The hidden duplication past of Arabidopsis thaliana.

Simillion, C., Vandepoele, K., Van Montagu, M., Zabeau, M., Van de Peer, Y.

Abstract

Analysis of the genome sequence of Arabidopsis thaliana shows that this genome, like that of many other eukaryotic organisms, has undergone large-scale gene duplications or even duplications of the entire genome. However, the high frequency of gene loss after duplication events reduces colinearity and therefore the chance of finding duplicated regions that, at the extreme, no longer share homologous genes. In this study we show that heavily degenerated block duplications that can no longer be recognized by directly comparing two segments because of differential gene loss, can still be detected through indirect comparison with other segments. When these so-called hidden duplications in Arabidopsis are taken into account, many homologous genomic regions can be found in five to eight copies. This finding strongly implies that Arabidopsis has undergone three, but probably no more, rounds of genome duplications. Therefore, adding such hidden blocks to the duplication landscape of Arabidopsis sheds light on the number of polyploidy events that this model plant genome has undergone in its evolutionary past.

Supplementary Data

Browse non-hidden duplications in Arabidopsis thaliana.

Non-hidden duplications are duplicated segments that still show conserved colinearity, i.e. conserved gene content and order.
Chromosome X Chromosome Y
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Browse multiplicons by multiplication level

A multiplicon is a set of genomic segments that are homologous to each other and have thus originated from the same ancestral segment through (multiple) duplications. The multiplication level is the number of segments in a multiplicon.
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Browse multiplicated segments

A multiplicated segment is a segment that is part of a multiplicon. You can browse these segments per chromosome or you can check if a specific locus (TIGR annotation, see remark below) is part of such a segment. If the locus you specify is not present in our dataset, the program will look for the nearest locus in our dataset.
Chromosome: TIGR Locus: Atg
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IMPORTANT! The genome annotation used in this study was the TIGR annotation of Aug. 10, 2001. Altough the gene identifiers (e.g. At3g15530) should still point to the same loci, it is possible that the mRNA and protein sequences of the genes are different from the current TIGR annotation.











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