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.