Abstract
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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Claims 8
Claim · model-written summary
Heterochromatic repeat arrays differed significantly among Arabidopsis populations, by up to twofold in the 180 bp repeat, 45S rDNA arrays and Athila retroelements.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianat0 - Outcome
- polymorphisme0
- Value
- a factor of twoe0
- Qualifier
- centromeric 180 bp repeat, in the 45S rDNA arrays and in the Athila retroelementse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Arabidopsis thaliana”
e0“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”
Claim · model-written summary
Loh-0 had more than twice as many 5S RNA gene copies as Col-0.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- Loh-0e0
- Gene
- 5S RNA genee0
- Outcome
- 5S RNA gene copiese0
- Direction
- increasee0
- Value
- more than a two-folde0
- Comparator
- Col-0e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Arabidopsis thaliana”
e0“Loh-0, we found more than a two-fold increase in 5S RNA gene copies relative to Col-0”
Claim · model-written summary
Fluorescence in situ hybridization supported 5S locus size polymorphism between Loh-0 and Col-0.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- Loh-0e0
- Gene
- 5S locie0
- Outcome
- size polymorphisme0
- Comparator
- Col-0e0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Arabidopsis thaliana”
e0“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”
Claim · model-written summary
Comparative genomic hybridization did not support enough contiguous protein-coding gene copy number variation to explain the genome size difference between Loh-0 and Col-0.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- Loh-0e0
- Outcome
- contiguous variation in copy number of protein-coding genese0
- Comparator
- Col-0e0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Arabidopsis thaliana”
e0“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”
Claim · model-written summary
Variation in repeat fractions could account for about 50% of genome size variance among accessions in the computational model.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- accessionse0
- Outcome
- variance in genome sizee0
- Value
- about 50%e0
- Qualifier
- variation we measured in the repeat fractionse1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Arabidopsis thaliana”
e0“this proposed relationship could account for about 50% of the variance in genome size among the accessions”
e1“variation we measured in the repeat fractions”
Claim · model-written summary
The authors concluded that 5S and 45S ribosomal gene repeat numbers vary substantially among Arabidopsis accessions.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- 5S and 45S ribosomal genese0
- Outcome
- repeat number polymorphisme0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Arabidopsis thaliana”
e0“substantial repeat number polymorphism for 5S and 45S ribosomal genes among accession of A. thaliana”
Claim · model-written summary
The authors suggested that centromeric and pericentromeric repeats also differ among accessions.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Outcome
- Differencese0
- Qualifier
- centromeric and pericentromeric repeatse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Arabidopsis thaliana”
e0“Differences are also suggested for centromeric and pericentromeric repeats”
Claim · model-written summary
The authors recommended independent validation of genome size in addition to flow cytometry.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Outcome
- independent validation of genome sizee0
- Comparator
- flow cytometric measurementse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Arabidopsis thaliana”
e0“independent validation of genome size should be sought in addition to flow cytometric measurements”