Biology subjects

VanBuren, R.

Publications and source records attributed to VanBuren, R..

30 records · Page 2Linked to original sources

bioRxiv2021

NDR1 and the Arabidopsis Plasma Membrane ATPase AHA5 are Required for Processes that Converge on Drought Tolerance and Immunity

NON-RACE-SPECIFIC DISEASE RISISTANCE1 (NDR1) is a key component of plant immune signaling, required for defense against the bacterial pathogen Pseudomonas syringae. Plant stress responses have overlapping molecular, physiological, and cell biology signatures, and given the central role of NDR1 during biotic stress perception and signaling, we hypothesized that NDR1 also functions in abiotic stress responses, including in a role that mediates signaling at the plasma membrane (PM) - cell wall (CW) continuum. Here, we demonstrate that NDR1 is required for the induction of drought stress responses in plants, a role that couples stress signaling in an abscisic acid-dependent manner. We show that NDR1 physically associates with the PM-localized H+-ATPases AHA1, AHA2, and AHA5 and is required for proper regulation of H+-ATPase activity and stomatal guard cell dynamics, providing a mechanistic function of NDR1 during drought responses. In the current study, we demonstrate that NDR1 functions in signaling processes associated with both biotic and abiotic stress response pathways, a function we hypothesize represents NDR1s role in the maintenance of cellular homeostasis during stress. We propose a role for NDR1 as a core transducer of signaling between cell membrane processes and intercellular stress response activation.

plant biology↗

bioRxiv2021

Lessons from 20 years of plant genome sequencing: an unprecedented resource in need of more diverse representation

The field of plant genomics has grown rapidly in the past 20 years, leading to dramatic increases in both the quantity and quality of publicly available genomic resources. With this ever-expanding wealth of genomic data from an increasingly diverse set of taxa, unprecedented potential exists to better understand the genome biology and evolution of plants. Here, we provide a contemporary view of plant genomics, including analyses on the quality of existing plant genome assemblies, the taxonomic distribution of sequenced species, and how national participation has influenced the fields development. We show that genome quality has increased dramatically in recent years, that substantial taxonomic gaps exist, and that the field has been dominated by affluent nations in the Global North and China, despite a wide geographic distribution of sequenced species. We identify multiple disconnects between the native range of focal species and the national affiliation of the researchers studying the plants, which we argue are rooted in colonialism--both past and present. However, falling sequencing costs paired with widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps, and, most importantly, empower a more global plant genomics community.

plant biology↗

bioRxiv2021

Diversification, Spread, and Admixture of Octoploid Strawberry in the Western Hemisphere

Premise of the studyOctoploid strawberry (Fragaria sp.) has a complex evolutionary history that has until recently been intractable due to limitations of available genomic resources. While recent work has further uncovered the evolutionary history of the octoploid strawberry, there are still open questions. Much is still unknown about the evolutionary relationship of the wild octoploid species, Fragaria virginiana and Fragaria chiloensis, and gene flow within and among species after the original formation of the octoploid genome. MethodsWe leveraged a diversity collection of wild octoploid eco-types of strawberry representing the recognized subspecies and ranging from Alaska to Southern Chile, and a high density SNP array to investigate wild octoploid strawberry evolution. Evolutionary relationships are interrogated with phylogenetic analysis and genetic clustering algorithms. Additionally, admixture among and within species is assessed with model-based and tree-based approaches. Key ResultsPhylogenetic analysis revealed that the two octoploid strawberry species are monophyletic sister lineages. The genetic clustering results show substructure between North Americana and South American F. chiloensis populations. Additionally, model-based and tree-based methods support gene flow within and among the two octoploid species, including newly identified admixture in the Hawaiian F. chiloensis subsp. sandwicensis population that appears to be from an ancestral F. chiloensis population. ConclusionF. virginiana and F. chiloensis are supported as monophyletic and sister lineages. All but one of the subspecies recognized within both octoploid species show extensive paraphyly. Furthermore, the phylogenetic relationship among F. chiloensis populations supports a single population range expansion southward from North America. The inter- and intraspecific relationships of octoploid strawberry are complex and suggest substantial and deep gene flow between sympatric populations among and within species.

evolutionary biology↗

bioRxiv2020

The Contributions of the Allopolyploid Parents of the Mesopolyploid Brassiceae are Evolutionarily Distinct but Functionally Compatible

The members of the tribe Brassiceae share a whole genome triplication (WGT), and one proposed model for its formation is a "two-step" pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using POInT (the Polyploidy Orthology Inference Tool). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring prior to the arrival of the third. We also, for the 90,000 individual genes in our study, make parental "subgenome" assignments, inferring, with measured uncertainty, which of the progenitor genomes of the allohexaploidy each gene derives from. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, where subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.

