Different Gene Families in Arabidopsis thaliana Transposed in Different Epochs and at Different Frequencies throughout the Rosids[W]

@article{Woodhouse2011DifferentGF,
  title={Different Gene Families in Arabidopsis thaliana Transposed in Different Epochs and at Different Frequencies throughout the Rosids[W]},
  author={Margaret R. Woodhouse and Haibao Tang and Michael Freeling},
  journal={Plant Cell},
  year={2011},
  volume={23},
  pages={4241 - 4253}
}
This work examines the chromosomal positional history of all genes in Arabidopsis thaliana through evolutionary time in the rosid superorder, finding that mobile gene families are under different selection pressure than syntenic gene families. Certain types of gene families, such as those encoding most families of transcription factors, maintain their chromosomal syntenic positions throughout angiosperm evolutionary time. Other nonsyntenic gene families are prone to deletion, tandem duplication… 

Figures and Tables from this paper

Gene family evolution in green plants with emphasis on the origination and evolution of Arabidopsis thaliana genes.
  • Ya-Long Guo
  • Biology
    The Plant journal : for cell and molecular biology
  • 2013
TLDR
Genome-wide insights are provided into evolutionary history and mechanisms of genes and gene families in green plants and especially in A. thaliana that are under stronger purifying selection and more conserved.
Whole Genome and Tandem Duplicate Retention Facilitated Glucosinolate Pathway Diversification in the Mustard Family
TLDR
It is shown that WGD and tandem duplication (TD) accelerated genetic versatility of plant secondary metabolism, exemplified with the glucosinolate (GS) pathway in the mustard family.
The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes
TLDR
A draft genome sequence of Brassica oleracea is described, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks.
Diversification of defensins and NLRs in Arabidopsis species by different evolutionary mechanisms
TLDR
The present analyses of NLRs expands previous studies in Arabidopsis thaliana and highlights contrasting patterns of purifying and diversifying selection affecting different gene regions.
GC content of plant genes is linked to past gene duplications
TLDR
A “biased gene duplication / biased mutation” (BDBM) model is proposed that may explain the origin and trajectory of the observed link between duplication and genic GC bias and is supported by empirical data based on joint analyses of 9 angiosperm species with their genes categorized by duplication status, GC content, methylation levels and functional classes.
Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants
TLDR
A comprehensive landscape of different modes of gene duplication across the plant kingdom is identified by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
A Complex Interplay of Tandem- and Whole-Genome Duplication Drives Expansion of the L-Type Lectin Receptor Kinase Gene Family in the Brassicaceae
TLDR
The evolutionary analyses of these plant immune components provide a framework to support future plant resistance breeding and it is demonstrated that the largest and most diverse L-type LecRK clades are lineage-specific.
The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification
TLDR
A systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events, and found a significant enrichment of essential genes was found among genes encoding for protein kinases.
A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants
TLDR
By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, this analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system.
MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans
TLDR
MCScanX-transposed is developed, a software package to detect transposed gene duplications that occurred within different epochs, based on execution of MCScanX within and between related genomes.
...
...

References

SHOWING 1-10 OF 58 REFERENCES
Many or most genes in Arabidopsis transposed after the origin of the order Brassicales.
TLDR
It is estimated that between one-fourth and three-fourths of the genes in Arabidopsis are transposed in the Brassicales, and a unique method involving transposition-rich regions of genome allowed for an indirect estimate of the positional stability of the average gene.
The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana
TLDR
Combining information about genomic segmental duplications, gene family phylogenies, and gene positions provides a method to evaluate contributions of tandem duplication and segmental genome duplication in the generation and maintenance of gene families.
Transposed Genes in Arabidopsis Are Often Associated with Flanking Repeats
TLDR
It is suggested that intrachromosomal recombination between tandemly duplicated sequences, and subsequent insertion of the circular product, is the predominant mechanism of gene transposition in Arabidopsis.
Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice
TLDR
Despite differences in the age distribution of tandem arrays, the striking similarities between rice and Arabidopsis indicate similar mechanisms of TAG generation and maintenance, which reflect an evolutionary trend in which successful tandem duplication involves genes either at the end of biochemical pathways or in flexible steps in a pathway, for which fluctuation in copy number is unlikely to affect downstream genes.
Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene.
Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels
TLDR
Putatively orthologous, shared single copy nuclear genes provide a vast source of new evidence for plant phylogenetics, genome mapping, and other applications, as well as a substantial class of genes for which functional characterization is needed.
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes.
TLDR
It is found that islands of retention contain "connected genes," those genes predicted-by the gene balance hypothesis-to be resistant to removal because the products they encode interact with other products in a dose-sensitive manner, creating a web of dependency.
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
TLDR
The 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47, based on 8.3× dideoxy sequence coverage, is reported, indicating pervasive selection for a smaller genome in this outcrossing species.
Chromosome evolution in eukaryotes: a multi-kingdom perspective.
Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication.
TLDR
Functional buffering may be especially important during "genomic turmoil" immediately after genome duplication but continues to act approximately 60 million years later, and its gradual deterioration may contribute cyclicality to genome duplication in some lineages.
...
...