A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants.

The vast majority of traditional almond varieties are self-incompatible, and the level of variability of the species is very high, resulting in a high-heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level.

The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants.

Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity.

Genome-wide identification of Reverse Transcriptase domains of recently inserted endogenous plant pararetrovirus ().

Endogenous viral elements (EVEs) are viral sequences that have been integrated into the nuclear chromosomes. Endogenous pararetrovirus (EPRV) are a class of EVEs derived from DNA viruses of the family . Previous works based on a limited number of genome assemblies demonstrated that EPRVs are abundant in plants and are present in several species.

Absence of major epigenetic and transcriptomic changes accompanying an interspecific cross between peach and almond.

Hybridization has been widely used in breeding of cultivated species showing low genetic variability, such as peach (). The merging of two different genomes in a hybrid often triggers a so-called "genomic shock" with changes in DNA methylation and in the induction of transposable element expression and mobilization. Here, we analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of and and in an F1 hybrid using high-throughput sequencing technologies.

Additional ORFs in Plant LTR-Retrotransposons.

LTR-retrotransposons share a common genomic organization in which the 5' long terminal repeat (LTR) is followed by the and genes and terminates with the 3' LTR. Although GAG-POL-encoded proteins are considered sufficient to accomplish the LTR-retrotransposon transposition, a number of elements carrying additional open reading frames (aORF) have been described. In some cases, the presence of an aORF can be explained by a phenomenon similar to retrovirus gene transduction, but in these cases the aORFs are present in only one or a few copies.

Impact of transposable elements on polyploid plant genomes.

Background: The growing wealth of knowledge on whole-plant genome sequences is highlighting the key role of transposable elements (TEs) in plant evolution, as a driver of drastic changes in genome size and as a source of an important number of new coding and regulatory sequences. Together with polyploidization events, TEs should thus be considered the major players in evolution of plants.

Scope: This review outlines the major mechanisms by which TEs impact plant genome evolution and how polyploidy events can affect these impacts, and vice versa.

Drought tolerance induced by sound in Arabidopsis plants.

We examined the responses of sound-treated arabidopsis adult plants to water deprivation and the associated changes on gene expression. The survival of drought-induced plants was significantly higher in the sound treated plants (24,8%) compared with plants kept in silence (13,3%). RNA-seq revealed significant upregulation of 87 genes including 32 genes involved in abiotic stress responses, 31 involved in pathogen responses, 11 involved in oxidation-reduction processes, 5 involved in the regulation of transcription, 2 genes involved in protein phosphorylation/dephosphorylation and 13 involved in jasmonic acid or ethylene synthesis or responses.

The effect of frequency-specific sound signals on the germination of maize seeds.

Objective: The effects of sound treatments on the germination of maize seeds were determined.

Results: White noise and bass sounds (300 Hz) had a positive effect on the germination rate. Only 3 h treatment produced an increase of about 8%, and 5 h increased germination in about 10%.

Use of ultrasonication to increase germination rates of Arabidopsis seeds.

Background: is widely used as model organism in plant biology. Although not of agronomic significance, it offers important advantages for basic research in genetics and molecular biology including the availability of a large number of mutants and genetically modified lines. However, Arabidopsis seed longevity is limited and seeds stored for more than 10 years usually show a very low capacity for germination.

The use of massive sequencing to detect differences between immature embryos of MON810 and a comparable non-GM maize variety.

The insect resistant maize YieldGard MON810 was studied to assess the extent to which introduction of a transgene may putatively alter the expression of endogenous genes by comparison of various GM lines vs. their non-transgenic counterparts. To assess the extent to which introduction of a transgene may putatively alter the expression of endogenous genes, GM lines of the insect resistant maize YieldGard MON810 were compared with non-transgenic counterparts.

Genetic diversity of maize germplasm assessed by retrotransposon-based markers.

Maize is one of the most important crops and also a model for grass genome research. Transposable elements comprise over 78% of the maize genome and their ability to generate new copies makes them good potential markers. Interretrotransposon-amplified polymorphism (IRAP) and retrotransposon microsatellite amplified polymorphism (REMAP) protocols were used for the first time in maize to study the genetic variability between maize cultivars.

The evolutionary conserved oil body associated protein OBAP1 participates in the regulation of oil body size.

A transcriptomic approach has been used to identify genes predominantly expressed in maize (Zea mays) scutellum during maturation. One of the identified genes is oil body associated protein1 (obap1), which is transcribed during seed maturation predominantly in the scutellum, and its expression decreases rapidly after germination. Proteins similar to OBAP1 are present in all plants, including primitive plants and mosses, and in some fungi and bacteria.

Identification of a type I Ca2+/Mg2+-dependent endonuclease induced in maize cells exposed to camptothecin.

Background: Camptothecin is a plant alkaloid that specifically binds topoisomerase I, inhibiting its activity and inducing double stranded breaks in DNA and activating the cell responses to DNA damage.

