Genome-Wide Identification, Phylogenetic Evolution, and Abiotic Stress Response Analyses of the Late Embryogenesis Abundant Gene Family in the Alpine Cold-Tolerant Medicinal Notopterygium Species

Late embryogenesis abundant (LEA) proteins are a class of proteins associated with osmotic regulation and plant tolerance to abiotic stress. However, studies on the <i>LEA</i> gene family in the alpine cold-tolerant herb are still limited, and the phylogenetic evolution and biological functions of its family members remain unclear. In this study, we conducted genome-wide identification, phylogenetic evolution, and abiotic stress response analyses of <i>LEA</i> family genes in <i>Notopterygium</i> species, alpine cold-tolerant medicinal herbs in the Qinghai-Tibet Plateau and adjacent regions. The gene family identification analysis showed that 23, 20, and 20 <i>LEA</i> genes were identified in three <i>Notopterygium</i> species, <i>N. franchetii</i>, <i>N. incisum</i>, and <i>N. forrestii</i>, respectively. All of these genes can be classified into six LEA subfamilies: LEA_1, LEA_2, LEA_5, LEA_6, DHN (Dehydrin), and SMP (seed maturation protein). The LEA proteins in the three <i>Notopterygium</i> species exhibited significant variations in the number of amino acids, physical and chemical properties, subcellular localization, and secondary structure characteristics, primarily demonstrating high hydrophilicity, different stability, and specific subcellular distribution patterns. Meanwhile, we found that the members of the same LEA subfamily shared similar exon-intron structures and conserved motifs. Interestingly, the chromosome distributions of <i>LEA</i> genes in <i>Notopterygium</i> species were scattered. The results of the collinearity analysis indicate that the expansion of the <i>LEA</i> gene family is primarily driven by gene duplication. A <i>Ka/Ks</i> analysis showed that paralogous gene pairs were under negative selection in <i>Notopterygium</i> species. A promoter <i>cis</i>-acting element analysis showed that most <i>LEA</i> genes possessed multiple <i>cis</i>-elements connected to plant growth and development, stress response, and plant hormone signal transduction. An expression pattern analysis demonstrated the species-specific and tissue-specific expression of <i>NinLEAs</i>. Experiments on abiotic stress responses indicated that the <i>NinLEAs</i> play a crucial role in the response to high-temperature and drought stresses in <i>N. franchetii</i> leaves and roots. These results provide novel insights for further understanding the functions of the <i>LEA</i> gene family in the alpine cold-tolerant <i>Notopterygium</i> species and also offer a scientific basis for in-depth research on the abiotic stress response mechanisms and stress-resistant breeding.