The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
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, Fanbo Meng, Ying Li, Lei Zhang, 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, Fanbo Meng, Ying Li, Lei Zhang, 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.
Pamela S. Soltis - One of the best experts on this subject based on the ideXlab platform.
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evolutionary trends in the floral transcriptome insights from one of the basalmost angiosperms the water lily nuphar advena nymphaeaceae
Plant Journal, 2010Co-Authors: Naomi Altman, Andre S Chanderbali, Pamela S. SoltisAbstract:Summary Current understanding of floral developmental genetics comes primarily from the core eudicot model Arabidopsis thaliana. Here, we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. We identify several thousand Nuphar genes with significantly upregulated floral expression, including homologs of the well-known ABCE floral regulators, deployed in broadly overlapping transcriptional programs across floral organ categories. Strong similarities in the expression profiles of different organ categories in Nuphar flowers are shared with the Magnoliid Persea americana (avocado), in contrast to the largely organ-specific transcriptional cascades evident in Arabidopsis, supporting the inference that this is the ancestral condition in angiosperms. In contrast to most eudicots, floral organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived, and correlate with a shift towards morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. Our findings suggest that the genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology.
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evolutionary trends in the floral transcriptome insights from one of the basalmost angiosperms the water lily nuphar advena nymphaeaceae
Plant Journal, 2010Co-Authors: Naomi Altman, Andre S Chanderbali, Pamela S. SoltisAbstract:Summary Current understanding of floral developmental genetics comes primarily from the core eudicot model Arabidopsis thaliana. Here, we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. We identify several thousand Nuphar genes with significantly upregulated floral expression, including homologs of the well-known ABCE floral regulators, deployed in broadly overlapping transcriptional programs across floral organ categories. Strong similarities in the expression profiles of different organ categories in Nuphar flowers are shared with the Magnoliid Persea americana (avocado), in contrast to the largely organ-specific transcriptional cascades evident in Arabidopsis, supporting the inference that this is the ancestral condition in angiosperms. In contrast to most eudicots, floral organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived, and correlate with a shift towards morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. Our findings suggest that the genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology.
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persea americana avocado bringing ancient flowers to fruit in the genomics era
BioEssays, 2008Co-Authors: Andre S Chanderbali, Douglas E Soltis, Victor A Albert, Vanessa E T M Ashworth, Michael T Clegg, Richard E Litz, Pamela S. SoltisAbstract:The avocado (Persea americana) is a major crop commodity worldwide. Moreover, avocado, a paleopolyploid, is an evolutionary "outpost" among flowering plants, representing a basal lineage (the Magnoliid clade) near the origin of the flowering plants themselves. Following centuries of selective breeding, avocado germplasm has been characterized at the level of microsatellite and RFLP markers. Nonetheless, little is known beyond these general diversity estimates, and much work remains to be done to develop avocado as a major subtropical-zone crop. Among the goals of avocado improvement are to develop varieties with fruit that will "store" better on the tree, show uniform ripening and have better post-harvest storage. Avocado transcriptome sequencing, genome mapping and partial genomic sequencing will represent a major step toward the goal of sequencing the entire avocado genome, which is expected to aid in improving avocado varieties and production, as well as understanding the evolution of flowers from non-flowering seed plants (gymnosperms). Additionally, continued evolutionary and other comparative studies of flower and fruit development in different avocado strains can be accomplished at the gene expression level, including in comparison with avocado relatives, and these should provide important insights into the genetic regulation of fruit development in basal angiosperms.
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Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms
Proceedings of the National Academy of Sciences of the United States of America, 2007Co-Authors: Michael J. Moore, Charles D. Bell, Pamela S. SoltisAbstract:Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, Magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes (≈42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence of Ceratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae + Magnoliids as sister to a well supported clade of monocots + (Ceratophyllum + eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 ± 4.8 and 140.3 ± 4.8 Mya.
