Phenylalanine ammonia lyase (PAL) is the first enzyme in the phenylpropanoid pathway and plays a critical role in plant growth, development and stress defence. However, there have been few reports of the PAL gene family in lucerne (also known as alfalfa, Medicago sativa L.), one of the most important forage legume species worldwide. In this study, we report that PAL in lucerne is encoded by a family of seven genes: MsPAL1–MsPAL7. Furthermore, a comprehensive genome-wide bioinformatics analysis of the MsPAL gene family is presented, including chromosomal locations, phylogenetic relationships, gene structures and conserved motifs. The cis-elements and potential biological functions of these genes were investigated, revealing the potential roles of MsPAL members in response to various stresses. RT-qPCR results showed that the expression of MsPAL6 was significantly upregulated under both salinity- and waterlogging-stress conditions. Other MsPAL members such as MsPAL1 and MsPAL2 were downregulated under saline conditions and upregulated significantly after waterlogging stress. Our findings provide useful information for further practical analyses and for the genetic improvement of abiotic stress tolerance of lucerne.

The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein–protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.