Recombination: an underappreciated factor in the evolution of plant genomes

Gaut, Brandon S.; Wright, Stephen I.; Rizzon, Carène; Dvořák, Jan; Anderson, Lorinda K.

doi:10.1038/nrg1970

Cited by 224 publications

(223 citation statements)

References 80 publications

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“…In contrast, a negative correlation between GR and gene density was detected in the euchromatic regions of Arabidopsis (Wright et al 2003). Why these genomes differ in this respect remains to be investigated (Gaut et al 2007). To date, the genome-wide estimates of GR rates have been derived for only two plant (Arabidopsis and rice) genomes by the comparison of genomic sequences and genetic maps (Zhang and Gaut 2003;Rizzon et al 2006).…”

Section: Discussionmentioning

confidence: 99%

“…Although the molecular mechanisms for the amplification and elimination of LTR-RTs are shared by plant genomes, the forces that regulate these mechanisms remain poorly understood. Both population-genetic and comparative approaches are needed to unravel these puzzles (Gaut et al 2007;Gaut and Ross-Ibarra 2008).…”

Section: Initial Frequencies Of Dna Loss By Ur and Irmentioning

confidence: 99%

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Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Tian

Rizzon²,

Du³

et al. 2009

Genome Res.

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In flowering plants, the accumulation of small deletions through unequal homologous recombination (UR) and illegitimate recombination (IR) is proposed to be the major process counteracting genome expansion, which is caused primarily by the periodic amplification of long terminal repeat retrotransposons (LTR-RTs). However, the full suite of evolutionary forces that govern the gain or loss of transposable elements (TEs) and their distribution within a genome remains unclear. Here, we investigated the distribution and structural variation of LTR-RTs in relation to the rates of local genetic recombination (GR) and gene densities in the rice (Oryza sativa) genome. Our data revealed a positive correlation between GR rates and gene densities and negative correlations between LTR-RT densities and both GR and gene densities. The data also indicate a tendency for LTR-RT elements and fragments to be shorter in regions with higher GR rates; the size reduction of LTR-RTs appears to be achieved primarily through solo LTR formation by UR. Comparison of indica and japonica rice revealed patterns and frequencies of LTR-RT gain and loss within different evolutionary timeframes. Different LTR-RT families exhibited variable distribution patterns and structural changes, but overall LTR-RT compositions and genes were organized according to the GR gradients of the genome. Further investigation of non-LTR-RTs and DNA transposons revealed a negative correlation between gene densities and the abundance of DNA transposons and a weak correlation between GR rates and the abundance of long interspersed nuclear elements (LINEs)/short interspersed nuclear elements (SINEs). Together, these observations suggest that GR and gene density play important roles in shaping the dynamic structure of the rice genome.

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Section: Discussionmentioning

confidence: 99%

Section: Initial Frequencies Of Dna Loss By Ur and Irmentioning

confidence: 99%

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Tian

Rizzon²,

Du³

et al. 2009

Genome Res.

Self Cite

146

176

View full text Add to dashboard Cite

show abstract

“…The extent and positions of crossovers is well-known in many plant species, but the frequency of gene conversion is mostly unknown in crops (Gaut et al, 2007). Recombination events in plants have been mapped using genetic markers.…”

Section: Durstewitz Et Al Identified 604 Snps Using 100 Est-based Ammentioning

confidence: 99%

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

et al. 2015

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SummaryThe growth of next generation DNA sequencing technologies has led to a rapid increase in sequence based genotyping, for applications including diversity assessment, genome structure validation and gene-trait association. With the reducing cost of sequence data generation and the increasing availability of reference genomes, there are opportunities to develop high density genotyping methods based on whole genome re-sequencing. We have established a skim-

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“…Recombination is a major mechanism underlying genetic diversity (Korol et al 1994;Gaut et al 2007;Wicker et al 2007;Morrell et al 2006). Tracking recombination events can illuminate the evolution of genes and genomes.…”

Section: Introductionmentioning

confidence: 99%

Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

et al. 2010

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INTRODUCTION: Recombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbors rich genetic resources for disease resistance. Lr10 is a leaf rust resistance gene encoding three domains: a coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NBS-LRR). RESULTS: Lr10 was sequenced from 58 accessions representing 12 diverse habitats in Israel. Diversity analysis revealed a high rate of synonymous and non-synonymous substitutions (d (S) = 0.029, d (N) = 0.018, respectively) in the NBS-LRR domains. Moreover, in contrast to other resistance genes, in Lr10 the CC domain was more diverse than the NBS-LRR domains (d (S) = 0.069 vs. 0.029, d (N) = 0.094 vs. 0.018) and was subjected to positive selection in some of the populations. Seventeen recombination events were detected between haplotypes, especially in the CC domain. Linkage disequilibrium (LD) analysis has shown a rapid decay from r (2) = 0.5 to r (2) = 0.1 within a 2-kb span. CONCLUSION: These results suggest that recombination is a diversifying force for the R-gene, Lr10, in the selfing species T. dicoccoides. This is the first report of a short-range LD decay in wild emmer wheat. AbstractRecombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbours rich genetic resources for disease resistance. Moreover, in contrast to other resistance genes, in Lr10 the CC domain was more diverse than the NBS-LRR domains ( d S = 0.069 vs. 0.029, d N =0.094 vs. 0.018) and was subjected to positive selection in some of the populations. Seventeen recombination events were detected between haplotypes, especially in the CC domain. Linkage disequilibrium (LD) analysis has shown a rapid decay from r 2 =0.5 to r 2 =0.1 within a 2 kb span. These results suggest that recombination is a diversifying force of the R-gene, Lr10, in the selfing species T. dicoccoides. This is the first report of a short range LD decay in wild emmer wheat.

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Recombination: an underappreciated factor in the evolution of plant genomes

Cited by 224 publications

References 80 publications

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

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