genomics↗

bioRxiv2020

Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves

Premise of studyLeaf morphology is dynamic, continuously deforming during leaf expansion and among leaves within a shoot. We measured leaf morphology from over 200 vines over four years, and modeled changes in leaf shape along the shoot to determine if a composite "shape of shapes" can better capture variation and predict species identity compared to individual leaves. MethodsUsing homologous universal landmarks found in grapevine leaves, we modeled various morphological features as a polynomial function of leaf node. The resulting functions are used to reconstruct modeled leaf shapes across shoots, generating composite leaves that comprehensively capture the spectrum of possible leaf morphologies. ResultsWe found that composite leaves are better predictors of species identity than individual leaves from the same plant. We were able to use composite leaves to predict species identity of previously unassigned vines, which were verified with genotyping. DiscussionObservations of individual leaf shape fail to capture the true diversity between species. Composite leaf shape--an assemblage of modeled leaf snapshots across the shoot--is a better representation of the dynamic and essential shapes of leaves, as well as serving as a better predictor of species identity than individual leaves.

plant biology↗

bioRxiv2020

Vein-to-blade ratio is an allometric indicator of climate-induced changes in grapevine leaf size and shape

PremiseAs a leaf expands, its shape dynamically changes. Previously, we documented an allometric relationship between vein and blade area in grapevine leaves. Larger leaves have a smaller ratio of primary and secondary vein area relative to blade area compared to smaller leaves. We sought to use allometry as an indicator of leaf size to measure the environmental effects of climate on grapevine leaf morphology. MethodsWe measure the ratio of vein-to-blade area in 8,412 leaves from the same 208 vines across four growing seasons (2013, 2015, 2016, and 2017) using 21 homologous landmarks. Matching leaves by vine and node, we correlate size and shape of grapevine leaves with climate variables. Key resultsVein-to-blade ratio varies strongly between years in ways that blade or vein area do not. Maximum daily temperature and to a lesser degree precipitation are the most strongly correlated climate variables with vein-to-blade ratio, indicating that smaller leaves are associated with heat waves and drought. Leaf count and overall leaf area of shoots and the vineyard population studied also diminish with heat and drought. Grapevine leaf primordia initiate in buds the year prior to when they emerge, and we find that climate during the previous growing season exerts the largest statistical effects over these relationships. ConclusionsOur results demonstrate the profound effects of heat and drought on the vegetative morphology of grapevines and show that vein-to-blade ratio is a strong allometric indicator of the effects of climate on grapevine leaf morphology.

plant biology↗

bioRxiv2019

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploidBrassica napus

Interspecific hybridization and allopolyploidization merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is "dominant" over the other subgenome, having a greater number of reatined duplicate genes and being more highly expressed. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we "replayed the evolutionary tape" with six isogenic resynthesized Brassica napus (rapeseed) allopolyploid lines and investigated subgenome dominance patterns over the first ten generations. We found that the same subgenome was consistently more dominantly expressed in all lines and generations. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the Brassica oleracea derived C subgenome in all lines and generations. These differences in gene expression and methylation were also found when comparing the progenitor genomes, suggesting subgenome dominance is related to inherited parental genome differences rather than a byproduct of allopolyploidization. Gene network analyses indicated an enrichment for network interactions and several biological functions for C subgenome biased pairs, but no enrichment was observed for A subgenome biased pairs. These findings demonstrate that "replaying the evolutionary tape" in allopolyploids results in repeatable and predictable subgenome expression dominance patterns based on preexisting genetic differences among the parental species. These findings have major implications regarding the genotypic and phenotypic diversity observed following plant hybridization in both ecological and agricultural contexts.

evolutionary biology↗

bioRxiv2019

Intertwined signatures of desiccation and drought tolerance in grasses

Grasses are among the most resilient plants and some can survive prolonged desiccation in semi-arid regions with seasonal rainfall. This vegetative desiccation tolerance has arisen independently multiple times within the grass family, but the genetic elements that differentiate desiccation tolerant and sensitive grasses are largely unknown. Here we leveraged comparative genomic approaches with the resurrection grass Eragrostis nindensis and the closely related desiccation sensitive cereal Eragrostis tef to identify changes underlying desiccation tolerance. We extended the analyses to include the grasses maize, sorghum, rice, and the model desiccation tolerant grass Oropetium thomaeum to identify broader evolutionary conservation and divergence. We identified changes in chromatin architecture and expression dynamics related to desiccation in E. nindensis. It was previously hypothesized that transcriptional re-wiring of seed desiccation pathways confers vegetative desiccation tolerance. We demonstrate that the majority of seed dehydration related genes show similar expression patterns in leaves of desiccation tolerant and sensitive species during dehydration. However, we discovered a small set of orthologs with expression specific to leaves of desiccation tolerant species, and seeds of sensitive species. This supports a nuanced role of seed-related genes where many overlap with typical drought responses but some crucial genes are desiccation specific in resurrection plants.

