Brandon S. Gaut
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View article: Human‐Mediated Dispersal Routes Structure Sahara Mustard Genomics
Human‐Mediated Dispersal Routes Structure Sahara Mustard Genomics Open
Humans have facilitated the spread and evolution of invasive species, a pattern that has accelerated with the globalisation of trade and societal development. Consequently, the invasiveness of a species may be determined not only by how ma…
View article: From juvenile to adult: investigating miRNAs, gene expression, and the juvenile cone in olive development
From juvenile to adult: investigating miRNAs, gene expression, and the juvenile cone in olive development Open
The long juvenile phase in perennials hinders rapid breeding, highlighting the need for early selection markers. Some species, such as the olive tree ( Olea europaea L.), develop a juvenile cone, where adult tissue forms in the upper and p…
View article: Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales
Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales Open
Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their a…
View article: The genetic basis of chloride exclusion in grapevines
The genetic basis of chloride exclusion in grapevines Open
Mediterranean regions are among the most important areas for global grape production, characterized by dry climates and frequent challenges associated with soil salinity. In these environments, chloride toxicity is a major factor limiting …
View article: Mentorship and acts of kindness
Mentorship and acts of kindness Open
As the inaugural recipient of the Genetics Society of America Mentorship Award, Gaut is being recognized for the mentorship of PhD students and postdocs in his lab and for being a dedicated advocate for mentees as an administrator at Unive…
View article: Quantifying the Evolution of SNPs That Affect RNA Secondary Structure in <i>Arabidopsis thaliana</i> Genes
Quantifying the Evolution of SNPs That Affect RNA Secondary Structure in <i>Arabidopsis thaliana</i> Genes Open
Single-stranded RNA molecules can form intramolecular bonds between nucleotides to create secondary structures. These structures can have phenotypic effects, meaning mutations that alter secondary structure may be subject to natural select…
View article: Mutational load and adaptive variation are shaped by climate and species range dynamics in <i>Vitis arizonica</i>
Mutational load and adaptive variation are shaped by climate and species range dynamics in <i>Vitis arizonica</i> Open
Summary Genetic load can reduce fitness and hinder adaptation. While its genetic underpinnings are well established, the influence of environmental variation on genetic load is less well characterized, as is the relationship between geneti…
View article: Impacts of reproductive systems on grapevine genome and breeding
Impacts of reproductive systems on grapevine genome and breeding Open
Diversified reproductive systems can be observed in the plant kingdom and applied in crop breeding; however, their impacts on crop genomic variation and breeding remain unclear. Grapevine (Vitis vinifera L.), a widely planted fruit tree, u…
View article: Early evidence of avocado domestication from El Gigante Rockshelter, Honduras
Early evidence of avocado domestication from El Gigante Rockshelter, Honduras Open
Molecular research suggests that avocados ( Persea americana Mill.) were domesticated multiple times in the Americas. Seed exchange, hybridization, and cloning have played an essential role across their wild distribution from Mexico to Sou…
View article: Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline
Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline Open
Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specifi c aligners or optimized for specifi c organisms, narrowing their…
View article: The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems
The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems Open
Hemizygous genes, which are 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, these genes can also occur on the autosomes o…
View article: Grapevine pangenome facilitates trait genetics and genomic breeding
Grapevine pangenome facilitates trait genetics and genomic breeding Open
Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemb…
View article: Pangenome analysis uncovers large hidden structural variants underlying fruit color and bacterial wilt resistance in eggplant
Pangenome analysis uncovers large hidden structural variants underlying fruit color and bacterial wilt resistance in eggplant Open
Large structural variants (SVs) underlying important agronomic traits remain largely unexplored in Solanaceae crops. Eggplant (Solanum melongena L.) is a globally important horticultural crop worldwide, belonging to the Solanaceae family. …
View article: Quantifying the evolution of SNPs that affect RNA secondary structure in <i>Arabidopsis thaliana</i> genes
Quantifying the evolution of SNPs that affect RNA secondary structure in <i>Arabidopsis thaliana</i> genes Open
Single-stranded RNA molecules can form intramolecular bonds between nucleotides to create secondary structures. These structures can have phenotypic effects, meaning mutations that alter secondary structure may be subject to natural select…
