyledons. The cotyledonary node elongates between the haustoria and the leaf blade to form a mesocotyl. • CONCLUSIONS To date, the absence or presence of a cotyledonary tube represents the only known qualitative morphological difference between the two major clades of Hydatellaceae. Cotyledons with a haustorium and leaf blade are unusual at the scale of seed plants and probably evolved due to homeosis. The mesocotyl of T. konkanensis resembles that of grasses and sedges. Seedling diversity in Hydatellaceae and other seed plants is linked with the principal physical and spatial constraint of their embryo structure, with the primary root and shoot apical meristems located at opposite poles, and haustorial cotyledon tips.
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Molecular phylogenetics of Hydatellaceae (Nymphaeales): Sexual-system homoplasy and a new sectional classification
American Journal of Botany, 2012Co-Authors: William J. D. Iles, Margarita V. Remizowa, Dmitry D. Sokoloff, Paula J. Rudall, Terry D. Macfarlane, Maria D. Logacheva, Sean W. GrahamAbstract:PREMISE OF THE STUDY: Species relationships are unknown in Hydatellaceae, a small family of dwarf aquatics related to water lilies that arose near the base of angiosperm phylogeny. Here we use molecular evidence to infer a species tree for the family and apply this to reconstructing major transitions in morphology and sexual system in this early branch of angiosperms. METHODS: We assembled plastid (atpB, matK, ndhF, rbcL) and nuclear (ribosomal ITS) data for 50 samples (including outgroups) and estimated a species tree for Hydatellaceae using a Bayesian multispecies coalescent approach. We reconstructed the evolution of several morphological characters, then tested for associations between sexual system and reproductive morphology using phylogenetic ANOVA. KEY RESULTS: Dioecious species of Hydatellaceae have significantly greater stamen number and anther length than do cosexual species, suggesting changes in male function. The perennial habit that defines one subclade likely represents a reversion from annuality. Species relationships do not fall along traditional morphological divisions, but new sections proposed here are supported by fruit and seed synapomorphies. The earliest split in the family is reflected in geography and climate (i.e., tropical vs. subtropical/temperate clades). We found limited evidence of incongruence between plastid and nuclear trees, with one exception involving gene-tree nonmonophyly for two close relatives (Trithuria submersa, T. bibracteata). CONCLUSIONS: While the direction of sexual-system evolution is ambiguous, transitions are significantly associated with changes in involucral phyllome length and proxies of pollen production. We propose a new sectional circumscription based on fruit, seed, and DNA evidence.
Yongzhi Yang - One of the best experts on this subject based on the ideXlab platform.
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prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution
Nature plants, 2020Co-Authors: Yongzhi Yang, Leke Lv, Dafu Ru, Donglei Wang, Xingxing Shen, Ying Li, Lei Zhang, Fanbo Meng, Beibei JiaoAbstract:Angiosperms represent one of the most spectacular terrestrial radiations on the planet1, but their early diversification and phylogenetic relationships remain uncertain2–5. A key reason for this impasse is the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of two aquatic species—prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales)—and expand the genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (that is, Nymphaeales, magnoliids, monocots, Ceratophyllales and eudicots). Furthermore, our phylogenomic analyses, which spanned multiple datasets and diverse methods, confirm that Amborella and Nymphaeales are successively sister to all other angiosperms. Furthermore, these genomes help to elucidate relationships among the major subclades within Mesangiospermae, which contain about 350,000 species. In particular, the species-poor lineage Ceratophyllales is supported as sister to eudicots, and monocots and magnoliids are placed as successively sister to Ceratophyllales and eudicots. Finally, our analyses indicate that incomplete lineage sorting may account for the incongruent phylogenetic placement of magnoliids between nuclear and plastid genomes. Genome assemblies of two aquatic species, prickly waterlily and rigid hornwort, clarify the early diversification and phylogeny of plants. Multiple independent polyploidization events are inferred in each of the five major angiosperm clades.
