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Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana

BACKGROUND: The composition of the individual eukaryote's genome and its variation within a species remain poorly defined. Even for a sequenced genome such as that of the model plant Arabidopsis thaliana accession Col-0, the large arrays of heterochromatic repeats are incompletely sequenced, wi...

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Autores principales: Davison, Jerry, Tyagi, Anand, Comai, Luca
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2000876/
https://www.ncbi.nlm.nih.gov/pubmed/17705842
http://dx.doi.org/10.1186/1471-2229-7-44
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author Davison, Jerry
Tyagi, Anand
Comai, Luca
author_facet Davison, Jerry
Tyagi, Anand
Comai, Luca
author_sort Davison, Jerry
collection PubMed
description BACKGROUND: The composition of the individual eukaryote's genome and its variation within a species remain poorly defined. Even for a sequenced genome such as that of the model plant Arabidopsis thaliana accession Col-0, the large arrays of heterochromatic repeats are incompletely sequenced, with gaps of uncertain size persisting in them. RESULTS: Using geographically separate populations of A. thaliana, we assayed variation in the heterochromatic repeat arrays using two independent methods and identified significant polymorphism among them, with variation by as much as a factor of two in the centromeric 180 bp repeat, in the 45S rDNA arrays and in the Athila retroelements. In the accession with highest genome size as measured by flow cytometry, Loh-0, we found more than a two-fold increase in 5S RNA gene copies relative to Col-0; results from fluorescence in situ hybridization with 5S probes were consistent with the existence of size polymorphism between Loh-0 and Col-0 at the 5S loci. Comparative genomic hybridization results of Loh-0 and Col-0 did not support contiguous variation in copy number of protein-coding genes on the scale needed to explain their observed genome size difference. We developed a computational data model to test whether the variation we measured in the repeat fractions could account for the different genome sizes determined with flow cytometry, and found that this proposed relationship could account for about 50% of the variance in genome size among the accessions. CONCLUSION: Our analyses are consistent with substantial repeat number polymorphism for 5S and 45S ribosomal genes among accession of A. thaliana. Differences are also suggested for centromeric and pericentromeric repeats. Our analysis also points to the difficulties in measuring the repeated fraction of the genome and suggests that independent validation of genome size should be sought in addition to flow cytometric measurements.
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spelling pubmed-20008762007-10-05 Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana Davison, Jerry Tyagi, Anand Comai, Luca BMC Plant Biol Research Article BACKGROUND: The composition of the individual eukaryote's genome and its variation within a species remain poorly defined. Even for a sequenced genome such as that of the model plant Arabidopsis thaliana accession Col-0, the large arrays of heterochromatic repeats are incompletely sequenced, with gaps of uncertain size persisting in them. RESULTS: Using geographically separate populations of A. thaliana, we assayed variation in the heterochromatic repeat arrays using two independent methods and identified significant polymorphism among them, with variation by as much as a factor of two in the centromeric 180 bp repeat, in the 45S rDNA arrays and in the Athila retroelements. In the accession with highest genome size as measured by flow cytometry, Loh-0, we found more than a two-fold increase in 5S RNA gene copies relative to Col-0; results from fluorescence in situ hybridization with 5S probes were consistent with the existence of size polymorphism between Loh-0 and Col-0 at the 5S loci. Comparative genomic hybridization results of Loh-0 and Col-0 did not support contiguous variation in copy number of protein-coding genes on the scale needed to explain their observed genome size difference. We developed a computational data model to test whether the variation we measured in the repeat fractions could account for the different genome sizes determined with flow cytometry, and found that this proposed relationship could account for about 50% of the variance in genome size among the accessions. CONCLUSION: Our analyses are consistent with substantial repeat number polymorphism for 5S and 45S ribosomal genes among accession of A. thaliana. Differences are also suggested for centromeric and pericentromeric repeats. Our analysis also points to the difficulties in measuring the repeated fraction of the genome and suggests that independent validation of genome size should be sought in addition to flow cytometric measurements. BioMed Central 2007-08-16 /pmc/articles/PMC2000876/ /pubmed/17705842 http://dx.doi.org/10.1186/1471-2229-7-44 Text en Copyright © 2007 Davison et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Davison, Jerry
Tyagi, Anand
Comai, Luca
Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
title Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
title_full Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
title_fullStr Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
title_full_unstemmed Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
title_short Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
title_sort large-scale polymorphism of heterochromatic repeats in the dna of arabidopsis thaliana
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2000876/
https://www.ncbi.nlm.nih.gov/pubmed/17705842
http://dx.doi.org/10.1186/1471-2229-7-44
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