The Experts below are selected from a list of 873 Experts worldwide ranked by ideXlab platform
Jeffrey D. Palmer - One of the best experts on this subject based on the ideXlab platform.
-
the complete moss mitochondrial genome in the angiosperm Amborella is a chimera derived from two moss whole genome transfers
PLOS ONE, 2015Co-Authors: Nathan Z Taylor, Danny W Rice, Jeffrey D. PalmerAbstract:Sequencing of the 4-Mb mitochondrial genome of the angiosperm Amborella trichopoda has shown that it contains unprecedented amounts of foreign mitochondrial DNA, including four blocks of sequences that together correspond almost perfectly to one entire moss mitochondrial genome. This implies whole-genome transfer from a single moss donor but conflicts with phylogenetic results from an earlier, PCR-based study that suggested three different moss donors to Amborella. To resolve this conflict, we conducted an expanded set of phylogenetic analyses with respect to both moss lineages and mitochondrial loci. The moss DNA in Amborella was consistently placed in either of two positions, depending on the locus analyzed, as sister to the Ptychomniales or within the Hookeriales. This agrees with two of the three previously suggested donors, whereas the third is no longer supported. These results, combined with synteny analyses and other considerations, lead us to favor a model involving two successive moss-to-Amborella whole-genome transfers, followed by recombination that produced a single intact and chimeric moss mitochondrial genome integrated in the Amborella mitochondrial genome. Eight subsequent recombination events account for the state of fragmentation, rearrangement, duplication, and deletion of this chimeric moss mitochondrial genome as it currently exists in Amborella. Five of these events are associated with short-to-intermediate sized repeats. Two of the five probably occurred by reciprocal homologous recombination, whereas the other three probably occurred in a non-reciprocal manner via microhomology-mediated break-induced replication (MMBIR). These findings reinforce and extend recent evidence for an important role of MMBIR in plant mitochondrial DNA evolution.
-
The Amborella Genome and the Evolution of Flowering Plants
Science, 2013Co-Authors: Victor A. Albert, Jeffrey D. Palmer, Claude W. Depamphilis, W. Bradley Barbazuk, Joshua P. Der, James Leebens-mack, Steve Rounsley, David Sankoff, Stephan C. Schuster, Douglas E. SoltisAbstract:Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication predating angiosperm diversification, without evidence of subsequent, lineage-specific genome duplications. Comparisons between Amborella and other angiosperms facilitated reconstruction of the ancestral angiosperm gene content and gene order in the MRCA of core eudicots. We identify new gene families, gene duplications, and floral protein-protein interactions that first appeared in the ancestral angiosperm. Transposable elements in Amborella are ancient and highly divergent, with no recent transposon radiations. Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications.
-
the Amborella genome an evolutionary reference for plant biology
Genome Biology, 2008Co-Authors: Douglas E. Soltis, Jeffrey D. Palmer, Jim Leebensmack, John E Carlson, Claude W. Depamphilis, Victor A. Albert, Rod A Wing, Naomi Altman, Sangtae KimAbstract:The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.
-
massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella
Proceedings of the National Academy of Sciences of the United States of America, 2004Co-Authors: Ulfar Bergthorsson, Aaron O Richardson, Gregory J Young, Leslie R Goertzen, Jeffrey D. PalmerAbstract:Several plants are known to have acquired a single mitochondrial gene by horizontal gene transfer (HGT), but whether these or any other plants have acquired many foreign genes is entirely unclear. To address this question, we focused on Amborella trichopoda, because it was already known to possess one horizontally acquired gene and because it was found in preliminary analyses to contain several more. We comprehensively sequenced the mitochondrial protein gene set of Amborella, sequenced a variable number of mitochondrial genes from 28 other diverse land plants, and conducted phylogenetic analyses of these sequences plus those already available, including the five sequenced mitochondrial genomes of angiosperms. Results indicate that Amborella has acquired one or more copies of 20 of its 31 known mitochondrial protein genes from other land plants, for a total of 26 foreign genes, whereas no evidence for HGT was found in the five sequenced genomes. Most of the Amborella transfers are from other angiosperms (especially eudicots), whereas others are from nonangiosperms, including six striking cases of transfer from (at least three different) moss donors. Most of the transferred genes are intact, consistent with functionality and/or recency of transfer. Amborella mtDNA has sustained proportionately more HGT than any other eukaryotic, or perhaps even prokaryotic, genome yet examined.
