Genomics of the NB genes in cassava: from gene expression to integrative biology

Proteins containing the NB (Nucleotide Binding) domain are intracellular receptors or co-receptors that recognize proteins from microorganisms directly or indirectly. Plant genomes contain a variable number of NB genes, but the function of most of them remains unknown. Cassava is a crucial staple crop, and given its drought-tolerant nature, it is a promising crop for addressing climate change. Here, we describe the manual curation of 262 NB genes present in the cassava genome. The corresponding proteins were classified according to the presence of additional domains such as TIR (Toll Interleukin-1 Receptor) and/or LRR (Leucine Rich Repeat). The gene expression of these genes was evaluated using several transcriptomic experiments available in databases. Our analysis revealed that most NB genes are expressed at low or very low levels, with around 20% of them showing high expression values. The differential expression analysis detected 26 differentially expressed NB genes of which nine correspond to NB proteins lacking one or two motifs present in the NB domain. An integrative approach that took into account gene expression, polymorphisms level, and co-expression network metrics demonstrated that some NB proteins lacking certain motifs play important roles in the network structure, despite their low expression. On the other hand, the same analysis highlights the importance of complete NB proteins that showed higher levels of fold change. Several NB genes represent excellent candidates for further functional validation studies and/or breeding programs.