plant biology↗

bioRxiv2019

Transcriptome-based prediction of complex traits in maize

The ability to predict traits from genome-wide sequence information (Genomic Prediction, GP), has improved our understanding of the genetic basis of complex traits and transformed breeding practices. Transcriptome data may also be useful for GP. However, it remains unclear how well transcript levels can predict traits, particularly when traits are scored at different development stages. Using maize genetic markers and transcript levels from seedlings to predict mature plant traits, we found transcript and genetic marker models have similar performance. Surprisingly, genetic markers important for predictions were not close to or identified as regulatory variants for important transcripts. Thus, transcript levels are predictive not simply due to genetic variation. Furthermore, genetic marker models identified only one of 14 benchmark flowering time genes, while transcript models identified five. Our findings highlight that transcriptome data is useful for GP and can provide a link between traits and variation that cannot be readily captured at the sequence level.

genetics↗

bioRxiv2019

Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia

Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Despite its overall importance to small-scale farmers and communities in Africa, teff suffers from low production compared to other cereals because of limited intensive selection and molecular breeding. Here we report a chromosome-scale genome assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintained as syntenic gene pairs. Through analyzing the history of transposable element activity, we estimate the teff polyploidy event occurred [~]1.1 million years ago (mya) and the two subgenomes diverged [~]5.0 mya. Despite this divergence, we detected no large-scale structural rearrangements, homoeologous exchanges, or bias gene loss, contrasting most other allopolyploid plant systems. The exceptional subgenome stability observed in teff may enable the ubiquitous and recurrent polyploidy within Chloridoideae, possibly contributing to the increased resilience and diversification of these grasses. The two teff subgenomes have partitioned their ancestral functions based on divergent expression patterns among homoeologous gene pairs across a diverse expression atlas. The most striking differences in homoeolog expression bias are observed during seed development and under abiotic stress, and thus may be related to agronomic traits. Together these genomic resources will be useful for accelerating breeding efforts of this underutilized grain crop and for acquiring fundamental insights into polyploid genome evolution.

plant biology↗

bioRxiv2018

A Draft Genome and High-Density Genetic Mapof European Hazelnut (Corylus avellana L.)

European hazelnut (Corylus avellana L.) is of global agricultural and economic significance, with genetic diversity existing in hundreds of accessions. Breeding efforts have focused on maximizing nut yield and quality and reducing susceptibility to diseases such as Eastern filbert blight (EFB). Here we present the first sequenced genome among the order Fagales, the EFB-resistant diploid hazelnut accession Jefferson (OSU 703.007). We assembled the highly heterozygous hazelnut genome using an Illumina only approach and the final assembly has a scaffold N50 of 21.5kb. We captured approximately 91 percent (345 Mb) of the flow-cytometry-determined genome size and identified 34,910 putative gene loci. In addition, we identified over 2 million polymorphisms across seven diverse hazelnut accessions and characterized t heir effect on coding sequences. We produced t wo high-density genetic maps with 3,209 markers from an F1 hazelnut population, representing a five-fold increase in marker density over previous maps. These genomic resources will aide in the discovery of molecular markers linked to genes of interest for hazelnut breeding efforts, and are available to the community at https://www.cavellanagenomeportal.com/.

genomics↗

bioRxiv2018

A chromosome scale assembly of the model desiccation tolerant grass Oropetium thomaeum

Oropetium thomaeum is an emerging model for desiccation tolerance and genome size evolution in grasses. A high-quality draft genome of Oropetium was recently sequenced, but the lack of a chromosome scale assembly has hindered comparative analyses and downstream functional genomics. Here, we reassembled Oropetium, and anchored the genome into ten chromosomes using Hi-C based chromatin interactions. A combination of high-resolution RNAseq data and homology-based gene prediction identified thousands of new, conserved gene models that were absent from the V1 assembly. This includes thousands of new genes with high expression across a desiccation timecourse. The sorghum and Oropetium genomes have a surprising degree of chromosome-level collinearity, and several chromosome pairs have near perfect synteny. Other chromosomes are collinear in the gene rich chromosome arms but have experienced pericentric translocations. Together, these resources will be useful for the grass comparative genomic community and further establish Oropetium as a model resurrection plant.

plant biology↗