-
genome scale data angiosperm relationships and ending incongruence a cautionary tale in phylogenetics
Trends in Plant Science, 2004Co-Authors: Douglas E. Soltis, Danny W Rice, Jeffrey D. Palmer, Khidir W. Hilu, Sasa Stefanovic, Victor A. Albert, Vincent Savolainen, Mark W Chase, James S Farris, Pamela S. SoltisAbstract:As systematists grapple with assembling the Tree of Life, recent studies have encouraged a genomic-scale approach, obtaining DNA sequence data for entire nuclear, plastid or mitochondrial genomes for a few exemplar taxa. Some have proclaimed that this comparative genomic strategy heralds the end of incongruence in phylogeny reconstruction. Although we applaud the use of many genes to resolve phylogenetic patterns, there is a significant caveat. In spite of, or even because of, the abundant data per taxon, whole-genome sequencing for a few exemplars can provide completely resolved and strongly supported, but incorrect, evolutionary reconstructions. We provide a conspicuous example that includes Amborella, the putative sister of all other extant angiosperms, highlighting the limits of phylogenetics when whole genomes are used but taxon sampling is poor.
Thomas Dresselhaus - One of the best experts on this subject based on the ideXlab platform.
-
transcriptomic and proteomic insights into Amborella trichopoda male gametophyte functions
Plant Physiology, 2020Co-Authors: Maria Florestornero, Frank Vogler, Marek Mutwil, David Potěsil, Ivana Ihnatova, Zbyněk Zdrahal, Stefanie Sprunck, Thomas DresselhausAbstract:Flowering plants (angiosperms) are characterized by pollen tubes (PTs; male gametophytes) carrying two immobile sperm cells that grow over long distances through the carpel toward the ovules, where double fertilization is executed. It is not understood how these reproductive structures evolved, which genes occur de novo in male gametophytes of angiosperms, and to which extent PT functions are conserved among angiosperms. To contribute to a deeper understanding of the evolution of gametophyte functions, we generated rna-sequencing/">RNA sequencing data from seven reproductive and two vegetative control tissues of the basal angiosperm Amborella trichopoda and complemented these with proteomic data of pollen grains (PGs) and PTs. The eudicot model plant Arabidopsis (Arabidopsis thaliana) served as a reference organism for data analysis, as more than 200 genes have been associated with male gametophyte functions in this species. We describe methods to collect bicellular A. trichopoda PGs, to induce their germination in vitro, and to monitor PT growth and germ cell division. Transcriptomic and proteomic analyses indicate that A. trichopoda PGs are prepared for germination requiring lipids, energy, but likely also reactive oxygen species, while PTs are especially characterized by catabolic/biosynthetic and transport processes including cell wall biosynthesis and gene regulation. Notably, a number of pollen-specific genes were lacking in Arabidopsis, and the number of genes involved in pollen signaling is significantly reduced in A. trichopoda In conclusion, we provide insight into male gametophyte functions of the most basal angiosperm and establish a valuable resource for future studies on the evolution of flowering plants.
-
Comparative analyses of angiosperm secretomes identify apoplastic pollen tube functions and novel secreted peptides
Plant Reproduction, 2020Co-Authors: María Flores-tornero, Frank Vogler, David Potěsil, Zbyněk Zdrahal, Stefanie Sprunck, Lele Wang, Said Hafidh, David Honys, Thomas DresselhausAbstract:Key message Analyses of secretomes of in vitro grown pollen tubes from Amborella, maize and tobacco identified many components of processes associated with the cell wall, signaling and metabolism as well as novel small secreted peptides. Abstract Flowering plants (angiosperms) generate pollen grains that germinate on the stigma and produce tubes to transport their sperm cells cargo deep into the maternal reproductive tissues toward the ovules for a double fertilization process. During their journey, pollen tubes secrete many proteins (secreted proteome or secretome) required, for example, for communication with the maternal reproductive tissues, to build a solid own cell wall that withstands their high turgor pressure while softening simultaneously maternal cell wall tissue. The composition and species specificity or family specificity of the pollen tube secretome is poorly understood. Here, we provide a suitable method to obtain the pollen tube secretome from in vitro grown pollen tubes of the basal angiosperm Amborella trichopoda (Amborella) and the Poaceae model maize. The previously published secretome of tobacco pollen tubes was used as an example of eudicotyledonous plants in this comparative study. The secretome of the three species is each strongly different compared to the respective protein composition of pollen grains and tubes. In Amborella and maize, about 40% proteins are secreted by the conventional “classic” pathway and 30% by unconventional pathways. The latter pathway is expanded in tobacco. Proteins enriched in the secretome are especially involved in functions associated with the cell wall, cell surface, energy and lipid metabolism, proteolysis and redox processes. Expansins, pectin methylesterase inhibitors and RALFs are enriched in maize, while tobacco secretes many proteins involved, for example, in proteolysis and signaling. While the majority of proteins detected in the secretome occur also in pollen grains and pollen tubes, and correlate in the number of mapped peptides with relative gene expression levels, some novel secreted small proteins were identified. Moreover, the identification of secreted proteins containing pro-peptides indicates that these are processed in the apoplast. In conclusion, we provide a proteome resource from three distinct angiosperm clades that can be utilized among others to study the localization, abundance and processing of known secreted proteins and help to identify novel pollen tube secreted proteins for functional studies.
