Integrated web portal for non-destructive salt sensitivity detection of seeds using fluorescent and visible light images coupled with machine learning algorithms.

Climate change has created unprecedented stresses in the agricultural sector, driving the necessity of adapting agricultural practices and developing novel solutions to the food crisis. (Camelina) is a recently emerging oilseed crop with high nutrient-density and economic potential. Camelina seeds are rich in essential fatty acids and contain potent antioxidants required to maintain a healthy diet.

Camelina sativa High-Throughput Phenotyping Under Normal and Salt Conditions Using a Plant Phenomics Platform.

Climate change and environmental pollution will have a great impact on food security worldwide. More than 30% of the world's irrigated areas are estimated to be perturbed by high salinity affecting the productivity of crops. Camelina sativa, also known as false flax, is a flowering plant that is mainly cultivated as an oilseed crop that has many potential economic benefits; it can be used in food products, in industrial applications, and in animal feed and converted into biofuel.

Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes.

Background: Transposable elements (TEs) are common and often present with high copy numbers in cellular genomes. Unlike in cellular organisms, TEs were previously thought to be either rare or absent in viruses. Almost all reported TEs display only one or two copies per viral genome.

Exaptation of transposable element coding sequences.

Transposable elements (TEs) are mobile genetic elements that were once perceived as merely selfish, but are now recognized as potent agents of adaptation. One way TEs contribute to genome evolution is through TE exaptation, a process whereby TEs, which usually persist by replicating in the genome, transform into novel host genes, which thereafter persist by conferring phenotypic benefits. Exapted TEs are known to contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet we have little understanding about the process of TE exaptation.

Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements.

Plant phenomics offers unique opportunities to accelerate our understanding of gene function and plant response to different environments, and may be particularly useful for studying previously uncharacterized genes. One important type of poorly characterized genes is those derived from transposable elements (TEs), which have departed from a mobility-driven lifestyle to attain new adaptive roles for the host (exapted TEs). We used phenomics approaches, coupled with reverse genetics, to analyze T-DNA insertion mutants of both previously reported and novel protein-coding exapted TEs in the model plant .

Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements.

Once perceived as merely selfish, transposable elements (TEs) are now recognized as potent agents of adaptation. One way TEs contribute to evolution is through TE exaptation, a process whereby TEs, which persist by replicating in the genome, transform into novel host genes, which persist by conferring phenotypic benefits. Known exapted TEs (ETEs) contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet little is known about this process.

A Comprehensive Approach to Assess Arabidopsis Survival Phenotype in Water-Limited Condition Using a Non-invasive High-Throughput Phenomics Platform.

With the rapid rise in global population and the challenges caused by climate changes, the maximization of plant productivity and the development of sustainable agriculture strategies are vital for food security. One of the resources more affected in this new environment will be the limitation of water. In this study, we describe the use of non-invasive technologies exploiting sensors for visible, fluorescent, and near-infrared lights to accurately screen survival phenotypes in Arabidopsis thaliana exposed to water-limited conditions.

A call for benchmarking transposable element annotation methods.

DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks-that is, no standard way to measure or compare their accuracy. This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation.

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.

Discovery of novel genes derived from transposable elements using integrative genomic analysis.

Complex eukaryotes contain millions of transposable elements (TEs), comprising large fractions of their nuclear genomes. TEs consist of structural, regulatory, and coding sequences that are ordinarily associated with transposition, but that occasionally confer on the organism a selective advantage and may thereby become exapted. Exapted transposable element genes (ETEs) are known to play critical roles in diverse systems, from vertebrate adaptive immunity to plant development.

Diversity and evolution of transposable elements in Arabidopsis.

Transposable elements are mobile genetic elements that have successfully populated eukaryotic genomes and show diversity in their structure and transposition mechanisms. Although first viewed solely as selfish, transposable elements are now known as important vectors to drive the adaptation and evolution of their host genome. Transposable elements can affect host gene structures, gene copy number, gene expression, and even as a source for novel genes.

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.

A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana.

The benefits of ever-growing numbers of sequenced eukaryotic genomes will not be fully realized until we learn to decipher vast stretches of noncoding DNA, largely composed of transposable elements. Transposable elements persist through self-replication, but some genes once encoded by transposable elements have, through a process called molecular domestication, evolved new functions that increase fitness. Although they have conferred numerous adaptations, the number of such domesticated transposable element genes remains unknown, so their evolutionary and functional impact cannot be fully assessed.

