Researchers have identified a set of genes that help control early drought response in a popular global crop...

The dynamics of local climates make development of agricultural strategies challenging. Yield improvement has progressed slowly, especially in drought-prone regions where annual crop production suffers from episodic aridity...

Effective implementation of technology that facilitates accurate and high-throughput screening of thousands of field-grown lines is critical for accelerating crop improvement and breeding strategies for higher yield and disease tolerance...

Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown...

Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution...

Black raspberry (Rubus occidentalis) is an important specialty fruit crop in the U.S. Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference...

A report on the 10 th plant genome meeting entitled ‘Plant genomes and biotechnology: from genes to networks’, held at Cold Spring Harbor Laboratory, 2–5 December, 2015.

Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly1. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE)2. Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum..

Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5...

Phenotyping has become the rate-limiting step in using large-scale genomic data to understand and improve agricultural crops. Here, the Bellwether Phenotyping Platform for controlled-environment plant growth and automated multimodal phenotyping is described. The system has capacity for 1140 plants, which pass daily through stations to record fluorescence, near-infrared, and visible images. Plant Computer Vision (PlantCV) was developed as open-source, hardware platform-independent software for quantitative image analysis...

We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance. Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace...

In recent years, high-throughput sequencing-based analysis of plant transcriptomes has suggested that up to ∼60% of plant gene loci encode alternatively spliced mature transcripts. These studies have also revealed that alternative splicing in plants can be regulated by cell type, developmental stage, the environment, and the circadian clock...

The goal of much of plant biology research is to understand and thus be able to manipulate phenotypes of important crop species. Decoding crop genomes has been a formidable challenge for many years due to their typically huge sizes, abundant repetitive regions, heterozygosity, and polyploidy. Therefore, plant biologists have heavily relied on studies of the reference plant, Arabidopsis, which has been the subject of a multitude of physiological, genetic, biochemical, molecular, and genomic studies. In recent years, next generation sequencing (NGS) has been a game changer in the field of crop science. NGS-based genomics overcomes many long-standing technical barriers that have made crop genomic challenging...

Artificial microRNAs (amiRNAs) are used for selective gene silencing in plants. However, current methods to produce amiRNA constructs for silencing transcripts in monocot species are not suitable for simple, cost-effective and large-scale synthesis. Here, a series of expression vectors based on Oryza sativa MIR390 (OsMIR390) precursor was developed for high-throughput cloning and high expression of amiRNAs in monocots.

Several factors affect the yield potential and geographical range of crops including the circadian clock, water availability, and seasonal temperature changes. In order to sustain and increase plant productivity on marginal land in the face of both biotic and abiotic stresses, we need to more efficiently generate stress-resistant crops through marker-assisted breeding, genetic modification, and new genome-editing technologies. To leverage these strategies for producing the next generation of crops, future transcriptomic data acquisition should be pursued with an appropriate temporal design and analyzed with a network-centric approach.

Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron retaining (IR) transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad range thermal cycles triggered a sharp increase in the long intron retaining CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought ...

The mechanisms ensuring balanced growth remain a critical question in developmental biology. In plants, this balance relies on spatiotemporal integration of hormonal signaling pathways, but the understanding of the precise contribution of each hormone is just beginning to take form. Brassinosteroid (BR) hormone is shown here to have opposing effects on root meristem size, depending on its site of action...

C₄ and C₃ photosynthesis differ in the efficiency with which they consume water and nitrogen. Engineering traits of the more efficient C₄ photosynthesis into C₃ crops could substantially increase crop yields in hot, arid conditions. To identify differences between C₄ and C₃ photosynthetic mechanisms, we profiled metabolites and gene expression in the developing leaves of Zea mays (maize), a C₄ plant, and Oryza sativa (rice), a C₃ plant, using a statistical method named the unified developmental model (UDM)...

The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. 

In plants, chloroplasts and the nucleus communicate with each other to regulate growth and adapt to environmental conditions. Signaling from the nucleus to chloroplasts, by which the nucleus programs chloroplast development, is called anterograde regulation.

We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly.

Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules.

Lignin is a significant barrier in the conversion of plant biomass to bioethanol. Cinnamyl alcohol dehydrogenase (CAD) and caffeic acid O-methyltransferase (COMT) catalyze key steps in the pathway of lignin monomer biosynthesis. We developed transgenic plants overexpressing artificial microRNA designed to silence BdCAD1 or BdCOMT4. Both transgenes caused altered flowering time and increased stem count and weight. Downregulation of BdCAD1 caused a leaf brown midrib phenotype, the first time this phenotype has been observed in a C3 plant. 

Modification of redox state caused a change in expression of a common set of about 750 genes, many of which are known stress-responsive genes. Among the most highly enriched promoter elements in the induced gene set were heat-shock elements (HSEs), known motifs that change gene expression in response to high temperature in many systems. Excess light regulates both the subcellular location of HSFA1D and its biochemical properties, making it a key early component of the excess light stress network of plants.

The global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. B. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants.

Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types.

It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba.

Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely-packed protuberances on its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.

High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops.

European hazelnut (Corylus avellana L.) is of worldwide agricultural significance, with breeding efforts focused on combining high nut yield and nut quality with resistance to diseases such as eastern filbert blight (EFB), a cause of severe crop loss in much of the United States.  We used Illumina ribonucleic acid sequencing (RNA-seq) to characterize complementary DNA (cDNA) libraries from four hazelnut tissues, including leaves, catkins, bark, and whole seedlings. 

Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29,213 single-nucleotide polymorphisms

Recent mapping of eukaryotic transcriptomes and spliceomes using massively parallel RNA sequencing (RNA-seq) has revealed that the extent of alternative splicing has been considerably underestimated. Our results demonstrate that unproductive alternative splicing is a widespread phenomenon among plant circadian clock genes that frequently generates mRNA isoforms harboring in-frame PTCs.

Pyrenophora tritici-repentis (Ptr), a necrotrophic fungus and the causal agent of tan spot of wheat, produces one or a combination of host-selective toxins (HSTs) necessary for disease development. Investigation of host responses induced by HSTs provides better insight into the nature of the host susceptibility.

Next-generation sequencing has enabled genome-wide studies of alternative pre-mRNA splicing, allowing for empirical determination, characterization, and quantification of the expressed RNAs in a sample in toto. As a result, RNA sequencing (RNA-seq) has shown tremendous power to drive biological discoveries.

Little is known about the potential of Brachypodium distachyon as a model for low temperature stress responses in Pooideae. The ice recrystallization inhibition proteins (IRIP) genes, fructosyltransferase (FST) genes, and many C-repeat binding factor (CBF) genes are Pooideae specific and important in low temperature responses. Here we use comparative analyses to study conservation and evolution of these gene families in B. distachyon to better understand B. distachyon's potential as a model species for agriculturally important temperate grasses

The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits.

Switchgrass (Panicum virgatum L.) is a C4 perennial grass that is widely popular as an important bioenergy crop.  Through next generation sequencing we estimate that 90% of the transcriptome has been covered in this analysis, which doubles the current publicly available ESTs.

A genome-wide SNP discovery study for the apple (Malus domestica) involving 27 cultivars is published.  A total of 2,113,120 SNPs were detected, 8k of which are now available in an SNP array as a genomic resource.  

Our study investigating the effects of methylation in Populus trichocarpa was published.  We found striking difference among tissues in methylation which were apparent at the chromosomal scale.

The circadian clock governs many daily rhythms in organisms, but the mechanisms behind this are not well understood.  Our study identifies over 1000 transcripts in the mammalian liver that exhibit circadian oscillations.

GENE-counter, a Perl-based computational pipeline for analyzing RNS-Seq data for differential gene expression, is published.  It is well suited for handling the unique characteristics of small sample sizes and the high variability in gene counts.

Snakes provide a unique vertebrate system for studying a diversity of extreme adaptations, but there are few genomic resources for studying them.  1 million transcriptome reads were assembled, characterized, and made available as a public resource.

Circadian regulated genes in poplar and rice were identified, which were found to be similar to those in Arabidopsis thaliana.  The major cis-regulator motifs were found to be strikingly conserved.

We We conducted a comprehensive assessment of genomic repeat content in two snake genomes, the venomous copperhead (Agkistrodon contortrix) and the Burmese python (Python molurus bivittatus).

Plants have two myosin classes, which are involved in molecular motor function. These transcripts were systematically investigated.

The genome of the woodland strawberry (Fragaria vesca), which is a close relative of the cultivated strawberry (Fragaria ananassa) is sequenced.  Several genes related to valuable horticultural traits were identified.  

Supersplat, an HTS specific splice junction discovery tool, is published.

A genetic linkage map for Brachypodium, a model organism for grasses, has been constructed.  This linkage map will be important in future molecular genetic analyses of this model system.

Over 56,000 transcripts were measured in our now published study on shoot organogenesis in Populus trichocarpa.  A total of 588 transcription factors across 45 gene families were differentially regulated. 

We published a brief communication detailing two proteins involved in de novo DNA methylation.

Alternative splicing is an essential characteristic of plant genomes.  Our recent analysis indicates that at least 42% of genes in Arabidopsis are alternatively spliced.

We characterized the population structure of the new grass model organism Brachypodium distachyon.  The genetic variation of this grass in California is much lower than in it's ancestral homelands in Eurasia, which is likely due to founder effects.

We investigated the effects of the plant disease caused by the microbe Pyrenophora tritici-repentis, Ptr ToxA, on wheat.  Our study supports previous research that indicates that ToxA induces cell death by impairing its photosynthetic machinery.  

High-throughput sequencing requires new types of assemblers that are adapted specifically to handling errors.  QSRA is one such assembly algorithm that takes advantage of quality scores.  This results in significant performance and quality increases.

Most organisms have circadian clocks that govern daily biological rhythms.  However, previous investigations in plants have been done with those that originate from temperate regions.  In a study with the tropical plant, Carica papaya, we identified that the genetic regulatory elements are largely conserved, and likely have been an integral part of plant evolution.  

Most organisms use daily light/dark cycles as timing cues to control many essential physiological processes.  In our paper, we identified a number of hormone associated genes that are co-expressed along with the overrepresentation of a cis-acting element (CACATG).  Our results indicated that the circadian clock controls growth by allowing phytohormone transcript levels to rise at the proper time of day.

Sequencing organellar DNA is important for evolutionary and population genetic studies; however, the conservative nature of these sequences limits these studies.  We developed a new method to simultaneously sequence multiple genomes efficiently while also maintaining high levels of quality.

We identified a novel zinc knuckle protein that carries a premature stop codon in one Arabidopsis accession.  Our study reveals that this protein controls blue light associated growth downstream of the circadian clock.

In a systematic study of Arabidopsis cis-regulatory elements involved in circadian gene expression, we identified several key motifs responsible for the observed cyclic patterns.  Of these we identified a previously unknown class of motifs terms the "midnight module, " since they are correlated with late night expression.

We have publicly released a suite of tools for the plat biology community that will facilitate cross-species comparisons.  The tools provide graphical web-based interfaces to viewing diurnal and circadian microarray data, modeling gene expression patterns, and identifying potential cis-regulator elements.