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Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes.

Ziolkowski PA, Koczyk G, Galganski L, Sadowski J - Nucleic Acids Res. (2009)

Bottom Line: Based on the resulting alignments large indels (>100 bp) within these two genomes were analysed.The results show that unequal recombination is not efficient in the removal of TEs within the pericentromeric regions.Moreover, we discovered an unexpectedly high influence of large indels on gene evolution pointing out significant differences between the various gene families.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland.

ABSTRACT
Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidopsis thaliana lines, Columbia (Col) and Landsberg erecta (Ler). Based on the resulting alignments large indels (>100 bp) within these two genomes were analysed. There are approximately 8500 large indels accounting for the differences between the two genomes. The genetic basis of their origin was distinguished as three main categories: unequal recombination (Urec)-derived, illegitimate recombination (Illrec)-derived and transposable elements (TE)-derived. A detailed study of their distribution and size variation along chromosomes, together with a correlation analyses, allowed us to demonstrate the impact of particular recombination-based mechanisms on the plant genome evolution. The results show that unequal recombination is not efficient in the removal of TEs within the pericentromeric regions. Moreover, we discovered an unexpectedly high influence of large indels on gene evolution pointing out significant differences between the various gene families. For the first time, we present convincing evidence that somatic events do play an important role in plant genome evolution.

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Indel distribution along Arabidopsis chromosomes. The x-axis represents the physical distance (Mb) along the chromosome. The y-axis represents the normalized numbers of indels counted for each 1.5 Mb chromosomal section. The bar represents the centromeric region.
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Figure 1: Indel distribution along Arabidopsis chromosomes. The x-axis represents the physical distance (Mb) along the chromosome. The y-axis represents the normalized numbers of indels counted for each 1.5 Mb chromosomal section. The bar represents the centromeric region.

Mentions: For non-terminal indels we were able to determine their length, and elucidate the probable evolutionary forces responsible for their appearance. All of the three main mechanisms (TE, Urec, and ILLrec) have some characteristics, which enable discrimination between them. However, in many cases an individual indel analysis delivered evidence of two or even more mechanisms being involved. Hence, we developed a heuristic approach, that takes into account a number of parameters and performs some additional analyses, such as the location of repeated elements within an insertion and searching for homologous sequences within genomic regions under consideration. Here, for simplicity, we focus on general mechanisms, and refer to the detailed categories in particular cases only, where it can be of a special interest. The presumable general mechanisms responsible for indels were divided into three classes: ILLrec, which includes sequence homology-independent recombination pathways, TE, which correspond to new insertions or the excisions of transposable elements (both perfectly conserved and slightly modified mainly by illegitimate recombination) and Urec, which originates from homologous recombination events involving two identical or highly similar sequences of >50 bp length. Unclear cases were classified to be in the unknown origin (Unk) category (this fourth class consists of mutations likely generated by mechanisms that can not be assigned to any of the above for some reason; it was not used in the analysis of mechanisms generating indel mutations). The distribution of various indel categories along particular chromosome is shown in Figure 1. Full information describing non-terminal indels detected is presented in Table S2.Figure 1.


Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes.

Ziolkowski PA, Koczyk G, Galganski L, Sadowski J - Nucleic Acids Res. (2009)

Indel distribution along Arabidopsis chromosomes. The x-axis represents the physical distance (Mb) along the chromosome. The y-axis represents the normalized numbers of indels counted for each 1.5 Mb chromosomal section. The bar represents the centromeric region.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2691826&req=5

Figure 1: Indel distribution along Arabidopsis chromosomes. The x-axis represents the physical distance (Mb) along the chromosome. The y-axis represents the normalized numbers of indels counted for each 1.5 Mb chromosomal section. The bar represents the centromeric region.
Mentions: For non-terminal indels we were able to determine their length, and elucidate the probable evolutionary forces responsible for their appearance. All of the three main mechanisms (TE, Urec, and ILLrec) have some characteristics, which enable discrimination between them. However, in many cases an individual indel analysis delivered evidence of two or even more mechanisms being involved. Hence, we developed a heuristic approach, that takes into account a number of parameters and performs some additional analyses, such as the location of repeated elements within an insertion and searching for homologous sequences within genomic regions under consideration. Here, for simplicity, we focus on general mechanisms, and refer to the detailed categories in particular cases only, where it can be of a special interest. The presumable general mechanisms responsible for indels were divided into three classes: ILLrec, which includes sequence homology-independent recombination pathways, TE, which correspond to new insertions or the excisions of transposable elements (both perfectly conserved and slightly modified mainly by illegitimate recombination) and Urec, which originates from homologous recombination events involving two identical or highly similar sequences of >50 bp length. Unclear cases were classified to be in the unknown origin (Unk) category (this fourth class consists of mutations likely generated by mechanisms that can not be assigned to any of the above for some reason; it was not used in the analysis of mechanisms generating indel mutations). The distribution of various indel categories along particular chromosome is shown in Figure 1. Full information describing non-terminal indels detected is presented in Table S2.Figure 1.

Bottom Line: Based on the resulting alignments large indels (>100 bp) within these two genomes were analysed.The results show that unequal recombination is not efficient in the removal of TEs within the pericentromeric regions.Moreover, we discovered an unexpectedly high influence of large indels on gene evolution pointing out significant differences between the various gene families.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland.

ABSTRACT
Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidopsis thaliana lines, Columbia (Col) and Landsberg erecta (Ler). Based on the resulting alignments large indels (>100 bp) within these two genomes were analysed. There are approximately 8500 large indels accounting for the differences between the two genomes. The genetic basis of their origin was distinguished as three main categories: unequal recombination (Urec)-derived, illegitimate recombination (Illrec)-derived and transposable elements (TE)-derived. A detailed study of their distribution and size variation along chromosomes, together with a correlation analyses, allowed us to demonstrate the impact of particular recombination-based mechanisms on the plant genome evolution. The results show that unequal recombination is not efficient in the removal of TEs within the pericentromeric regions. Moreover, we discovered an unexpectedly high influence of large indels on gene evolution pointing out significant differences between the various gene families. For the first time, we present convincing evidence that somatic events do play an important role in plant genome evolution.

Show MeSH