Genome-wide identification of PYL/PYR-PP2C (A)-SnRK2 genes in Eutrema and their co-expression analysis in response to ABA and abiotic stresses

ABA signaling core components PYR/PYL, group A PP2C and SnRK2 play important roles in various environmental stress responses of plants. This study identified 14 PYR/PYL, 9 PP2C (A), and 10 SnRK2 genes from halophytic Eutrema. Phylogenetic analysis showed 4 EsPYR/PYL, 4 EsPP2C (A) and 3 EsSnRK2 subfamilies characterized, which was supported by their gene structures and protein motifs. Large-scale segmental duplication event was demonstrated to be a major contributor to expansion of the EsPYL-PP2C (A)-SnRK2 gene families. Synteny relationship analysis revealed more orthologous PYL-PP2C (A)-SnRK2 gene pairs located in collinear blocks between Eutrema and Brassica than that between Eutrema and Arabidopsis. RNA-seq and qRT-PCR revealed EsABI1, EsABI2 and EsHAL2 showed a significantly up-regulated expression in leaves and roots in response to ABA, NaCl or cold stress. Three markedly co-expression modules of ABA/R-brown, NaCl/L-lightsteelblue1 and Cold/R-lightgreen were uncovered to contain EsPYL-PP2C (A)-SnRK2 genes by WGCNA analysis. GO and KEGG analysis indicated that the genes of ABA/R-brown module containing EsHAB1, EsHAI2 and EsSnRK2.6 were enriched in proteasome pathway. Further, EsHAI2-OE transgenic Arabidopsis lines showed significantly enhanced seeds germination and seedlings growth. This work provides a new insight for elucidating potential molecular functions of PYL-PP2C (A)-SnRK2 responding to ABA and abiotic stresses.

Automated summary

This study identified and classified 14 PYR/PYL genes, 9 PP2C (A) genes, and 10 SnRK2 genes from the halophytic plant Eutrema. The phylogenetic analysis and gene structure analysis supported the existence of 4 EsPYR/PYL, 4 EsPP2C (A), and 3 EsSnRK2 subfamilies. Furthermore, it was demonstrated that a large-scale segmental duplication event played a major role in the expansion of these gene families. Comparative synteny analysis revealed more orthologous gene pairs between Eutrema and Brassica than between Eutrema and Arabidopsis. RNA-seq and qRT-PCR experiments confirmed the up-regulated expression of several genes in response to ABA, NaCl, or cold stress. Additionally, WGCNA analysis uncovered several co-expression modules containing the PYL-PP2C (A)-SnRK2 genes, providing new insights into their potential molecular functions.