Modulation of auxin-binding protein 1 gene expression in maize and the teosintes by transposon insertions in its promoter.

Auxin plays crucial roles in plant development. Auxin-binding protein 1 (ABP1) is an auxin receptor required to coordinate cell division and expansion during postembryonic shoot development, and differential auxin responses during root growth. While ABP1 is encoded by a single gene in maize, multiple gene copies exist in teosinte, the wild relatives of maize.

Bs1, a new chimeric gene formed by retrotransposon-mediated exon shuffling in maize.

Transposons are major components of all eukaryotic genomes. Although traditionally regarded as causes of detrimental mutations, recent evidence suggests that transposons may play a role in host gene diversification and evolution. For example, host gene transduction by retroelements has been suggested to be both common and to have the potential to create new chimeric genes by the shuffling of existing sequences.

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.

Rice, the primary source of dietary calories for half of humanity, is the first crop plant for which a high-quality reference genome sequence from a single variety was produced. We used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference genome for 20 diverse varieties and landraces that capture the impressive genotypic and phenotypic diversity of domesticated rice. Here, we report the distribution of 160,000 nonredundant SNPs.

Sequence diversity of a domesticated transposase gene, MUG1, in Oryza species.

MUG1 is a MULE transposon-related domesticated gene in plants. We assessed the sequence diversity, neutrality, expression, and phylogenetics of the MUG1 gene among Oryza ssp. We found MUG1 expression in all tissues analyzed, with different levels in O.

The Rice Annotation Project Database (RAP-DB): 2008 update.

The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide.

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare.

Transposon-mediated expansion and diversification of a family of ULP-like genes.

Transposons comprise a major component of eukaryotic genomes, yet it remains controversial whether they are merely genetic parasites or instead significant contributors to organismal function and evolution. In plants, thousands of DNA transposons were recently shown to contain duplicated cellular gene fragments, a process termed transduplication. Although transduplication is a potentially rich source of novel coding sequences, virtually all appear to be pseudogenes in rice.

The evolutionary fate of MULE-mediated duplications of host gene fragments in rice.

DNA transposons are known to frequently capture duplicated fragments of host genes. The evolutionary impact of this phenomenon depends on how frequently the fragments retain protein-coding function as opposed to becoming pseudogenes. Gene fragment duplication by Mutator-like elements (MULEs) has previously been documented in maize, Arabidopsis, and rice.

Genomic mutation in lines of Arabidopsis thaliana exposed to ultraviolet-B radiation.

Studies that have attempted to estimate the rate of deleterious mutation have typically been conducted under low levels of ultraviolet-B (UV-B) radiation, a naturally occurring mutagen. We conducted experiments to test whether the inclusion of natural levels of UV-B radiation in mutation-accumulation (MA) experiments influences the rate and effects of mildly deleterious mutation in the plant Arabidopsis thaliana. Ten generations of MA proved insufficient to observe significant changes in means or among-line variances in experimental lines maintained either with or without supplemental UV-B radiation.

MUSTANG is a novel family of domesticated transposase genes found in diverse angiosperms.

While transposons have traditionally been viewed as genomic parasites or "junk DNA," the discovery of transposon-derived host genes has fueled an ongoing debate over the evolutionary role of transposons. In particular, while mobility-related open reading frames have been known to acquire host functions, the contribution of these types of events to the evolution of genes is not well understood. Here we report that genome-wide searches for Mutator transposase-derived host genes in Arabidopsis thaliana (Columbia-0) and Oryza sativa ssp.

Transposable element annotation of the rice genome.

Motivation: The high content of repetitive sequences in the genomes of many higher eukaryotes renders the task of annotating them computationally intensive. Presently, the only widely accepted method of searching and annotating transposable elements (TEs) in large genomic sequences is the use of the RepeatMasker program, which identifies new copies of TEs by pairwise sequence comparisons with a library of known TEs. Profile hidden Markov models (HMMs) have been used successfully in discovering distant homologs of known proteins in large protein databases, but this approach has only rarely been applied to known model TE families in genomic DNA.