Results: Maize cultured cells were incubated in the presence of different concentrations of camptothecin. Camptothecin inhibits cultured cell growth, induces genomic DNA degradation, and induces a 32 kDa Ca2+/Mg2+-dependent nuclease activity.

ZmPTR1, a maize peptide transporter expressed in the epithelial cells of the scutellum during germination.

In plants, peptide transporter/nitrate transporter 1 (PTR/NRT1) family proteins transport a variety of substrates such as nitrate, di- and tripepetides, auxin and carboxylates across membranes. We isolated and characterized ZmPTR1, a maize member of this family. ZmPTR1 protein sequence is highly homologous to the previously characterized di- and tripeptide Arabidopsis transporters AtPTR2, AtPTR4 and AtPTR6.

Grande retrotransposons contain an accessory gene in the unusually long 3'-internal region that encodes a nuclear protein transcribed from its own promoter.

LTR retrotransposons are major components of plant genomes playing important roles in the evolution of their host genomes, for example, generating new genes or providing new promoters to existing genes. The Grande family of retrotransposons is present in Zea species and is characterized by an unusually long internal region due to the presence of a 7-kbp region between the gag-pol coding region and the 3'LTR. We demonstrate here that such unusual sequence is present in the great majority of Grande copies in maize genome.

Expression profile of maize (Zea mays) scutellar epithelium during imbibition.

The scutellum is a shield-shaped structure surrounding the embryo axis in grass species. The scutellar epithelium (Sep) is a monolayer of cells in contact with the endosperm. The Sep plays an important role during seed germination in the secretion of gibberellins and hydrolytic enzymes and in the transport of the hydrolized products to the growing embryo.

Transcriptomic and proteomic profiling of maize embryos exposed to camptothecin.

Background: Camptothecin is a plant alkaloid that specifically binds topoisomerase I, inhibiting its activity and inducing double stranded breaks in DNA, activating the cell responses to DNA damage and, in response to severe treatments, triggering cell death.

Results: Comparative transcriptomic and proteomic analyses of maize embryos that had been exposed to camptothecin were conducted. Under the conditions used in this study, camptothecin did not induce extensive degradation in the genomic DNA but induced the transcription of genes involved in DNA repair and repressed genes involved in cell division.

Protein composition analysis of oil bodies from maize embryos during germination.

Seed oil bodies (OBs) are intracellular particles that store lipids. In maize embryos, the oil bodies are accumulated mainly in the scutellum. Oil bodies were purified from the scutellum of germinating maize seeds and the associated proteins were extracted and subjected to 2-DE analysis followed by LC-MS/MS for protein identification.

Transcriptional activity of transposable elements in maize.

Background: Mobile genetic elements represent a high proportion of the Eukaryote genomes. In maize, 85% of genome is composed by transposable elements of several families. First step in transposable element life cycle is the synthesis of an RNA, but few is known about the regulation of transcription for most of the maize transposable element families.

Stability of the MON 810 transgene in maize.

We analysed the DNA variability of the transgene insert and its flanking regions in maize MON 810 commercial varieties. Southern analysis demonstrates that breeding, since the initial transformation event more than 10 years ago, has not resulted in any rearrangements. A detailed analysis on the DNA variability at the nucleotide level, using DNA mismatch endonuclease assays, showed the lack of polymorphisms in the transgene insert.

Genetic, molecular and cellular approaches to the analysis of maize embryo development.

The development of embryo structures in plants is essential for the formation of the adult plant organs. In cereals, this process has distinct features which have attracted attention from different points of view. Differential gene expression analyses have been used in order to identify genes useful as molecular markers of certain physiological, molecular or developmental processes.

Characterization of polyadenylated cryIA(b) transcripts in maize MON810 commercial varieties.

The Zea mays L. event MON810 is one of the major commercialized genetically modified crops. The inserted expression cassette has a 3' truncation partially affecting the cryIA(b) coding sequence, resulting in the lack of the NOS terminator, with transcription of the transgene reported to read-through 3'-past the truncation site.

Maize embryogenesis.

Plant embryo development is a complex process that includes several coordinated events. Maize mature embryos consist of a well-differentiated embryonic axis surrounded by a single massive cotyledon called scutellum. Mature embryo axis also includes lateral roots and several developed leaves.

Life without GAG: the BARE-2 retrotransposon as a parasite's parasite.

A large proportion of the plant LTR (Long Terminal Repeat) retrotransposons are partly or completely unable to synthesize their own machinery for transposition. However, most of these inactive or non-autonomous elements are likely able to retrotranspose, based on their insertional polymorphism. Therefore, they must be parasitic on one or more active partners.

Integrase diversity and transcription of the maize retrotransposon Grande.

Grande is an abundant gypsy-like retrotransposon present in the genera Zea and Tripsacum. Related retro transposon families can be found in sorghum, rice, and barley, but not in wheat or rye. We have amplified and sequenced several copies of part of the integrase domain derived from the Zea mays, Zea diploperennis, and Tripsacum dactyloides genomes.