A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome.

By Guillaume Le Blanc, Karsten Hokamp, Kenneth H. Wolfe. Genome Research, 2003

741 citations recorded by the source corpus.

The Arabidopsis genome contains numerous large duplicated chromosomal segments, but the different approaches used in previous analyses led to different interpretations regarding the number and timing of ancestral large-scale duplication events. Here, using more appropriate methodology and a more recent version of the genome sequence annotation, we investigate the scale and timing of segmental duplications in Arabidopsis. We used protein sequence similarity searches to detect duplicated blocks in the genome, used the level of synonymous substitution between duplicated genes to estimate the relative ages of the blocks containing them, and analyzed the degree of overlap between adjacent duplicated blocks. We conclude that the Arabidopsis lineage underwent at least two distinct episodes of duplication. One was a polyploidy that occurred much more recently than estimated previously, before the Arabidopsis/Brassica rapa split and probably during the early emergence of the crucifer family (24-40 Mya). An older set of duplicated blocks was formed after the monocot/dicot divergence, and the relatively low level of overlap among these blocks indicates that at least some of them are remnants of a larger duplication such as a polyploidy or aneuploidy.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/fdee62399212577665d17837a2c6db961900e297

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Plant Science

Citations in the corpus

Widespread genome duplications throughout the history of flowering plants. (2006, background): “…Harbor Laboratory Press; ISSN 1088-9051/06; www.genome.org genome duplications from segmental and tandem duplications by mapping chromosomal locations of duplicate genes or blocks of genes (Simillion et al. 2002; Blanc et al. 2003; Bowers et al. 2003; Cannon et al. 2004; Paterson et al. 2004b).”
Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution (2004, methodology): “%) of the genome (Simillion et al., 2002; Blanc et al., 2003; Bowers et al., 2003).”
Phylogenetic Analysis of the Plant Endo-β-1,4-Glucanase Gene Family (2004, background): “ie/athal/dup as described by Blanc et al. (2003).”
Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice (2004, background): “The most recent large-scale duplications that likely involved the whole genome occurred before the Arabidopsis–Brassica split and after the Malvaceae– Brassiceae split 14.5 to 40 million years ago (Blanc et al., 2003; Bowers et al., 2003).”
Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice (2006, background): “The duplicated chromosomal regions retain ;25% of their genes as duplicates [3], with the remaining duplicate pairs having lost one copy to deletion or pseudogenization.”
Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice[W] (2006, background): “Since the density of the duplicated genes in recently duplicated segmental chromosomes was reported to be 28.0% 6 7.8% (Blanc et al., 2003), the duplicated pairs of ERF genes have been preferentially retained compared with other genes.”
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. (2008, methodology): “In this step, we need to use a “reference” gene order as the basis for stacking the tracks; we then describe the aligned synteny blocks as “threaded by the reference order,” a procedure inspired by TBA aligner (Blanchette et al. 2004).”
DAGchainer: a tool for mining segmental genome duplications and synteny (2004, methodology): “Using the latest release (version 5) of the Arabidopsis genome annotation (available at ftp://ftp.tigr.org/pub/data/a_thaliana/ath1), DAGchainer was employed to identify genes found in chromosomal segmental duplications (Fig.”