Predmoter-cross-species prediction of plant promoter and enhancer regions.

Motivation: Identifying -regulatory elements (CREs) is crucial for analyzing gene regulatory networks. Next generation sequencing methods were developed to identify CREs but represent a considerable expenditure for targeted analysis of few genomic loci. Thus, predicting the outputs of these methods would significantly cut costs and time investment.

A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity.

Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits.

Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning.

Motivation: Current state-of-the-art tools for the de novo annotation of genes in eukaryotic genomes have to be specifically fitted for each species and still often produce annotations that can be improved much further. The fundamental algorithmic architecture for these tools has remained largely unchanged for about two decades, limiting learning capabilities. Here, we set out to improve the cross-species annotation of genes from DNA sequence alone with the help of deep learning.

Phosphate starvation causes different stress responses in the lipid metabolism of tomato leaves and roots.

Plants have evolved various acclimation responses to cope with phosphate depletion, including several changes in lipid metabolism. Thereby membrane phospholipids are dephosphorylated and can be used as an internal phosphate source, while galactolipids are incorporated into the membrane to maintain membrane functionality. Still little is known about the lipidomic and transcriptomic response of plants other than Arabidopsis thaliana upon phosphate starvation.

Transcriptomic and proteomic data in developing tomato fruit.

Transcriptomic and proteomic analyses were performed on three replicates of tomato fruit pericarp samples collected at nine developmental stages, each replicate resulting from the pooling of at least 15 fruits. For transcriptome analysis, Illumina-sequenced libraries were mapped on the tomato genome with the aim to obtain absolute quantification of mRNA abundance. To achieve this, spikes were added at the beginning of the RNA extraction procedure.

Modeling Protein Destiny in Developing Fruit.

Protein synthesis and degradation are essential processes that regulate cell status. Because labeling in bulky organs, such as fruits, is difficult, we developed a modeling approach to study protein turnover at the global scale in developing tomato () fruit. Quantitative data were collected for transcripts and proteins during fruit development.

Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris.

A parasitic lifestyle, where plants procure some or all of their nutrients from other living plants, has evolved independently in many dicotyledonous plant families and is a major threat for agriculture globally. Nevertheless, no genome sequence of a parasitic plant has been reported to date. Here we describe the genome sequence of the parasitic field dodder, Cuscuta campestris.

De Novo Assembly of a New Accession Using Nanopore Sequencing.

Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species We describe the assembly of its genome to a contig N50 of 2.

Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes.

Strawberry fruits (Fragaria vesca) are valued for their sweet fruity flavor, juicy texture, and characteristic red color caused by anthocyanin pigments. To gain a deeper insight into the regulation of anthocyanin biosynthesis, we performed comparative metabolite profiling and transcriptome analyses of one red-fruited and two natural white-fruited strawberry varieties in two tissues and three ripening stages. Developing fruit of the three genotypes showed a distinctive pattern of polyphenol accumulation already in green receptacle and achenes.

Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data.

The high efficiency of C photosynthesis relies on spatial division of labor, classically with initial carbon fixation in the mesophyll and carbon reduction in the bundle sheath. By employing grinding and serial filtration over liquid nitrogen, we enriched C tissues along a developing leaf gradient. This method treats both C tissues in an integrity-preserving and consistent manner, while allowing complementary measurements of metabolite abundance and enzyme activity, thus providing a comprehensive data set.

Understanding metabolite transport and metabolism in C4 plants through RNA-seq.

RNA-seq, the measurement of steady-state RNA levels by next generation sequencing, has enabled quantitative transcriptome analyses of complex traits in many species without requiring the parallel sequencing of their genomes. The complex trait of C4 photosynthesis, which increases photosynthetic efficiency via a biochemical pump that concentrates CO2 around RubisCO, has evolved convergently multiple times. Due to these interesting properties, C4 photosynthesis has been analyzed in a series of comparative RNA-seq projects.

Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress responsive and experience frequent response gains.

Background: Green algae belong to a group of photosynthetic organisms that occupy diverse habitats, are closely related to land plants, and have been studied as sources of food and biofuel. Although multiple green algal genomes are available, a global comparative study of algal gene families has not been carried out. To investigate how gene families and gene expression have evolved, particularly in the context of stress response that have been shown to correlate with gene family expansion in multiple eukaryotes, we characterized the expansion patterns of gene families in nine green algal species, and examined evolution of stress response among gene duplicates in Chlamydomonas reinhardtii.

Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species.

C(4) photosynthesis outperforms the ancestral C(3) state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C(3) backgrounds. However, the genetic architecture of C(4) photosynthesis remains largely unknown.

Predicting C4 photosynthesis evolution: modular, individually adaptive steps on a Mount Fuji fitness landscape.

An ultimate goal of evolutionary biology is the prediction and experimental verification of adaptive trajectories on macroevolutionary timescales. This aim has rarely been achieved for complex biological systems, as models usually lack clear correlates of organismal fitness. Here, we simulate the fitness landscape connecting two carbon fixation systems: C3 photosynthesis, used by most plant species, and the C4 system, which is more efficient at ambient CO2 levels and elevated temperatures and which repeatedly evolved from C3.

C₄ photosynthesis: from evolutionary analyses to strategies for synthetic reconstruction of the trait.

C₄ photosynthesis represents the most productive modes of photosynthesis in land plants and some of the most productive crops on the planet, such as maize and sugarcane, and many ecologically important native plants use this type of photosynthesis. Despite its ecological and economic importance, the genetic basis of C₄ photosynthesis remains largely unknown. Even many fundamental aspects of C₄ biochemistry, such as the molecular identity of solute transporters, and many aspects of C₄ plant leaf development, such as the Kranz anatomy, are currently not understood.

Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation.

We systematically analyzed a developmental gradient of the third maize (Zea mays) leaf from the point of emergence into the light to the tip in 10 continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, and photosynthetic rate measurements showed that the maize leaf undergoes a sink-to-source transition without an intermediate phase of C(3) photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination, showed continuous gradients for all analyzed items.