Tag: Genomics

Experiments using large germplasm collections are prone to contamination. With dropping sequencing costs, it becomes easier to validate the genotype using minimal sequencing coverage. Pisupati and colleagues developed an open-source python pipeline, called SNPmatch, allowing identification of 930 Arabidopsis…

Transposable elements are a major part of plant genomes. Long-terminal repeat retrotransposons (LTR (LTR-RTs) alone make up 78% of the maize genome (retrotransposons use a “copy and paste” transposition method meaning that a single source element can generate numerous clones of itself, leading to…

DNA methylation is instrumental in promoting transcriptional silencing at repetitive elements, inhibiting illegitimate recombination and establishing genomic imprinting. In plants, DNA methylation profiles are stably inherited over generations through the activities of cytosine DNA methyltransferases…

Cis-regulatory elements direct transcriptional output during cell differentiation and coordinate adaptive responses to environmental stress. DNA becomes open and accessible when nucleosomes are displaced by DNA-binding proteins, indicating a correlation between open chromatin regions and transcriptional…

Plants are highly plastic and can modulate their growth and development to better respond to abiotic and biotic surroundings. Among the molecules involved in the adaptation to the environment, a crucial role is played by small secreted peptides (SSPs). In their paper, integrating 144 transcriptomic experiments,…

Rust fungi represent an important group of plant pathogens, many of which have heteroecious lifestyles (meaning that they require two alternate hosts). However, the molecular mechanisms used by these pathogens for suppression and colonization of multiple hosts are poorly understood.  Lorrain et al.…

Three-dimensional organization of the genome is critical for proper gene expression. Comparison of the extremely compact genome of Arabidopsis with mammalian genomes revealed reduced local intra-chromosomal contacts (also know as Topologically Associated Domains, TADs) and fewer chromatin loops in the…

Many plants are polyploid, meaning that instead of the normal, diploid “2n” complement of chromosomes (one from each parent), they have more than 2n. Following whole-genome duplication, redundancy can allow the duplicated regions to diverge or become silenced. In some cases, silencing occurs preferentially…