57 research outputs found
On the genetics and genomics of Arabidopsis thaliana and its relatives
Plant genomes are sculpted by the combined influences of mutation, selection, and genetic drift. As a result of these processes, genome size, as well as the overall architecture of genomes, is constantly fluctuating. A species’ genomic architecture can impact what types of genetic variants give rise to phenotypic variation, including variation in hybridization efficiency which can lead to the formation of genetic barriers. The genomic, phenotypic, and reproductive consequences of genome evolution in Arabidopsis thaliana and its relatives were examined and three major findings are discussed.
1. Transposable elements (TEs) are a major source of variation in genome architecture and their fast, often lineage-specific, evolution can swiftly alter a species’ epigenetic landscape as a result of their tightly linked epigenetic marks, including DNA methylation. As a result of this rapid evolution, any TE-induced phenotypic consequences are not maintained for long periods of time.
2. The contribution of genetic drift and selection to generating or maintaining the genetic variants underlying hybrid phenotypes was evaluated in a large collection of first generation hybrids. Mutation-selection balance is not sufficient to explain the detected loci, and either genetic bottlenecks or adaptive processes are also contributing to the variants underlying hybrid phenotypes.
3. The species-wide frequency of intraspecific genetic barriers that arise as a byproduct of genome evolution was characterized in Arabidopsis thaliana. A molecular signature of hybrid dysfunction, segregation distortion, was surveyed in a large set of genetically diverse F¬2 populations and distorted loci were uncovered in 12-24% of populations, indicating that a number of genetic barriers are segregating in this species
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A Dominance Hypothesis Argument for Historical Genetic Gains and the Fixation of Heterosis in Octoploid Strawberry.
Heterosis was the catalyst for the domestication of cultivated strawberry (Fragaria Ă— ananassa), an interspecific hybrid species that originated in the 1700s. The hybrid origin was discovered because the phenotypes of spontaneous hybrids transgressed those of their parent species. The transgressions included fruit yield increases and other genetic gains in the twentieth century that sparked the global expansion of strawberry production. The importance of heterosis to the agricultural success of the hybrid species, however, has remained a mystery. Here we show that heterosis has disappeared (become fixed) among improved hybrids within a population (the California population) that has been under long-term selection for increased fruit yield, weight, and firmness. We found that the highest yielding hybrids are among the most highly inbred (59-79%), which seems counterintuitive for a highly heterozygous, outbreeder carrying heavy genetic loads. Although faint remnants of heterosis were discovered, the between-parent allele frequency differences and dispersed favorable dominant alleles necessary for heterosis have decreased nearly genome-wide within the California population. Conversely, heterosis was prevalent and significant among wide hybrids, especially for fruit count, a significant driver of genetic gains for fruit yield. We attributed the disappearance (fixation) of heterosis within the California population to increased homozygosity of favorable dominant alleles and inbreeding associated with selection, random genetic drift, and selective sweeps. Despite historical inbreeding, the highest yielding hybrids reported to-date are estimated to be heterozygous for 20,370-44,280 of 97,000-108,000 genes in the octoploid genome, the equivalent of an entire diploid genome or more
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The genomic diversification of grapevine clones.
BACKGROUND:Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03. RESULTS:Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones. CONCLUSIONS:These data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome
The Evolutionary Dynamics of Orthologs That Shift in Gene Body Methylation between Arabidopsis Species
Aly_class_all.out
Ath/Aly/Cgr_metL.out<br>Methylation levels in the three species in gene bodies (from start to stop codons)<br>1st col: gene ID<br>2nd col: CG methylation levels<br>3rd: col: CHG<br>4th col: CHH<br><br>Ath/Aly/Cgr_class.out<br>gbM levels are categorized into three: BM, IM and UM.<br>Please see Takuno and Gaut (2012) MBE; Takuno and Gaut (2013) PNAS<br>Takuno et al. (2017) MBE.<br><br>1st col: gene ID<br>2nd col: CG<br><br>3rd: col: CHG<br>4th col: CHH<br><br>AthAlyCgra1.out<br>The three-way ortholog
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Gene body methylation is under selection in Arabidopsis thaliana.
In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation (gbM). It has been controversial whether this phenomenon has any functional role. Here, we took advantage of the availability of 876 leaf methylomes in Arabidopsis thaliana to characterize the population frequency of methylation at the gene level and to estimate the site-frequency spectrum of allelic states. Using a population genetics model specifically designed for epigenetic data, we found that genes with ancestral gbM are under significant selection to remain methylated. Conversely, ancestrally unmethylated genes were under selection to remain unmethylated. Repeating the analyses at the level of individual cytosines confirmed these results. Estimated selection coefficients were small, on the order of 4 Nes = 1.4, which is similar to the magnitude of selection acting on codon usage. We also estimated that A. thaliana is losing gbM threefold more rapidly than gaining it, which could be due to a recent reduction in the efficacy of selection after a switch to selfing. Finally, we investigated the potential function of gbM through its link with gene expression. Across genes with polymorphic methylation states, the expression of gene body methylated alleles was consistently and significantly higher than unmethylated alleles. Although it is difficult to disentangle genetic from epigenetic effects, our work suggests that gbM has a small but measurable effect on fitness, perhaps due to its association to a phenotype-like gene expression
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