Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.

Background: Efforts to characterize regulatory elements in plant genomes traditionally rely on evolutionary conservation and chromatin accessibility. Recently, intergenic bi-directional nascent transcript has emerged as a putative hallmark of active enhancers. Here, we integrate these approaches to better define the cis-regulatory landscape of the rice genome.

Structural Variants Contribute to Phenotypic Variation in Maize.

Comprehensively identifying the loci shaping trait variation has been challenging, in part because standard approaches often miss many types of genetic variants. Structural variants (SVs), especially transposable elements (TEs), are likely to affect phenotypic variation but we lack methods that can detect polymorphic SVs and TEs using short-read sequencing data. Here, we used a whole genome alignment between two maize genotypes to identify polymorphic SVs and then genotyped a large maize diversity panel for these variants using short-read sequencing data.

Exploring genetic diversity, population structure, and subgenome differences in the allopolyploid : implications for future breeding and research studies.

Camelina (), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, "alongside an understanding of the genetic diversity" and population structure of material present within breeding programs. We conducted population genetic analyses of a diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs.

Identification and analysis of imprinted genes in wild strawberry uncover a regulatory pathway in endosperm development.

Fertilization is a fundamental process that triggers seed and fruit development, but the molecular mechanisms underlying fertilization-induced seed development are poorly understood. Previous research has established AGamous-Like62 (AGL62) activation and auxin biosynthesis in the endosperm as key events following fertilization in Arabidopsis (Arabidopsis thaliana) and wild strawberry (Fragaria vesca). To test the hypothesis that epigenetic mechanisms are critical in mediating the effect of fertilization on the activation of AGL62 and auxin biosynthesis in the endosperm, we first identified and analyzed imprinted genes from the endosperm of wild strawberries.

Structural variants contribute to phenotypic variation in maize.

Comprehensively identifying the loci shaping trait variation has been challenging, in part because standard approaches often miss many types of genetic variants. Structural variants (SVs), especially transposable elements (TEs), are likely to affect phenotypic variation but we lack methods that can detect polymorphic structural variants and TEs using short-read sequencing data. Here, we used a whole genome alignment between two maize genotypes to identify polymorphic structural variants and then genotyped a large maize diversity panel for these variants using short-read sequencing data.

Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry.

Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes).

Uncovering genetic and metabolite markers associated with resistance against anthracnose fruit rot in northern highbush blueberry.

Anthracnose fruit rot (AFR), caused by the fungal pathogen is among the most destructive and widespread fruit disease of blueberry, impacting both yield and overall fruit quality. Blueberry cultivars have highly variable resistance against AFR. To date, this pathogen is largely controlled by applying various fungicides; thus, a more cost-effective and environmentally conscious solution for AFR is needed.

Vaccinium as a comparative system for understanding of complex flavonoid accumulation profiles and regulation in fruit.

The genus Vaccinium L. (Ericaceae) contains premium berryfruit crops, including blueberry, cranberry, bilberry, and lingonberry. Consumption of Vaccinium berries is strongly associated with various potential health benefits, many of which are attributed to the relatively high concentrations of flavonoids, including the anthocyanins that provide the attractive red and blue berry colors.

Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum).

Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter-specific, and inter-ploidy admixture of its genome and lack of in depth genome-wide inheritance and comparative structural studies. Here we describe a new high-quality, phased, chromosome-scale genome of a diploid blueberry, clone W85.

Evolutionary history and pan-genome dynamics of strawberry ( spp.).

Strawberry ( spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y.

In the presence of population structure: From genomics to candidate genes underlying local adaptation.

Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles.

The strength and pattern of natural selection on gene expression in rice.

Levels of gene expression underpin organismal phenotypes, but the nature of selection that acts on gene expression and its role in adaptive evolution remain unknown. Here we assayed gene expression in rice (Oryza sativa), and used phenotypic selection analysis to estimate the type and strength of selection on the levels of more than 15,000 transcripts. Variation in most transcripts appears (nearly) neutral or under very weak stabilizing selection in wet paddy conditions (with median standardized selection differentials near zero), but selection is stronger under drought conditions.

An inferred fitness consequence map of the rice genome.

The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa).

Assembly of the Pokeweed Genome Provides Insight Into Pokeweed Antiviral Protein (PAP) Gene Expression.

Ribosome-inactivating proteins (RIPs) are RNA glycosidases thought to function in defense against pathogens. These enzymes remove purine bases from RNAs, including rRNA; the latter activity decreases protein synthesis , which is hypothesized to limit pathogen proliferation by causing host cell death. Pokeweed antiviral protein (PAP) is a RIP synthesized by the American pokeweed plant ().

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower.

Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant, having retained more genes and being more highly expressed, a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of emergence of subgenome dominance, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural, <140-year-old allopolyploid (), a resynthesized interspecies triploid hybrid (), a resynthesized allopolyploid (), and progenitor species ( and ).

The butterfly plant arms-race escalated by gene and genome duplications.

Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race.

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris.

Whole-genome duplication (WGD) events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection, and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole-genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm.

Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora.

The extent that both positive and negative selection vary across different portions of plant genomes remains poorly understood. Here, we sequence whole genomes of 13 Capsella grandiflora individuals and quantify the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we show that selection is strong in coding regions, but weak in most noncoding regions, with the exception of 5' and 3' untranslated regions (UTRs).

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.

Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions.

The Capsella rubella genome and the genomic consequences of rapid mating system evolution.

The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C.