-
transcriptomic and proteomic insights into Amborella trichopoda male gametophyte functions
Plant Physiology, 2020Co-Authors: Maria Florestornero, Frank Vogler, Marek Mutwil, David Potěsil, Ivana Ihnatova, Zbyněk Zdrahal, Stefanie Sprunck, Thomas DresselhausAbstract:Flowering plants (angiosperms) are characterized by pollen tubes (male gametophytes) carrying two immobile sperm cells that grow over long distances through the carpel towards the ovules where double fertilization is executed. It is not understood how these reproductive structures evolved, which genes occur de novo in male gametophytes of angiosperms, and to which extent pollen tube functions are conserved among angiosperms. To contribute to a deeper understanding of the evolution of gametophyte functions, we generated RNA-seq data from seven reproductive and two vegetative control tissues of the basal angiosperm Amborella (Amborella trichopoda) and complemented these with proteomic data of pollen grains and pollen tubes. The eudicot model plant Arabidopsis (Arabidopsis thaliana) served as a reference organism for data analysis, as more than 200 genes have been associated with male gametophyte functions in this species. We describe methods to collect bi-cellular Amborella pollen grains, to induce their germination in vitro, and to monitor pollen tube growth and germ cell division. Transcriptomic and proteomic analyses indicate that Amborella pollen grains are prepared for germination requiring lipids, energy, but likely also reactive oxygen species, while pollen tubes are especially characterized by catabolic/biosynthetic and transport processes including cell wall biosynthesis and gene regulation. Notably, a number of pollen-specific genes were lacking in Arabidopsis and the number of genes involved in pollen signaling is significantly reduced in Amborella. In conclusion, we provide insight into male gametophyte functions of the most basal angiosperm and establish a valuable resource for future studies on the evolution of flowering plants.
-
correction to transcriptomics of manually isolated Amborella trichopoda egg apparatus cells
Sexual Plant Reproduction, 2019Co-Authors: Maria Florestornero, Charles P. Scutt, Marek Mutwil, Thomas Dresselhaus, Sebastian Proost, Stefanie SprunckAbstract:The article Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells, written by Maria Flores-Tornero, Sebastian Proost, Marek Mutwil, Charles P. Scutt, Thomas Dresselhaus, Stefanie Sprunck, was originally published electronically on the publisher’s internet portal (currently SpringerLink) on 1 February 2019 without open access
-
transcriptomics of manually isolated Amborella trichopoda egg apparatus cells
Sexual Plant Reproduction, 2019Co-Authors: Maria Florestornero, Charles P. Scutt, Marek Mutwil, Thomas Dresselhaus, Sebastian Proost, Stefanie SprunckAbstract:A protocol for the isolation of egg apparatus cells from the basal angiosperm Amborella trichopoda to generate RNA-seq data for evolutionary studies of fertilization-associated genes. Sexual reproduction is particularly complex in flowering plants (angiosperms). Studies in eudicot and monocot model species have significantly contributed to our knowledge on cell fate specification of gametophytic cells and on the numerous cellular communication events necessary to deliver the two sperm cells into the embryo sac and to accomplish double fertilization. However, for a deeper understanding of the evolution of these processes, morphological, genomic and gene expression studies in extant basal angiosperms are inevitable. The basal angiosperm Amborella trichopoda is of special importance for evolutionary studies, as it is likely sister to all other living angiosperms. Here, we report about a method to isolate Amborella egg apparatus cells and on genome-wide gene expression profiles in these cells. Our transcriptomics data revealed Amborella-specific genes and genes conserved in eudicots and monocots. Gene products include secreted proteins, such as small cysteine-rich proteins previously reported to act as extracellular signaling molecules with important roles during double fertilization. The detection of transcripts encoding EGG CELL 1 (EC1) and related prolamin-like family proteins in Amborella egg cells demonstrates the potential of the generated data set to study conserved molecular mechanisms and the evolution of fertilization-related genes and their encoded proteins.
