Biology subjects

Gaut, B.

Publications and source records attributed to Gaut, B..

5 recordsLinked to original sources

bioRxiv2024

The genomic and epigenomic dynamics of hemizygous genes across crops with contrasting mating systems

Hemizygous genes, which present on only one of the two homologous chromosomes of diploid organisms, have been mainly studied in the context of sex chromosomes and sex-linked genes. However, structural variants (SVs), such as a deletion/insertion of one allele, can lead to hemizygous genes, a phenomenon largely unexplored in plants. Here, we investigated the genomic and epigenomic landscapes of hemizygous genes across 22 genomes with varying propagation histories: eleven clonal lineages, seven outcrossed samples and four inbred and putatively homozygous genomes. We identified SVs leading to genic hemizygosity. As expected, very few genes (0.01%-1.2%) were hemizygous in the homozygous genomes, representing negative controls. Hemizygosity was appreciable among outcrossed lineages, averaging 8.7% of genes, but consistently elevated for the clonal samples at 13.8% genes, likely reflecting heterozygous SVs accumulation during clonal propagation. Compared to diploid genes, hemizygous genes were more often situated in centromeric than telomeric regions and underlying weaker purifying selection. They also had reduced levels of expression, averaging [~]20% of the expression levels of diploid genes, violating the evolutionary model of dosage compensation. We also detected higher DNA methylation levels, in hemizygous genes and transposable elements, which may contribute to the reduced expression of hemizygous genes. Finally, expression profiles showed that hemizygous genes were more specifically expressed in contexts related to fruit development, organ differentiation and stress responses. Overall, hemizygous genes accumulate in clonally propagated lineages and display distinct genetic, and epigenetic features compared to diploid genes, shedding new insights on genetic studies and breeding programs of clonal crops.

plant biology↗

bioRxiv2023

A reference-unbiased super-pangenome of the North American wild grape species (Vitis spp.) reveals genus-wide association with adaptive traits

Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which were phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierces disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short-reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.

genomics↗

bioRxiv2020

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. 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 estimated the site-frequency spectrum of allelic states (epialleles). Using a population genetics model specifically designed for epigenetic data, we found that genes with ancestral gene body methylation are under significant selection to remain methylated. Conversely, all genes taken together were inferred to be under selection to be unmethylated. The estimated selection coefficients were small, similar to the magnitude of selection acting on codon usage. We also estimated that A. thaliana is losing gene body methylation three-fold 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 gene body methylation through its link with gene expression level. 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.

genetics↗

bioRxiv2019

The genomic diversification of clonally propagated grapevines

Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better understand the consequences of clonal propagation 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.\n\nThough 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 genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and the increased likelihood of methylated cytosines to 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.\n\nThese data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clonal propagation is associated with the accumulation of putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions such that mutations are less frequent in coding than noncoding regions of the genome.

genomics↗

bioRxiv2016

Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects on Escherichia coli gene expression

Modifications to transcriptional regulators play a major role in adaptation. Here we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase {beta} subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adaptive mutations in numerous E. coli evolution experiments but particularly in our previous large-scale thermal stress experiment, where the two genes characterized two alternative adaptive pathways. To compare the effects of beneficial mutations, we engineered four advantageous mutations into each of the two genes and measured their effects on fitness, growth, gene expression and transcriptional termination at 42.2{degrees}C. Among the eight mutations, two rho mutations had no detectable effect on relative fitness, suggesting they were beneficial only in the context of epistatic interactions. The remaining six mutations had an average relative fitness benefit of [~]20%. The rpoB mutations altered the expression of [~]1700 genes; rho mutations altered the expression of fewer genes, most of which were a subset of the genes altered by rpoB. Across our eight mutants, relative fitness correlated with the degree to which a mutation restored gene expression back to the unstressed, 37.0{degrees}C state. The rho mutations do not enhance transcriptional termination in known rho-terminated regions, but the genome-wide effects of mutations in both genes was to enhance termination. Although beneficial mutations in the two genes did not have identical effects on fitness, growth or gene expression, they acted predominantly through parallel phenotypic effects on gene expression and transcriptional termination.

evolutionary biology↗