Phylogeny, Expression Profiling, and Coexpression Networks Reveals the Critical Roles of Nucleotide-BindingLeucine-Rich Repeats on <i>Valsa</i> Canker Resistance

Abstract

Rosaceae is one of the major families in the plant kingdom with important economic value. However, many of them are attacked by Valsa canker, resulting in serious loss of production and profits. Nucleotide-binding leucine-rich repeats (NLRs) play a key role in the plant immune response as the largest class of resistance genes. Currently, we performed a genome-wide identification of NLR genes in Rosaceae and revealed some NLR genes in response to Valsa canker using multispecies bioinformatics including co-expression network analysis and RNASeq data. A total of 3718 NLR genes were identified from genomes of 19 plant species (include 9 Rosaceae plants) and classified them into 15 clades. The NLRs display species- and group-specific expansions that are derived from both the whole genome duplication and the tandem duplication. Additionally, the expression of some NLR members was low under normal growth conditions in various plant tissues, while significantly enhanced after the infection of Valsa canker. Furthermore, co-expression network analysis shows that the 13 NLR members were distributed in key nodes of differentially expressed genes which could be considered as promosing key regulators for the resistance of Valsa canker. Therefore, our findings provide a reference for the evolution of NLR genes in Rosaceae and the key regulators of Valsa canker resistance.

Keywords

• genome-wide analysis
• rosaceae
• expansion rate
• gene duplication
• gene expression