Danny W Rice - One of the best experts on this subject based on the ideXlab platform.
-
the complete moss mitochondrial genome in the angiosperm Amborella is a chimera derived from two moss whole genome transfers
PLOS ONE, 2015Co-Authors: Nathan Z Taylor, Danny W Rice, Jeffrey D. PalmerAbstract:Sequencing of the 4-Mb mitochondrial genome of the angiosperm Amborella trichopoda has shown that it contains unprecedented amounts of foreign mitochondrial DNA, including four blocks of sequences that together correspond almost perfectly to one entire moss mitochondrial genome. This implies whole-genome transfer from a single moss donor but conflicts with phylogenetic results from an earlier, PCR-based study that suggested three different moss donors to Amborella. To resolve this conflict, we conducted an expanded set of phylogenetic analyses with respect to both moss lineages and mitochondrial loci. The moss DNA in Amborella was consistently placed in either of two positions, depending on the locus analyzed, as sister to the Ptychomniales or within the Hookeriales. This agrees with two of the three previously suggested donors, whereas the third is no longer supported. These results, combined with synteny analyses and other considerations, lead us to favor a model involving two successive moss-to-Amborella whole-genome transfers, followed by recombination that produced a single intact and chimeric moss mitochondrial genome integrated in the Amborella mitochondrial genome. Eight subsequent recombination events account for the state of fragmentation, rearrangement, duplication, and deletion of this chimeric moss mitochondrial genome as it currently exists in Amborella. Five of these events are associated with short-to-intermediate sized repeats. Two of the five probably occurred by reciprocal homologous recombination, whereas the other three probably occurred in a non-reciprocal manner via microhomology-mediated break-induced replication (MMBIR). These findings reinforce and extend recent evidence for an important role of MMBIR in plant mitochondrial DNA evolution.
-
horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella
Science, 2013Co-Authors: Danny W Rice, Aaron O Richardson, Gregory J Young, Jerome Munzinger, Andrew J Alverson, Virginia M Sanchezpuerta, Kerrie Barry, Jeffrey L Boore, Yan Zhang, Claude W. DepamphilisAbstract:Amborella trichopoda is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by [Adams][1] ). To validate and assemble the sequence, Chamala et al. (p. [1516][2]) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The Amborella Genome Project (p. [10.1126/science.1241089][3]) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and Rice et al. (p. [1468][4]) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae. [1]: /lookup/doi/10.1126/science.1248709 [2]: /lookup/doi/10.1126/science.1241130 [3]: /lookup/doi/10.1126/science.1241089 [4]: /lookup/doi/10.1126/science.1246275
-
genome scale data angiosperm relationships and ending incongruence a cautionary tale in phylogenetics
Trends in Plant Science, 2004Co-Authors: Douglas E. Soltis, Danny W Rice, Jeffrey D. Palmer, Khidir W. Hilu, Sasa Stefanovic, Victor A. Albert, Vincent Savolainen, Mark W Chase, James S Farris, Pamela S. SoltisAbstract:As systematists grapple with assembling the Tree of Life, recent studies have encouraged a genomic-scale approach, obtaining DNA sequence data for entire nuclear, plastid or mitochondrial genomes for a few exemplar taxa. Some have proclaimed that this comparative genomic strategy heralds the end of incongruence in phylogeny reconstruction. Although we applaud the use of many genes to resolve phylogenetic patterns, there is a significant caveat. In spite of, or even because of, the abundant data per taxon, whole-genome sequencing for a few exemplars can provide completely resolved and strongly supported, but incorrect, evolutionary reconstructions. We provide a conspicuous example that includes Amborella, the putative sister of all other extant angiosperms, highlighting the limits of phylogenetics when whole genomes are used but taxon sampling is poor.
