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Patrick S Herendeen - One of the best experts on this subject based on the ideXlab platform.
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the origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the cretaceous paleogene k pg mass extinction event
2021Co-Authors: Erik J M Koenen, Dario I Ojeda, Freek T Bakker, Jan J Wieringa, Catherine A Kidner, Olivier J Hardy, Toby R Pennington, Patrick S HerendeenAbstract:The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for Allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or Allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous-Paleogene (K-Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events].
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the origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the cretaceous paleogene k pg mass extinction event
2020Co-Authors: Erik J M Koenen, Dario I Ojeda, Freek T Bakker, Jan J Wieringa, Catherine A Kidner, Olivier J Hardy, Toby R Pennington, Patrick S HerendeenAbstract:The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for Allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or Allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic.
Catherine A Kidner - One of the best experts on this subject based on the ideXlab platform.
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the origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the cretaceous paleogene k pg mass extinction event
2021Co-Authors: Erik J M Koenen, Dario I Ojeda, Freek T Bakker, Jan J Wieringa, Catherine A Kidner, Olivier J Hardy, Toby R Pennington, Patrick S HerendeenAbstract:The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for Allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or Allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous-Paleogene (K-Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events].
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the origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the cretaceous paleogene k pg mass extinction event
2020Co-Authors: Erik J M Koenen, Dario I Ojeda, Freek T Bakker, Jan J Wieringa, Catherine A Kidner, Olivier J Hardy, Toby R Pennington, Patrick S HerendeenAbstract:The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for Allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or Allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic.
Toby R Pennington - One of the best experts on this subject based on the ideXlab platform.
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the origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the cretaceous paleogene k pg mass extinction event
2021Co-Authors: Erik J M Koenen, Dario I Ojeda, Freek T Bakker, Jan J Wieringa, Catherine A Kidner, Olivier J Hardy, Toby R Pennington, Patrick S HerendeenAbstract:The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for Allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or Allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous-Paleogene (K-Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events].
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the origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the cretaceous paleogene k pg mass extinction event
2020Co-Authors: Erik J M Koenen, Dario I Ojeda, Freek T Bakker, Jan J Wieringa, Catherine A Kidner, Olivier J Hardy, Toby R Pennington, Patrick S HerendeenAbstract:The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for Allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or Allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic.
Tsuyoshi Tanaka - One of the best experts on this subject based on the ideXlab platform.
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Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris
2018Co-Authors: Tatsuhiro Nomaguchi, Yoshiaki Maeda, Tomoko Yoshino, Toru Asahi, Leila Tirichine, Chris Bowler, Tsuyoshi TanakaAbstract:BACKGROUND: Allopolyploidy is a genomic structure wherein two or more sets of chromosomes derived from divergent parental species coexist within an organism. It is a prevalent genomic configuration in plants, as an important source of genetic variation, and also frequently confers environmental adaptability and increased crop productivity. We previously reported the oleaginous marine diatom Fistulifera solaris JPCC DA0580 to be a promising host for biofuel production and that its genome is allopolyploid, which had never previously been reported in eukaryotic microalgae. However, the study of Allopolyploidy in F. solaris was hindered by the difficulty in classifying the homoeologous genes based on their progenitor origins, owing to the shortage of diatom genomic references. RESULTS: In this study, the allopolyploid genome of F. solaris was tentatively classified into two pseudo-parental subgenomes using sequence analysis based on GC content and codon frequency in each homoeologous gene pair. This approach clearly separated the genome into two distinct fractions, subgenome Fso_h and Fso_l, which also showed the potency of codon usage analysis to differentiate the allopolyploid subgenome. Subsequent homoeolog expression bias analysis revealed that, although both subgenomes appear to contribute to global transcription, there were subgenomic preferences in approximately 61% of homoeologous gene pairs, and the majority of these genes showed continuous bias towards a specific subgenome during lipid accumulation. Additional promoter analysis indicated the possibility of promoter motifs involved in biased transcription of homoeologous genes. Among these subgenomic preferences, genes involved in lipid metabolic pathways showed interesting patterns in that biosynthetic and degradative pathways showed opposite subgenomic preferences, suggesting the possibility that the oleaginous characteristics of F. solaris derived from one of its progenitors. CONCLUSIONS: We report the detailed genomic structure and expression patterns in the allopolyploid eukaryotic microalga F. solaris. The allele-specific patterns reported may contribute to the oleaginous characteristics of F. solaris and also suggest the robust oleaginous characteristics of one of its progenitors. Our data reveal novel aspects of Allopolyploidy in a diatom that is not only important for evolutionary studies but may also be advantageous for biofuel production in microalgae.
Jonathan F Wendel - One of the best experts on this subject based on the ideXlab platform.