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prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution
Nature plants, 2020Co-Authors: Yongzhi Yang, Leke Lv, Dafu Ru, Donglei Wang, Xingxing Shen, Ying Li, Lei Zhang, Fanbo Meng, Beibei JiaoAbstract:Angiosperms represent one of the most spectacular terrestrial radiations on the planet1, but their early diversification and phylogenetic relationships remain uncertain2–5. A key reason for this impasse is the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of two aquatic species—prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales)—and expand the genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (that is, Nymphaeales, magnoliids, monocots, Ceratophyllales and eudicots). Furthermore, our phylogenomic analyses, which spanned multiple datasets and diverse methods, confirm that Amborella and Nymphaeales are successively sister to all other angiosperms. Furthermore, these genomes help to elucidate relationships among the major subclades within Mesangiospermae, which contain about 350,000 species. In particular, the species-poor lineage Ceratophyllales is supported as sister to eudicots, and monocots and magnoliids are placed as successively sister to Ceratophyllales and eudicots. Finally, our analyses indicate that incomplete lineage sorting may account for the incongruent phylogenetic placement of magnoliids between nuclear and plastid genomes. Genome assemblies of two aquatic species, prickly waterlily and rigid hornwort, clarify the early diversification and phylogeny of plants. Multiple independent polyploidization events are inferred in each of the five major angiosperm clades.
Sarah Mathews - One of the best experts on this subject based on the ideXlab platform.
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water lily nymphaea thermarum genome reveals variable genomic signatures of ancient vascular cambium losses
Proceedings of the National Academy of Sciences of the United States of America, 2020Co-Authors: Rebecca A Povilus, Jeffrey M Dacosta, Prasad R V Satyaki, Morgan Moeglein, Johan Jaenisch, Christopher J Grassa, Zhenxiang Xi, Sarah MathewsAbstract:For more than 225 million y, all seed plants were woody trees, shrubs, or vines. Shortly after the origin of angiosperms ∼140 million y ago (MYA), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium, the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem, which are produced by apical meristems and retained in nearly all seed plants. Here, we sequenced and assembled a draft genome of the water lily Nymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compared it to genomes from other cambium-bearing and cambium-less lineages (e.g., monocots and Nelumbo). This revealed lineage-specific patterns of gene loss and divergence. Nymphaea is characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss of REVOLUTA, which influences cambial activity in other angiosperms. We also found the Nymphaea and monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids. Nelumbo displays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent loss of vascular cambium reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent events of trait loss. Our results shed light on the evolution of herbaceousness—one of the key biological innovations associated with the earliest phases of angiosperm evolution.
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water lily nymphaea thermarum draft genome reveals variable genomic signatures of ancient vascular cambium losses
bioRxiv, 2019Co-Authors: Rebecca A Povilus, Jeffrey M Dacosta, Prasad R V Satyaki, Morgan Moeglein, Johan Jaenisch, Christopher J Grassa, Sarah Mathews, Zhenxiang Xi, Mary Gehring, Charles C DavisAbstract:For more than 225 million years, all seed plants were woody trees, shrubs, or vines (1,2,3,4). Shortly after the origin of angiosperms ~135 million years ago (MYA) (5), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium (6), the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem (7,8,9), which are produced by apical meristems and retained in nearly all seed plants. Here we sequence and assemble a draft genome of the water lily Nymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compare it to genomes from other cambium-bearing and cambium-less lineages (like monocots and Nelumbo). This reveals lineage-specific patterns of gene loss and divergence. Nymphaea is characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss of REVOLUTA, which influences cambial activity in other angiosperms. We also find the Nymphaea and monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids. Nelumbo displays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent vascular cambium loss reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent trait loss events. Our results shed light on the evolution of herbaceousness,which is one of the key biological innovations associated with the earliest phases of angiosperm evolution.
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the root of angiosperm phylogeny inferred from duplicate phytochrome genes
Science, 1999Co-Authors: Sarah Mathews, Michael J DonoghueAbstract:An analysis of duplicate phytochrome genes (PHYA and PHYC) is used to root the angiosperms, thereby avoiding the inclusion of highly diverged outgroup sequences. The results unambiguously place the root near Amborella (one species, New Caledonia) and resolve water lilies (Nymphaeales, ∼70 species, cosmopolitan), followed by Austrobaileya (one species, Australia), as early branches. These findings bear directly on the interpretation of morphological evolution and diversification within angiosperms.