-
Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
BMC Evolutionary Biology, 2004Co-Authors: Saša Stefanović, Danny W Rice, Jeffrey D. PalmerAbstract:Background Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella , as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol . 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for monocots as the deepest angiosperms relative to Amborella , Calycanthus , and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent monocots. Results We used two main approaches to test this hypothesis. First, we sequenced a large number of chloroplast genes from the monocot Acorus and added these plus previously sequenced Acorus genes to the Goremykin et al. (2003) dataset in order to explore the effects of altered monocot sampling under the same analytical conditions used in their study. With Acorus alone representing monocots, strongly supported Amborella -sister trees were obtained in all maximum likelihood and parsimony analyses, and in some distance-based analyses. Trees with both Acorus and grasses gave either a well-supported Amborella -sister topology or else a highly unlikely topology with 100% support for grasses-sister and paraphyly of monocots (i.e., Acorus sister to "dicots" rather than to grasses). Second, we reanalyzed the Goremykin et al. (2003) dataset focusing on methods designed to account for rate heterogeneity. These analyses supported an Amborella -sister hypothesis, with bootstrap support values often conflicting strongly with cognate analyses performed without allowing for rate heterogeneity. In addition, we carried out a limited set of analyses that included the chloroplast genome of Nymphaea , whose position as a basal angiosperm was also, and very recently, challenged. Conclusions These analyses show that Amborella (or Amborella plus Nymphaea ), but not monocots, is the sister group of all other angiosperms among this limited set of taxa and that the grasses-sister topology is a long-branch-attraction artifact leading to incorrect rooting of angiosperms. These results highlight the danger of having lots of characters but too few and, especially, molecularly divergent taxa, a situation long recognized as potentially producing strongly misleading molecular trees. They also emphasize the importance in phylogenetic analysis of using appropriate evolutionary models.
-
long branch attraction taxon sampling and the earliest angiosperms Amborella or monocots
BMC Evolutionary Biology, 2004Co-Authors: Saša Stefanović, Danny W Rice, Jeffrey D. PalmerAbstract:Background Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella, as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol. 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for monocots as the deepest angiosperms relative to Amborella, Calycanthus, and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent monocots.
Saša Stefanović - One of the best experts on this subject based on the ideXlab platform.
-
Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
BMC Evolutionary Biology, 2004Co-Authors: Saša Stefanović, Danny W Rice, Jeffrey D. PalmerAbstract:Background Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella , as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol . 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for monocots as the deepest angiosperms relative to Amborella , Calycanthus , and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent monocots. Results We used two main approaches to test this hypothesis. First, we sequenced a large number of chloroplast genes from the monocot Acorus and added these plus previously sequenced Acorus genes to the Goremykin et al. (2003) dataset in order to explore the effects of altered monocot sampling under the same analytical conditions used in their study. With Acorus alone representing monocots, strongly supported Amborella -sister trees were obtained in all maximum likelihood and parsimony analyses, and in some distance-based analyses. Trees with both Acorus and grasses gave either a well-supported Amborella -sister topology or else a highly unlikely topology with 100% support for grasses-sister and paraphyly of monocots (i.e., Acorus sister to "dicots" rather than to grasses). Second, we reanalyzed the Goremykin et al. (2003) dataset focusing on methods designed to account for rate heterogeneity. These analyses supported an Amborella -sister hypothesis, with bootstrap support values often conflicting strongly with cognate analyses performed without allowing for rate heterogeneity. In addition, we carried out a limited set of analyses that included the chloroplast genome of Nymphaea , whose position as a basal angiosperm was also, and very recently, challenged. Conclusions These analyses show that Amborella (or Amborella plus Nymphaea ), but not monocots, is the sister group of all other angiosperms among this limited set of taxa and that the grasses-sister topology is a long-branch-attraction artifact leading to incorrect rooting of angiosperms. These results highlight the danger of having lots of characters but too few and, especially, molecularly divergent taxa, a situation long recognized as potentially producing strongly misleading molecular trees. They also emphasize the importance in phylogenetic analysis of using appropriate evolutionary models.
-
long branch attraction taxon sampling and the earliest angiosperms Amborella or monocots
BMC Evolutionary Biology, 2004Co-Authors: Saša Stefanović, Danny W Rice, Jeffrey D. PalmerAbstract:Background Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella, as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol. 20:1499–1505), whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for monocots as the deepest angiosperms relative to Amborella, Calycanthus, and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent monocots.
Valerie Poncet - One of the best experts on this subject based on the ideXlab platform.
