Phylogenomic dataset used for evolutionary rate covariation analyses in Forsythe et al.

Nuclear and plastid (chloroplast) genomes experience different mutation
rates, levels of selection, and transmission modes, yet key cellular
functions depend on coordinated interactions between proteins encoded in
both genomes. Functionally related proteins often show correlated changes
in rates of sequence evolution across a phylogeny (evolutionary rate
covariation or ERC), offering a means to detect previously unidentified
suites of coevolving and cofunctional genes. We performed phylogenomic
analyses across angiosperm diversity, scanning the nuclear genome for
genes that exhibit ERC with plastid genes. As expected, the strongest hits
are highly enriched for plastid-targeted proteins, providing evidence that
cytonuclear interactions affect rates of molecular evolution at
genome-wide scales. Many identified nuclear genes function in
post-transcriptional regulation and the maintenance of protein homeostasis
(proteostasis), including protein translation (in both the plastid and
cytosol), import, quality control and turnover. We also identified nuclear
genes that exhibit strong signatures of coevolution with the plastid
genome but lack organellar-targeting annotations, making them candidates
for having previously underibed roles in plastids. In sum, our genome-wide
analyses reveal that plastid-nuclear coevolution extends beyond the
intimate molecular interactions within chloroplast enzyme complexes and
may be driven by frequent rewiring of the machinery responsible for
maintenance of plastid proteostasis in angiosperms.