Dating the Monocot?Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes

Chaw, Shu‐Miaw; Chang, Chien-Chang; Chen, Hsin‐Liang; Li, Wen‐Hsiung

doi:10.1007/s00239-003-2564-9

Cited by 370 publications

(137 citation statements)

References 56 publications

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“…A total of 102 genes spanned all eight of the species that were retained for analysis. The plant dataset was taken from a larger dataset comprising 61 genes from 12 taxa [ 39]. Nine species were selected in accordance with the stipulation that their phylogeny was known with almost complete certainty.…”

Section: Resultsmentioning

confidence: 99%

Relaxed Phylogenetics and Dating with Confidence

et al. 2006

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In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

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Section: Resultsmentioning

confidence: 99%

Relaxed Phylogenetics and Dating with Confidence

et al. 2006

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“…We identified three dicot-specific groups (G6, 10, 15) and six grass-specific groups (G27, G32, G35, G43, G45, G46) plus G3.b. These non-conserved groups likely evolved after the divergence of eudicots and grasses 140 to 150 million years ago [10-12]. In addition, poplar possesses four unique subgroups (G38, G39, G40, G48).…”

Section: Resultsmentioning

confidence: 99%

“…R2R3 MYBs likely evolved from progenitor 3R MYB proteins by losing the R1 repeat [10]. The family subsequently underwent a dramatic expansion after the origin of land plants but before the divergence of dicots and grasses [10-12]. The whole-genome complements of R2R3 MYB proteins has been investigated in several plant species, including Arabidopsis, rice ( Oryza sativa ), poplar ( Populus trichocarpa ), grapevine ( Vitis vinifera ), and maize ( Zea mays ), often with the goals of identifying orthologous groups and species-diverged clades [13-17].…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass

Zhao

Bartley

2014

BMC Plant Biol

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BackgroundR2R3 MYB proteins constitute one of the largest plant transcription factor clades and regulate diverse plant-specific processes. Several R2R3 MYB proteins act as regulators of secondary cell wall (SCW) biosynthesis in Arabidopsis thaliana (At), a dicotyledenous plant. Relatively few studies have examined SCW R2R3 MYB function in grasses, which may have diverged from dicots in terms of SCW regulatory mechanisms, as they have in cell wall composition and patterning. Understanding cell wall regulation is especially important for improving lignocellulosic bioenergy crops, such as switchgrass.ResultsHere, we describe the results of applying phylogenic, OrthoMCL, and sequence identity analyses to classify the R2R3 MYB family proteins from the annotated proteomes of Arabidposis, poplar, rice, maize and the initial genome (v0.0) and translated transcriptome of switchgrass (Panicum virgatum). We find that the R2R3 MYB proteins of the five species fall into 48 subgroups, including three dicot-specific, six grass-specific, and two panicoid grass-expanded subgroups. We observe four classes of phylogenetic relationships within the subgroups of known SCW-regulating MYB proteins between Arabidopsis and rice, ranging from likely one-to-one orthology (for AtMYB26, AtMYB103, AtMYB69) to no homologs identifiable (for AtMYB75). Microarray data for putative switchgrass SCW MYBs indicate that many maintain similar expression patterns with the Arabidopsis SCW regulators. However, some of the switchgrass-expanded candidate SCW MYBs exhibit differences in gene expression patterns among paralogs, consistent with subfunctionalization. Furthermore, some switchgrass representatives of grass-expanded clades have gene expression patterns consistent with regulating SCW development.ConclusionsOur analysis suggests that no single comparative genomics tool is able to provide a complete picture of the R2R3 MYB protein family without leaving ambiguities, and establishing likely false-negative and -positive relationships, but that used together a relatively clear view emerges. Generally, we find that most R2R3 MYBs that regulate SCW in Arabidopsis are likely conserved in the grasses. This comparative analysis of the R2R3 MYB family will facilitate transfer of understanding of regulatory mechanisms among species and enable control of SCW biosynthesis in switchgrass toward improving its biomass quality.

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“…The phylogenetic relationships between different plant groups are based on earlier studies [3][4][5][6][7]. The estimated divergence times are based on previous studies [8][9][10][11]. See also the main text for more details.…”

Section: The History Of Land Plants (A) Overview Of Land Plant Evolutionmentioning

confidence: 99%

Morphological evolution in land plants: new designs with old genes

Pires

Dolan

2012

Phil. Trans. R. Soc. B

204

189

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The colonization and radiation of multicellular plants on land that started over 470 Ma was one of the defining events in the history of this planet. For the first time, large amounts of primary productivity occurred on the continental surface, paving the way for the evolution of complex terrestrial ecosystems and altering global biogeochemical cycles; increased weathering of continental silicates and organic carbon burial resulted in a 90 per cent reduction in atmospheric carbon dioxide levels. The evolution of plants on land was itself characterized by a series of radical transformations of their body plans that included the formation of three-dimensional tissues, de novo evolution of a multicellular diploid sporophyte generation, evolution of multicellular meristems, and the development of specialized tissues and organ systems such as vasculature, roots, leaves, seeds and flowers. In this review, we discuss the evolution of the genes and developmental mechanisms that drove the explosion of plant morphologies on land. Recent studies indicate that many of the gene families which control development in extant plants were already present in the earliest land plants. This suggests that the evolution of novel morphologies was to a large degree driven by the reassembly and reuse of pre-existing genetic mechanisms.

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Dating the Monocot?Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes

Cited by 370 publications

References 56 publications

Relaxed Phylogenetics and Dating with Confidence

Relaxed Phylogenetics and Dating with Confidence

Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass

Morphological evolution in land plants: new designs with old genes

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