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Phylogenetic analyses and perianth evolution in basal angiosperms
Annals of the Missouri Botanical Garden, 2003Co-Authors: Michael J. Zanis, Pamela S. Soltis, Elizabeth A ZimmerAbstract:Using a compartmentalization approach, we conducted phylogenetic analyses of the basalmost extant angiosperms using sequences from six genes (over 12,000 bp per taxon) from all three genomes (chloroplast-atpB, rbcL; nuclear- 18S rDNA, 26S rDNA; mitochondrial-matR, atpA). Trees resulting from parsimony and maximum likelihood analyses of the compartmentalized data are identical. We find strong support (100% for each node) for the earliest-branching angiosperms: Amborellaceae, Nymphaeaceae, and an Austrobaileyales clade (Illiciaceae, Schisandraceae, Trimeniaceae, Austrobaileyaceae). Whereas most recent studies using multiple genes provided poor resolution and support for relationships among the remaining basal angiosperms (Ceratophyllaceae, Chloranthaceae, Canellales ( = Winterales), Piperales, monocots, Magnoliales, Laurales), with compartmentalization, we find high levels (> 90%) of bootstrap support for relationships among these clades. Canellales and Piperales form a strongly supported (100%) sister group that is, in turn, sister to a well-supported (100%) clade of Laurales and Magnoliales. Canellales + Piperales and Magnoliales + Laurales form a well-supported Magnoliid clade. Ceratophyllaceae are strongly supported (100%) as sister to the monocots; the monocot/Ceratophyllaceae clade is well supported (86%) as sister to all remaining angiosperms (Chloranthaceae, the Magnoliid clade, and eudicots). The addition of entire 26S rDNA sequences clearly contributed to this increased internal support. We examined the diversification of perianth phyllotaxis, merosity, and differentiation using our phylogenetic hypothesis for angiosperms. Ancestral perianth phyllotaxis and merosity are equivocal for each node of the Amborellaceae, Nymphaeaceae, Austrobaileyales grade; however, an undifferentiated perianth is reconstructed as the ancestral state for the angiosperms. Trimery and whorled perianth phyllotaxis have played a major role in basal angiosperm perianth evolution and represent the ancestral states for the large Glade comprising all angiosperms other than Amborella, Nymphaeaceae, and Austrobaileyales. A differentiated perianth has apparently evolved multiple times.
Beibei Jiao - 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, Fanbo Meng, Ying Li, Lei Zhang, 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, Fanbo Meng, Ying Li, Lei Zhang, 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.
Juan M Losada - One of the best experts on this subject based on the ideXlab platform.
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pollen pistil interaction in pawpaw asimina triloba the northernmost species of the mainly tropical family annonaceae
American Journal of Botany, 2017Co-Authors: Juan M Losada, J. Ignacio Hormaza, Jorge LoraAbstract:PREMISE OF THE STUDY: The pawpaw, Asimina triloba, is an underutilized fruit crop native to North America that belongs to the mainly tropical, early-divergent family Annonaceae. Asimina is the only genus within the Annonaceae with species adapted to cold climates. A thorough analysis of its reproductive biology, specifically pollen-pistil interaction during the progamic phase, is essential to understand both its adaptation to cold climates and how to optimize its fertilization and fruit set. METHODS: We characterized pollen-pistil interaction in Asimina triloba, including the floral cycle and anatomy, stigmatic receptivity, and the pollen tube pathway. We used a combination of histological, cytological, and immunolocalization approaches. KEY RESULTS: Asimina triloba has a gynoecium formed by plicate carpels with a short stylar canal. Unicellular papillae form a continuous tissue covered by a copious secretion from the stigma to the ovary, which is most prominent on the stigma surface where it forms an extragynoecial compitum. Compared to the stigmas of other species in the Annonaceae, the stigmas of A. triloba show a long stigmatic receptivity associated with a long flowering cycle. Stigmatic receptivity is concomitant with the secretion of cell-wall-related arabinogalactan proteins (AGPs). CONCLUSIONS: A long female phase with a long period of stigmatic receptivity is unusual among protogynous flowers of the Magnoliid clade, suggesting a derived condition of A. triloba within the Annonaceae. This phase further correlates with the presence of cell-wall-related arabinogalactan proteins in the secretion, which may indicate the conservation of these glycoproteins during stigmatic receptivity and pollen tube growth in angiosperms.