-
Amborella bearing witness to the past
Annual Plant Reviews Online, 2019Co-Authors: Valerie Poncet, Gildas Gâteble, Bruno Fogliani, Tanguy Jaffré, Alexandre De ,kochko, Philippe Birnbaum, Valerie Burtetsarramegna, Sandrine Isnard, Dominique JobAbstract:Amborella trichopoda (Amborellaceae) is a shrub endemic to New Caledonia in the Southwest Pacific region. This plant suddenly became famous when molecular phylogenetic studies revealed that this sole species is likely the sister taxon to all other angiosperms. It has thus been a prime research model for reconstructing plant evolution and gaining insight into what the earliest angiosperms looked like. A wealth of studies on Amborella have now shed considerable light on its genome, morphology, anatomy, physiology, development, and architecture – this research is reviewed in this article. While Amborella likely retained some ancestral traits, critical character reconstructions have also highlighted some derived and sometimes unique characters in this species. The history of Amborella is also tied to the South Pacific archipelago of New Caledonia, its homeland. It was part of the New Caledonian biogeography puzzle and its genetic history shed light on the dynamics of its ecosystem, the rainforest understorey. Amborella is now cultivated in botanical gardens and has been the focus of some conservation measures that will also benefit other species in this biodiversity hotspot.
-
Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda
PLoS ONE, 2017Co-Authors: Rémi Tournebize, Alexandre De ,kochko, Francois Munoz, Stéphanie Manel, Yves Vigouroux, Valerie PoncetAbstract:Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict plant endemic to New Caledonia, widely distributed in the understory of non-ultramafic rainforests. We assessed the influence of the last glacial climates on the demographic history and the paleo-distribution of 12 Amborella populations covering the whole current distribution. We performed coalescent genetic modelling of these dynamics, based on both whole-genome resequencing and microsatellite genotyping data. We found that the two main genetic groups of Amborella were shaped by the divergence of two ancestral populations during the last glacial maximum. From 12,800 years BP, the South ancestral population has expanded 6.3-fold while the size of the North population has remained stable. Recent asymmetric gene flow between the groups further contributed to the phylogeographical pattern. Spatially explicit coalescent modelling allowed us to estimate the location of ancestral populations with good accuracy (< 22 km) and provided indications regarding the mid-elevation pathways that facilitated post-glacial expansion.
-
Variations in Amborella trichopoda effective size and variations in the δ13C isotopic ratio.
2017Co-Authors: Rémi Tournebize, Alexandre De ,kochko, Francois Munoz, Stéphanie Manel, Yves Vigouroux, Valerie PoncetAbstract:(A) Best demo-genomic model (2M) estimated from the whole-genomic sequence dataset. The radii of demographic pipes are scaled by the corresponding effective population sizes. The dotted interspace depicts gene flow. (B) Variations in the effective size of Amborella (black solid line) from present time to 25,000 years BP as estimated from the best demo-genomic model. The orange solid line (left y-axis) is the smoothing spline of the δ13C isotopic ratio obtained from Hellstrom et al. [44], a proxy of dense lowland forest productivity in Northern New Zealand, ~2,000 km south of New Caledonia. Consistent demographic and δ13C isotope ratio variation trends suggest a positive lag time between the post-refugial expansion of Amborella and the re-expansion of forests in Northern New Zealand.
-
Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda - Fig 4
2017Co-Authors: Rémi Tournebize, Alexandre De ,kochko, Francois Munoz, Stéphanie Manel, Yves Vigouroux, Valerie PoncetAbstract:Habitat suitability for Amborella in New Caledonia under (A) the Last Glacial Maximum, ~21,000 years BP and (B) the mid-Holocene, ~6,000 years BP. Paleo-habitat projections were performed using MIROC paleo-climatic layers.
-
Topography of New Caledonia and geographical distribution of the 12 studied populations spanning the whole natural distribution of Amborella trichopoda at present (black line polygon) [13].
2017Co-Authors: Rémi Tournebize, Alexandre De ,kochko, Francois Munoz, Stéphanie Manel, Yves Vigouroux, Valerie PoncetAbstract:Black points represent populations present in both re-sequencing and microsatellite datasets; blue points in the re-sequencing dataset only; red points in the microsatellite dataset only. Population names are coloured according to their genetic group assignment (blue for the North group, red for the South, black when undetermined). The topography of New Caledonia ranges from sea level up to 1,630 m ASL (Mont Panié). Amborella currently grows between 100 and 1,000 m ASL.