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homoeologous exchanges segmental Allopolyploidy and polyploid genome evolution
2020Co-Authors: Annaliese S Mason, Jonathan F WendelAbstract:Polyploidy is a major force in plant evolution and speciation. In newly formed allopolyploids, pairing between related chromosomes from different subgenomes (homoeologous chromosomes) during meiosis is common. The initial stages of allopolyploid formation are characterized by a spectrum of saltational genomic and regulatory alterations that are responsible for evolutionary novelty. Here we highlight the possible effects and roles of recombination between homoeologous chromosomes during the early stages of allopolyploid stabilization. Homoeologous exchanges (HEs) have been reported in young allopolyploids from across the angiosperms. Although all lineages undergo karyotype change via chromosome rearrangements over time, the early generations after allopolyploid formation are predicted to show an accelerated rate of genomic change. HEs can also cause changes in allele dosage, genome-wide methylation patterns, and downstream phenotypes, and can hence be responsible for speciation and genome stabilization events. Additionally, we propose that fixation of duplication - deletion events resulting from HEs could lead to the production of genomes which appear to be a mix of autopolyploid and allopolyploid segments, sometimes termed "segmental allopolyploids." We discuss the implications of these findings for our understanding of the relationship between genome instability in novel polyploids and genome evolution.
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the utility of graph clustering of 5s ribosomal dna homoeologs in plant allopolyploids homoploid hybrids and cryptic introgressants
2020Co-Authors: Malika L Ainouche, Jonathan F Wendel, Sonia Garcia, Natalia Borowskazuchowska, Alena Kuderova, Ales KovarikAbstract:Introduction: Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer pipeline to analyse homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant genera, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups. Results: (i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graphs complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harbouring introgressed genomes exhibit exceptionally complex graph structures. Conclusion: We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organisation and intragenomic homogenity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RepeatExplorer pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.
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genetic and epigenetic aspects of polyploid evolution in plants
2013Co-Authors: Andreas Madlung, Jonathan F WendelAbstract:Polyploidy, the condition of possessing more than 2 complete chromosome sets in the same nucleus, is frequent in nature and has implications for a species' prospects for evolution. Newly formed polyploids, so-called neopolyploids, undergo a wide spectrum of genomic changes upon genome merger and duplication. Here, we review recent literature describing genomic and transcriptomic changes along the pathway from neoallopolyploid formation to the stabilization of species and diversification at the allopolyploid level. We begin by reviewing pathways of polyploid formation and discuss the effects of genome doubling and hybridization on chromosome pairing. We then review our knowledge of epigenetic changes in allopolyploids, followed by a consideration of the effects of these structural genomic and epigenetic changes on the transcriptional activity of genes in allopolyploids. We discuss the effects of changes in gene expression in polyploids with respect to current evolutionary theory. Finally, we draw attention to the general question of the relationships between genomic and transcriptomic alteration and incipient diversification among sibling polyploid lines and populations.
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genomically biased accumulation of seed storage proteins in allopolyploid cotton
2011Co-Authors: Norma L Houston, Dharminder Pathak, Linnea Schmidt, Jay J Thelen, Jonathan F WendelAbstract:Allopolyploidy is an important process during plant evolution that results in the reunion of two divergent genomes into a common nucleus. Many of the immediate as well as longer-term genomic and epigenetic responses to polyploidy have become appreciated. To investigate the modifications of gene expression at the proteome level caused by allopolyploid formation, we conducted a comparative analysis of cotton seed proteomes from the allopolyploid Gossypium hirsutum (AD genome) and its model A-genome and D-genome diploid progenitors. An unexpectedly high level of divergence among the three proteomes was found, with about one-third of all protein forms being genome specific. Comparative analysis showed that there is a higher degree of proteomic similarity between the allopolyploid and its D-genome donor than its A-genome donor, reflecting a biased accumulation of seed proteins in the allopolyploid. Protein identification and genetic characterization of high-abundance proteins revealed that two classes of seed storage proteins, vicilins and legumins, compose the major component of cotton seed proteomes. Analyses further indicate differential regulation or modification of homoeologous gene products, as well as novel patterns in the polyploid proteome that may result from the interaction between homoeologous gene products. Our findings demonstrate that genomic merger and doubling have consequences that extend beyond the transcriptome into the realm of the proteome and that unequal expression of proteins from diploid parental genomes may occur in allopolyploids.
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evolutionary rate variation genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation
2010Co-Authors: Lex E Flagel, Jonathan F WendelAbstract:Here, we describe the evolution of gene expression among a diversified cohort of five allopolyploid species in the cotton genus (Gossypium). Using this phylogenetic framework and comparisons with expression changes accompanying F(1) hybridization, we provide a temporal perspective on expression diversification following a shared genome duplication. Global patterns of gene expression were studied by the hybridization of petal RNAs to a custom microarray. This platform measures total expression for c. 42 000 duplicated genes, and genome-specific expression for c. 1400 homoeologs (genes duplicated by polyploidy). We report homoeolog expression bias favoring the allopolyploid D genome over the A genome in all species (among five polyploid species, D biases ranging from c. 54 to 60%), in addition to conservation of biases among genes. Furthermore, we find surprising levels of transgressive up- and down-regulation in the allopolyploids, a diminution of the level of bias in genomic expression dominance but not in its magnitude, and high levels of rate variation among allotetraploid species. We illustrate how phylogenetic and temporal components of expression evolution may be partitioned and revealed following Allopolyploidy. Overall patterns of expression evolution are similar among the Gossypium allotetraploids, notwithstanding a high level of interspecific rate variation, but differ strikingly from the direction of genomic expression dominance patterns in the synthetic F(1) hybrid.