Volume 14, Issue 4, April 2024

Duckweeds are among the fastest reproducing plants on the planet. One species, Spirodela polyrhiza, has lost key genes involved in de novo methylation of DNA at sites often associated with repetitive DNA, and within genes. However symmetrical DNA methylation and heterochromatin is maintained.

Nagle et al. explored the genetic basis of plant regeneration, an essential aspect of plant propagation and transgenic plant production, by conducting a genome-wide association study (GWAS) of callus and shoot regeneration in the model tree Populus trichocarpa. To enable large-scale phenotyping of developing tissues during regeneration, the authors employed a novel computer vision system. They identified over 200 candidate genes involved in key processes including cell adhesion, stress signaling, and hormonal pathways, offering potential strategies for advancing biotechnology in difficult-to-regenerate plants.

Wilson et al. combined information across trials and applied genomic prediction to tetraploid potato, while evaluating different modelling strategies and application scenarios.

Reference genome assemblies have been created from multiple lineages within the Canidae family, however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, Armstrong et al. present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases (Mb), respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern US and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of prdm9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.