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Arabinogalactan proteins mark stigmatic receptivity in the protogynous flowers of Magnolia virginiana (Magnoliaceae)
American journal of botany, 2014Co-Authors: Juan M Losada, J. Ignacio Hormaza, Maria Herrero, William E. FriedmanAbstract:PREMISE OF THE STUDY Factors affecting floral receptivity in angiosperms remain opaque, but recent studies suggest that the acquisition of stigmatic receptivity associated with cell-wall-related arabinogalactan proteins (AGPs) may be a widespread feature of flowering plants. Here, the time during which a stigma is receptive is evaluated and related to the secretion of AGPs in Magnolia virginiana, a protogynous member of an early-divergent angiosperm clade (Magnoliids) with a clearly discernible female receptive phase. METHODS Magnolia virginiana flower phenology was documented, and histochemical changes in the stigma before and after pollination were examined. Stigmatic receptivity was evaluated in relation to the secretion of AGPs detected in whole mounts and immunolocalized in sectioned stigmas. KEY RESULTS Protogynous Magnolia flowers had a precise window of stigmatic receptivity, which is concomitant with the secretion of two AGPs labeled for different epitopes. After pollen germination and tube growth, these two AGPs could no longer be detected in the stigmas, suggesting that these AGPs interact with the growing male gametophytes and could be markers of stigmatic receptivity. CONCLUSIONS These results show that the period of stigmatic receptivity is finely coordinated with the secretion of two arabinogalactan proteins on stigmas of flowers of M. virginiana. This first report of AGP presence in stigmatic tissues in a member of the Magnoliids, together with recently described similar patterns in eudicots, monocots, and members of early-divergent lineages of flowering plants, suggests an ancient and widespread role for AGPs on stigmatic receptivity in angiosperms.
Andre S Chanderbali - One of the best experts on this subject based on the ideXlab platform.
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evolutionary trends in the floral transcriptome insights from one of the basalmost angiosperms the water lily nuphar advena nymphaeaceae
Plant Journal, 2010Co-Authors: Naomi Altman, Andre S Chanderbali, Pamela S. SoltisAbstract:Summary Current understanding of floral developmental genetics comes primarily from the core eudicot model Arabidopsis thaliana. Here, we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. We identify several thousand Nuphar genes with significantly upregulated floral expression, including homologs of the well-known ABCE floral regulators, deployed in broadly overlapping transcriptional programs across floral organ categories. Strong similarities in the expression profiles of different organ categories in Nuphar flowers are shared with the Magnoliid Persea americana (avocado), in contrast to the largely organ-specific transcriptional cascades evident in Arabidopsis, supporting the inference that this is the ancestral condition in angiosperms. In contrast to most eudicots, floral organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived, and correlate with a shift towards morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. Our findings suggest that the genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology.
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evolutionary trends in the floral transcriptome insights from one of the basalmost angiosperms the water lily nuphar advena nymphaeaceae
Plant Journal, 2010Co-Authors: Naomi Altman, Andre S Chanderbali, Pamela S. SoltisAbstract:Summary Current understanding of floral developmental genetics comes primarily from the core eudicot model Arabidopsis thaliana. Here, we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. We identify several thousand Nuphar genes with significantly upregulated floral expression, including homologs of the well-known ABCE floral regulators, deployed in broadly overlapping transcriptional programs across floral organ categories. Strong similarities in the expression profiles of different organ categories in Nuphar flowers are shared with the Magnoliid Persea americana (avocado), in contrast to the largely organ-specific transcriptional cascades evident in Arabidopsis, supporting the inference that this is the ancestral condition in angiosperms. In contrast to most eudicots, floral organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived, and correlate with a shift towards morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. Our findings suggest that the genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology.
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persea americana avocado bringing ancient flowers to fruit in the genomics era
BioEssays, 2008Co-Authors: Andre S Chanderbali, Douglas E Soltis, Victor A Albert, Vanessa E T M Ashworth, Michael T Clegg, Richard E Litz, Pamela S. SoltisAbstract:The avocado (Persea americana) is a major crop commodity worldwide. Moreover, avocado, a paleopolyploid, is an evolutionary "outpost" among flowering plants, representing a basal lineage (the Magnoliid clade) near the origin of the flowering plants themselves. Following centuries of selective breeding, avocado germplasm has been characterized at the level of microsatellite and RFLP markers. Nonetheless, little is known beyond these general diversity estimates, and much work remains to be done to develop avocado as a major subtropical-zone crop. Among the goals of avocado improvement are to develop varieties with fruit that will "store" better on the tree, show uniform ripening and have better post-harvest storage. Avocado transcriptome sequencing, genome mapping and partial genomic sequencing will represent a major step toward the goal of sequencing the entire avocado genome, which is expected to aid in improving avocado varieties and production, as well as understanding the evolution of flowers from non-flowering seed plants (gymnosperms). Additionally, continued evolutionary and other comparative studies of flower and fruit development in different avocado strains can be accomplished at the gene expression level, including in comparison with avocado relatives, and these should provide important insights into the genetic regulation of fruit development in basal angiosperms.