Correlation and expression pattern analyses of immune receptor genes in cotton

To investigate the correlation of cell-surface and intracellular immune receptor genes, 29 cotton tribe species that include 28 Gossypium species and Gossypium sister genus Gossypioides kirkii were selected to identify the PRR (LRR-RLK and LysM-RLK) and NLR (NB-ARC) protein gene families. In total, we identified 10,654 LRR-RLKs, 374 LysM-RLKs, and 9,524 NB-ARCs from 29 cotton tribe species. Compared to A. thaliana, almost all the cotton tribe species showed a slight expansion of the LysM-RLK family, but Gossypium D group species had a significant expansion of the LRR-RLK family. Among them, the LRR-RLK-I subfamily showed dramatic contraction, while two LRR-RLK (XI-1 and XII) subfamilies exhibited significant expansion in Gossypieae species. In addition, %LRR-RLKs showed a strong positive linear correlation (Pearson’s r = 0.8363), but %LysM-RLKs showed no correlation with %NB-ARC (Pearson’s r = -0.1837). Two subfamilies, LRR-RLK-VIII_2 and LRR-RLK-XII, formed the two most positive correlations with %NB-ARCs (Pearson’s r = 0.8156 and 0.7485), indicating that LRR-RLK-VIII_2 and LRR-RLK-XII gene families co-expand or co-contract with NB-ARC gene families in Gossypieae species. In addition, members of LRR-RLK-VIII_2, LRR-RLK-XII, LysM-RLK and NB-ARC family genes showed high expression levels in the leaves or roots of Upland cotton and Sea Island cotton based on the transcriptome data. The low correlations of the expression levels between root and leaf in LRR-RLK-VIII_2 and LRR-RLK-XII family genes indicated that LRR-RLK genes may be involved in the local immune response process in cotton. On the contrary, the high correlations of expression levels between root and leaf tissues in LysM-RLK and NB-ARC family genes suggested they might be involved in global immune response. Our results provided new insights into correlation and expression pattern analyses and narrowed the range of immune receptor genes that may be involved in pathogen recognition in cotton plants.