Genome-Wide Identification and Codon Bias of NBS-LRR Gene Family in Banana

Abstract As the largest family of plant resistance (R) proteins, nucleotide binding site-leucine-rich repeat ( NBS-LRR ) proteins play an important role in pathogen defense. In order to identify and get the codon usage bias of NBS-LRR gene family in banana. Using software MEGA11, TBtools and CodonW to analyze the codon preference and its influencing factors on genome-wide data from banana. The 74 NBS-LRR genes were divided into 6 subfamilies, 5 conserved motifs and 14 domains were identified. The more similar domain structures in the same phylogenetic tree subfamily and less consistent structures between different subfamilies. It was also found that when the G/C base appears at the third position of the codon, it had a higher usage rate. We identified 16 codons, including UCC and CCC, as the optimal codons. All of the 16 optimal codons ended with G or C, which indicated that the banana genome NBS-LRR gene prefers to use G or C terminated codons. Most of the gene points in the GC3s-ENC distribution map fell near the expected curve, mutation and natural selection during gene expression affected codon selection. The results of PR2-plot showed that most of the genes fell on the upper right side of the plane, and neutrality plot result showed that there was not significant correlation between C12 and GC3, which indicated the main factor of codon preference was natural selection. The results provide scientific basis for codon optimization of exogenous genes and improvement of their expression efficiency.