Biology subjects

Gaut, B. S.

Publications and source records attributed to Gaut, B. S..

24 records · Page 2Linked to original sources

bioRxiv2019

Gene capture by transposable elements leads to epigenetic conflict

Plant transposable elements (TEs) regularly capture fragments of genes. When the host silences these TEs, siRNAs homologous to the captured regions may also target the genes. This epigenetic cross-talk establishes an intragenomic conflict: silencing the TEs has the cost of silencing the genes. If genes are important, however, natural selection may maintain function by moderating the silencing response, which may also advantage the TEs. Here, we examined this model by focusing on three TE families in maize: Helitrons, Pack-MULEs and Sirevirus LTR retrotransposons. We documented 1,263 TEs containing exon fragments from 1,629 donor genes. Consistent with epigenetic conflict, donor genes mapped more siRNAs and were more methylated than genes with no evidence of capture. However, these patterns differed between syntelog vs. translocated donor genes. Syntelogs appeared to maintain function, as measured by gene expression, consistent with moderation of silencing for functionally important genes. Epigenetic marks did not spread beyond their captured regions and 24nt cross-talk siRNAs were linked with CHH methylation. Translocated genes, in contrast, bore the signature of silencing by being highly methylated and less expressed. They were also overrepresented among donor genes, suggesting a link between capture and gene movement. The evidence for an advantage to TEs was less obvious. TEs with captured fragments were older, mapped fewer siRNAs and were slightly less methylated than TEs without captured fragments but showed no evidence of increased copy numbers. Altogether, our results demonstrate that TE capture triggers an epigenetic conflict for important genes, but it may lead to pseudogenization for less constrained genes.

genomics↗

bioRxiv2019

Phylogenetic shifts in gene body methylation correlate with gene expression and reflect trait conservation

A subset of genes in plant genomes are labeled with DNA methylation specifically at CG residues. These genes, known as gene-body methylated (gbM), have a number of associated characteristics. They tend to have longer sequences, to be enriched for intermediate expression levels, and to be associated with slower rates of molecular evolution. Most importantly, gbM genes tend to maintain their level of DNA methylation between species, suggesting that this trait is under evolutionary constraint. Given the degree of conservation in gbM, we still know surprisingly little about its function in plant genomes or whether gbM is itself a target of selection. To address these questions, we surveyed DNA methylation across eight grass (Poaceae) species that span a gradient of genome sizes. We first established that genome size correlates with genome-wide DNA methylation levels, but less so for genic levels. We then leveraged genomic data to identify a set of 2,982 putative orthologs among the eight species and examined shifts of methylation status for each ortholog in a phylogenetic context. A total of 55% of orthologs exhibited a shift in gbM, but these shifts occurred predominantly on terminal branches, indicating that shifts in gbM are rarely conveyed over time. Finally, we found that the degree of conservation of gbM across species is associated with increased gene length, reduced rates of molecular evolution, and increased gene expression level, but reduced gene expression variation across species. Overall, these observations suggest a basis for evolutionary pressure to maintain gbM status over evolutionary time.

evolutionary biology↗

bioRxiv2019

The Genomics of Selfing in Maize (Zea mays ssp. mays): Catching Purging in the Act

In plants, self-fertilization is both an important reproductive strategy and a valuable genetic tool. In theory, selfing increases homozygosity at a rate of 0.50 per generation. Increased homozygosity can uncover recessive deleterious variants and lead to inbreeding depression, unless it is countered by the loss of these variants by genetic purging. Here we investigated the dynamics of purging on genomic scale by testing three predictions. The first was that heterozygous, putatively deleterious SNPs were preferentially lost from the genome during continued selfing. The second was that the loss of deleterious SNPs varied as a function of recombination rate, because recombination increases the efficacy of selection by uncoupling linked variants. Finally, we predicted that genome size (GS) decreases during selfing, due to the purging of deleterious transposable element (TE) insertions. We tested these three predictions by following GS and SNP variants in a series of selfed maize (Zea mays ssp. mays) lines over six generations. In these lines, putatively deleterious alleles were purged, and purging was more pronounced in highly recombining regions. Homozygosity increased more slowly than expected; instead of increasing by 50% each generation, it increased by 35% to 40%. Finally, three lines showed dramatic decreases in GS, losing an average of 398 Mb from their genomes over the short timeframe of our experiment. TEs were the principal component of loss, and GS loss was more likely for lineages that began with more TE and more chromosomal knob repeats. Overall, this study documented remarkable GS loss - as much DNA as three Arabidopsis thaliana genomes, on average - in only a few generations of selfing.

genomics↗

bioRxiv2018

Structural variants, clonal propagation, and genome evolution in grapevine (Vitis vinifera)

Little is known about the type and numbers of structural variants (SVs) in plant genomes, the evolutionary processes that shape SV variation, or their effects on phenotypes. Here we assembled the 605Mb genome of the Chardonnay grape (Vitis vinifera ssp. sativa), which we use to catalog SVs within and between genomes and also across 69 cultivars and wild accessions. SVs underlie widespread hemizygosity of protein coding genes within Chardonnay and genic presence-absence variation between cultivars. Negative selection acts against all SV types, but they also accrue as heterozygous, recessive mutations in clonally propagated grapevines. SV hotspots in the sex determination region and the berry color locus illustrate their impact on phenotype and the role of SVs as drivers of convergent phenotypic evolution.

evolutionary biology↗

bioRxiv2017

Was maize domesticated in the Balsas Basin? Complex patterns of genetic divergence, gene flow and ancestral introgressions among Zea subspecies suggest an alternative scenario

The study of maize domestication has overlooked the genetic structure within maizes wild relative teosinte. Prior to investigating the domestication history of maize (Zea mays subspecies mays), one should first understand the population history of teosintes and how they relate to maize. To achieve this, we used 32,739 SNPs obtained from a broad sampling of teosinte populations and 46 maize landraces and a) inferred current and past gene flow among teosinte populations and maize, b) analyzed the degree of introgression among Zea mays subspecies, and c) explored the putative domestication location of maize. We found geographic structure and introgression between Zea mays taxa. Teosinte subspecies have diverged significantly from maize, which indicates that current teosinte populations have evolved mainly independently from maize since the domestication. Our results further suggest that the likely ancestor of maize may maybe have come from Jalisco or the Pacific coast.\n\nOne Sentence SummaryShared polymorphism in teosinte suggests a Jalisco origin of maize domestication.

evolutionary biology↗

bioRxiv2017

The Evolutionary Genomics of Grape (Vitis vinifera ssp. vinifera) Domestication

We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ~22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne) thereafter. The long decline may reflect low intensity management by humans prior to domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development and stress responses. In contrast, candidate selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.\n\nSignificance StatementWe generated genomic data to estimate the population history of grapes, the most economically important horticultural crop in the world. Domesticated grapes experienced a protracted, 22,000 year population decline prior to domestication; we hypothesize that this decline reflects low intensity cultivation by humans prior to domestication. Domestication altered the mating system of grapes. The sex determination region is detectable as a region of heightened genetic divergence between wild and cultivated accessions. Based on gene expression analyses, we propose new candidate genes that alter sex determination. Finally, grapes contain more deleterious mutations in heterozygous states than their wild ancestors. The accumulation of deleterious mutations is due in part to clonal propagation, which shelters deleterious, recessive mutations.

evolutionary biology↗