Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants

Freeling, Michael; Woodhouse, Margaret R.; Subramaniam, Sabarinath; Turco, Gina; Lisch, Damon; Schnable, James C.

doi:10.1016/j.pbi.2012.01.015

Cited by 195 publications

(179 citation statements)

References 63 publications

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“…These major plant families are also characterized by having independent ancient polyploidy events at their origins (Soltis et al, 2009;Schranz et al, 2012;Tank et al, 2015). Morphological changes could thus be tied to these ancient polyploidy events or specific gene transposition events that place key regulatory factors into new genomic contexts (Soltis et al, 2009;Freeling et al, 2012). Our synteny network approach can identify such lineage-specific transposition events for genes by clustering and phylogenetic profiling.…”

Section: Section I: Lineage-specific Synteny Relationshipsmentioning

confidence: 99%

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

et al. 2017

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Conserved genomic context provides critical information for comparative evolutionary analysis. With the increase in numbers of sequenced plant genomes, synteny analysis can provide new insights into gene family evolution. Here, we exploit a network analysis approach to organize and interpret massive pairwise syntenic relationships. Specifically, we analyzed synteny networks of the MADS-box transcription factor gene family using 51 completed plant genomes. In combination with phylogenetic profiling, several novel evolutionary patterns were inferred and visualized from synteny network clusters. We found lineage-specific clusters that derive from transposition events for the regulators of floral development (APETALA3 and PI) and flowering time (FLC) in the Brassicales and for the regulators of root development (AGL17) in Poales. We also identified two large gene clusters that jointly encompass many key phenotypic regulatory Type II MADS-box gene clades (SEP1, SQUA, TM8, SEP3, FLC, AGL6, and TM3). Gene clustering and gene trees support the idea that these genes are derived from an ancient tandem gene duplication that likely predates the radiation of the seed plants and then expanded by subsequent polyploidy events. We also identified angiosperm-wide conservation of synteny of several other less studied clades. Combined, these findings provide new hypotheses for the genomic origins, biological conservation, and divergence of MADS-box gene family members.

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Section: Section I: Lineage-specific Synteny Relationshipsmentioning

confidence: 99%

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

et al. 2017

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“…As researchers have utilized complete genome sequences and high-quality transcriptomes that allow resolution of duplicate gene pairs, it has become clear that many allopolyploids exhibit genome dominance such that one of the two subgenomes plays a greater functional role than the other (Thomas et al, 2006;Flagel and Wendel, 2010;Woodhouse et al, 2010Woodhouse et al, , 2014Wang et al, 2011;Freeling et al, 2012). This was initially observed through the analysis of the retention of genes in the two subgenomes, but subsequent work has found evidence for preferential transcription and functional impact of genes in one subgenome .…”

Section: Chromatin-based Long-term Contributions To Regulatory Diversmentioning

confidence: 99%

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Springer

Lisch

2016

Plant Cell

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ORCID IDs: 0000-0002-7301-4759 (N.M.S.); 0000-0003-3232-9479 (Q.L.)Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that the current structure of a genome is the result of various TE bursts and WGDs and it is likely that the silencing mechanisms and the chromatin structure of a genome have been shaped by these events. This suggests that the specific mechanisms targeting chromatin modifications and epigenomic patterns may vary among different species. Many crop species have likely evolved chromatin-based mechanisms to tolerate silenced TEs near actively expressed genes. These interactions of heterochromatin and euchromatin are likely to have important roles in modulating gene expression and variability within species.

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“…This difference may be due to reduced negative selection against altered dosage of chromosomes that carry fewer genes (there are eight arenosa instead of five thaliana chromosomes) or could stem from more regular meiotic partitioning of one genome compared with the other. Alternatively, the two parental genomes in this allopolyploid may differ in overall epigenetic state leading to different overall expression levels and observed aneuploidy (Freeling et al, 2012).…”

Section: Dosage Imbalance Is Widespreadmentioning

confidence: 99%

The BOY NAMED SUE Quantitative Trait Locus Confers Increased Meiotic Stability to an Adapted Natural Allopolyploid of Arabidopsis

et al. 2014

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Whole-genome duplication resulting from polyploidy is ubiquitous in the evolutionary history of plant species. Yet, polyploids must overcome the meiotic challenge of pairing, recombining, and segregating more than two sets of chromosomes. Using genomic sequencing of synthetic and natural allopolyploids of Arabidopsis thaliana and Arabidopsis arenosa, we determined that dosage variation and chromosomal translocations consistent with homoeologous pairing were more frequent in the synthetic allopolyploids. To test the role of structural chromosomal differentiation versus genetic regulation of meiotic pairing, we performed sequenced-based, high-density genetic mapping in F2 hybrids between synthetic and natural lines. This F2 population displayed frequent dosage variation and deleterious homoeologous recombination. The genetic map derived from this population provided no indication of structural evolution of the genome of the natural allopolyploid Arabidopsis suecica, compared with its predicted parents. The F2 population displayed variation in meiotic regularity and pollen viability that correlated with a single quantitative trait locus, which we named BOY NAMED SUE, and whose beneficial allele was contributed by A. suecica. This demonstrates that an additive, gain-of-function allele contributes to meiotic stability and fertility in a recently established allopolyploid and provides an Arabidopsis system to decipher evolutionary and molecular mechanisms of meiotic regularity in polyploids.

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Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants

Cited by 195 publications

References 63 publications

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

The BOY NAMED SUE Quantitative Trait Locus Confers Increased Meiotic Stability to an Adapted Natural Allopolyploid of Arabidopsis

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