Structural evolution drives diversification of the large LRR-RLK gene family

Cells are continuously exposed to chemical signals that they must
discriminate between and respond to appropriately. In embryophytes, the
Leucine-Rich Repeat Receptor-Like Kinases (LRR-RLKs) are signal receptors
critical in development and defense. LRR-RLKs have diversified to hundreds
of genes in many plant genomes. Although intensively studied, a
well-resolved LRR-RLK gene tree has remained elusive.  To resolve
the LRR-RLK gene tree, we developed an improved gene discovery method
based on iterative Hidden Markov Model (HMM)-searching and phylogenetic
inference. We used this method to infer complete gene trees for each of
the LRR-RLK subclades, and reconstructed the deepest nodes of the full
gene family. We discovered that the LRR-RLK gene family is even larger
than previously thought, and that protein domain gains and losses are
prevalent. These structural modifications, some of which likely predate
embryophyte diversification, led to misclassification of some LRR-RLK
variants as members of other gene families. Our work corrects this
misclassification. Our results reveal ongoing structural evolution
generating novel LRR-RLK genes. These new genes are raw material for the
diversification of signaling in development and defense. Our methods also
enable phylogenetic reconstruction in any large gene family.