| 1. |
- Charlesworth, Deborah, et al.
(author)
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Trans-specificity at Loci Near the Self-Incompatibility Loci in Arabidopsis
- 2006
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In: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 172:4, s. 2699-2704
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Journal article (peer-reviewed)abstract
- We compared allele sequences of two loci near the Arabidopsis lyrata self-incompatibility (S) loci with sequences of A. thaliana orthologs and found high numbers of shared polymorphisms, even excluding singletons and sites likely to be highly mutable. This suggests maintenance of entire S-haplotypes for long evolutionary times and extreme recombination suppression in the region.
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| 2. |
- Hagenblad, Jenny, 1974-, et al.
(author)
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Linkage Disequilibrium Between Incompatibility Locus Region Genes
- 2006
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In: Genetics. - Baltimore, MD, USA : The Genetics Society. - 0016-6731 .- 1943-2631. ; 173, s. 1057-1073
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Journal article (peer-reviewed)abstract
- We have studied diversity in Arabidopsis lyrata of sequencesorthologous to the ARK3 gene of A. thaliana. Our main goal wasto test for recombination in the S-locus region. In A. thaliana,the single-copy ARK3 gene is closely linked to the non-functionalcopies of the self-incompatibility loci, and the ortholog inA. lyrata (a self-incompatible species) is in the homologousgenome region and is known as Aly8. It is thus of interest totest whether Aly8 sequence diversity is elevated due to closelinkage to the highly polymorphic incompatibility locus, asis theoretically predicted. However, Aly8 is not a single-copygene, and the presence of paralogs could also lead to the appearanceof elevated diversity. We established a typing approach basedon different lengths of Aly8 PCR products and show that mostA. lyrata haplotypes have a single copy, but some have two genecopies, both closely linked to the incompatibility locus, onebeing a pseudogene. We determined the phase of multiple haplotypesin families of plants from Icelandic and other populations.Different Aly8 sequence types are associated with differentSRK alleles, while haplotypes with the same SRK sequences tendto have the same Aly8 sequence. There is evidence of some exchangeof sequences between different Aly8 sequences, making it difficultto determine which ones are allelic or to estimate the diversity.However, the homogeneity of the Aly8 sequences of each S-haplotypesuggests that recombination between the loci has been very infrequentover the evolutionary history of these populations. Overall,the results suggest that recombination rarely occurs in theinterval between the S-loci and Aly8 and that linkage to theS-loci can probably account for the observed high Aly8 diversity.
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| 3. |
- Kawabe, Akira, et al.
(author)
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Centromere Locations and Associated Chromosome Rearrangements in Arabidopsis lyrata and A. thaliana
- 2006
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In: Genetics. - Baltimore, MD, USA : The Genetics Society. - 0016-6731 .- 1943-2631. ; 173:3, s. 1613-1619
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Journal article (peer-reviewed)abstract
- We analyzed linkage and chromosomal positions of genes in A. lyrata ssp. petraea that are located near the centromere (CEN) regions of A. thaliana, using at least two genes from the short and long arms of each chromosome. In our map, genes from all 10 A. thaliana chromosome arms are also tightly linked in A. lyrata. Genes from the regions on the two sides of CEN5 have distant map localizations in A. lyrata (genes on the A. thaliana short-arm genes are on linkage group AL6, and long-arm genes are on AL7), but genes from the other four A. thaliana centromere regions remain closely linked in A. lyrata. The observation of complete linkage between short- and long-arm centromere genes, but not between genes in other genome regions that are separated by similar physical distances, suggests that crossing-over frequencies near the A. lyrata ssp. petraea centromere regions are low, as in A. thaliana. Thus, the centromere positions appear to be conserved between A. thaliana and A. lyrata, even though three centromeres have been lost in A. thaliana, and the core satellite sequences in the two species are very different. We can now definitively identify the three centromeres that were eliminated in the fusions that formed the A. thaliana chromosomes. However, we cannot tell whether genes were lost along with these centromeres, because such genes are absent from the A. thaliana genome, which is the sole source of markers for our mapping.
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| 4. |
- Kawabe, Akira, et al.
(author)
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Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV : Evolutionary history, rearrangements and local recombination rates
- 2006
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In: Genetical Research. - 0016-6723 .- 1469-5073. ; 88:1, s. 45-56
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Journal article (peer-reviewed)abstract
- We have increased the density of genetic markers on the Arabidopsis lyrata chromosomes AL6 and AL7 corresponding to the A. thaliana chromosome IV, in order to determine chromosome rearrangements between these two species, and to compare recombination fractions across the same intervals. We confirm the two rearrangements previously inferred (a reciprocal translocation and a large inversion, which we infer to be pericentric). By including markers around the centromere regions of A. thaliana chromosomes IV and V, we localize the AL6 centromere, and can localize the breakpoints of these chromosome rearrangements more precisely than previously. One translocation breakpoint was close to the centromere, and the other coincided with one end of the inversion, suggesting that a single event caused both rearrangements. At the resolution of our mapping, apart from these rearrangements, all other markers are in the same order in A. lyrata and A. thaliana. We could thus compare recombination rates in the two species. We found slightly higher values in A. thaliana, and a minimum estimate for regions not close to a centromere in A. lyrata is 4-5 centimorgans per megabase. The mapped region of AL7 includes the self-incompatibility loci (S-loci), and this region has been predicted to have lower recombination than elsewhere in the genome. We mapped 17 markers in a region of 1·23 Mb surrounding these loci, and compared the approximately 600 kb closest to the S-loci with the surrounding region of approximately the same size. There were significantly fewer recombination events in the closer than the more distant region, supporting the above prediction, but showing that the low recombination region is very limited in size. © 2006 Cambridge University Press.
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| 5. |
- Qiu, Suo, et al.
(author)
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Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species
- 2011
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 3, s. 868-880
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Journal article (peer-reviewed)abstract
- Population genetic theory predicts that the efficacy of natural selection in a self-fertilizing species should be lower than its outcrossing relatives because of the reduction in the effective population size (N(e)) in the former brought about by inbreeding. However, previous analyses comparing Arabidopsis thaliana (selfer) with A. lyrata (outcrosser) have not found conclusive support for this prediction. In this study, we addressed this issue by examining silent site polymorphisms (synonymous and intronic), which are expected to be informative about changes in N(e). Two comparisons were made: A. thaliana versus A. lyrata and Capsella rubella (selfer) versus C. grandiflora (outcrosser). Extensive polymorphism data sets were obtained by compiling published data from the literature and by sequencing 354 exon loci in C. rubella and 89 additional loci in C. grandiflora. To extract information from the data effectively for studying these questions, we extended two recently developed models in order to investigate detailed selective differences between synonymous codons, mutational biases, and biased gene conversion (BGC), taking into account the effects of recent changes in population size. We found evidence that selection on synonymous codons is significantly weaker in the selfers compared with the outcrossers and that this difference cannot be fully accounted for by mutational biases or BGC.
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