View article: Patterns of Fitness and Gene Expression Epistasis Generated by Beneficial Mutations in the <i>rho</i> and <i>rpoB</i> Genes of <i>Escherichia coli</i> during High-Temperature Adaptation
Patterns of Fitness and Gene Expression Epistasis Generated by Beneficial Mutations in the <i>rho</i> and <i>rpoB</i> Genes of <i>Escherichia coli</i> during High-Temperature Adaptation Open
Epistasis is caused by genetic interactions among mutations that affect fitness. To characterize properties and potential mechanisms of epistasis, we engineered eight double mutants that combined mutations from the rho and rpoB genes of Es…
View article: Climate, population size, and dispersal influences mutational load across the landscape in<i>Vitis arizonica</i>
Climate, population size, and dispersal influences mutational load across the landscape in<i>Vitis arizonica</i> Open
The interplay between genetics and the environment determines a population’s ability to survive. Plants, being immobile, are particularly vulnerable to environmental shifts and must adapt to their local environment or face extinction. Whil…
View article: The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems
The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems Open
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/ins…
View article: <i>Sphingomonas</i> clade and functional distribution with simulated climate change
<i>Sphingomonas</i> clade and functional distribution with simulated climate change Open
Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response o…
View article: Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution
Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution Open
We are launching a series to celebrate the 40th anniversary of the first issue of Molecular Biology and Evolution. In 2024, we will publish virtual issues containing selected papers published in the Society for Molecular Biology and Evolut…
View article: Modeling transposable elements dynamics during polyploidization in plants
Modeling transposable elements dynamics during polyploidization in plants Open
In this work we study the proliferation of transposable elements (TEs) and the epigenetic response of plants during the process of polyploidization. Through a deterministic model, expanding on our previous work on TE proliferation under ep…
View article: Reply to Blanco-Pastor: Introgression and heterozygosity complicated grapevine domestication
Reply to Blanco-Pastor: Introgression and heterozygosity complicated grapevine domestication Open
Micro-nano plastics originating from the prevalent usage of plastics have raised increasingly alarming concerns worldwide. However, there remains a fundamental knowledge gap in nanoplastics because of the lack of effective analytical ...Pl…
View article: miRNA-like secondary structures in maize ( <i>Zea mays</i> ) genes and transposable elements correlate with small RNAs, methylation, and expression
miRNA-like secondary structures in maize ( <i>Zea mays</i> ) genes and transposable elements correlate with small RNAs, methylation, and expression Open
RNA molecules carry information in their primary sequence and also their secondary structure. Secondary structure can confer important functional information, but it is also a signal for an RNAi-like host epigenetic response mediated by sm…
View article: Sampling effect in predicting the evolutionary response of populations to climate change
Sampling effect in predicting the evolutionary response of populations to climate change Open
Genomic data and machine learning approaches have gained interest due to their potential to identify adaptive genetic variation across populations and to assess species vulnerability to climate change. By identifying gene–environment assoc…
View article: A super-pangenome of the North American wild grape species
A super-pangenome of the North American wild grape species Open
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. Gen…
View article: Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history
Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history Open
‘ Candidatus Liberibacter’ is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific…
View article: Adaptive and maladaptive introgression in grapevine domestication
Adaptive and maladaptive introgression in grapevine domestication Open
Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these…
View article: Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate
Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate Open
Xylella fastidiosa is a bacterium that infects crops like grapevines, coffee, almonds, citrus and olives. There is little understanding of the genes that contribute to plant resistance, the genomic architecture of resistance, and the poten…
View article: Phenotypic and Genotypic Adaptation of <i>Escherichia coli</i> to Thermal Stress is Contingent on Genetic Background
Phenotypic and Genotypic Adaptation of <i>Escherichia coli</i> to Thermal Stress is Contingent on Genetic Background Open
Evolution can be contingent on history, but we do not yet have a clear understanding of the processes and dynamics that govern contingency. Here, we performed the second phase of a two-phase evolution experiment to investigate features of …