Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with different susceptibilities to Ralstonia solanacearum
Authors: Franco Ortega, S., James, S. R., Gilbert, L., Hogg, K., Stevens, H., Daff, J., Friman, V. P., Harper, A. L.
The study generated de‑novo genome assemblies for the resistant wild relative Solanum dulcamara and the susceptible Solanum nigrum using a hybrid Oxford Nanopore and Illumina sequencing strategy. Comparative genomic analyses identified auxin‑transport genes and novel pattern recognition receptor orthogroups unique to resistant species, as well as differential gene‑body methylation that may underlie resistance to Ralstonia solanacearum.
The study examined transposable element (TE) silencing in the duckweed Spirodela polyrhiza, which exhibits unusually low DNA methylation, scarce 24‑nt siRNAs, and missing RdDM components. While degenerated TEs lack DNA methylation and H3K9me2, they retain heterochromatin marks H3K9me1 and H3K27me1, whereas the few intact TEs show high DNA methylation and H3K9me2, indicating a shift in RdDM focus toward potentially active TEs and suggesting heterochromatin can be maintained independently of DNA methylation in flowering plants.