Systematic analysis of the expansin gene family in Nelumbo reveals candidate seed development responsive members in lotus (Nelumbo nucifera)

•Systematic identification and comparative analysis of 62 EXP genes in Nelumbo.•Segmental duplication as the main drivers of EXP gene family expansion in lotus.•Lotus EXP proteins were localized in the cell wall.•Expression profiling and co-expression analysis revealed the potential biological function of NnEXP genes.•NnEXPA2 positively regulates cell expansion in lotus seeds. Expansins (EXPs) are plant cell wall proteins that not only induce cell wall extension in a pH-dependent manner, but also regulate plant growth and development process, as well as stress tolerance. This study systematically analyzed the EXP gene family in Nelumbo, and 62 genes, including 29 and 33 members were identified in the N. nucifera and N. lutea genomes, respectively. These genes could be classified into four subfamilies, including α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB), with 40, 11, 5, and 6 members, respectively. Physicochemical analysis, motif structure, and chromosomal distribution of these genes were evaluated. Evolutionary analysis within or between the two Nelumbo genomes revealed strong purifying selection among the EXP genes, with segmental duplication emerging as the primary driver of the EXP gene family expansion in lotus. Moreover, synteny analysis conducted between lotus and other species has revealed that EXP genes exhibit varying evolutionary patterns across different plant species. Subcellular localization assay demonstrated that NnEXP proteins were localized in the cell wall. NnEXP gene expression analysis revealed that most members were expressed in at least one lotus tissue, and qRT-PCR indicated that some genes were differently expressed in lotus seeds at different developmental stages. Furthermore, the transient overexpression of NnEXPA2 has been demonstrated to enhance cell expansion during the early development of lotus seed cotyledons. This study not only forms a basis for functional characterization of lotus EXP genes, but also provides useful genetic resources for future lotus breeding.