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The nuclear pore complex (NPC), comprised of individual nucleoporin (Nup) proteins, controls nucleo-cytoplasmic transport of RNA and protein, and is important for regulating plant growth and development. However, there are no reports on this complex in fruit tree species. In this study, we identified 38 apple Nups and named them based on the known  Arabidopsis thaliana  homologs. We also completed bioinformatics analyses of the intron and exon structural data for apple Nups. The proteins encoded by the apple Nups lacked a universally conserved domain. Moreover, a phylogenetic analysis separated the apple and  A. thaliana  Nups into three groups. The phylogenetic tree indicated that  MdNup54  and  MdNup62  are most closely related to genes in other Rosaceae species. To characterize the 38 candidate  Malus domestica  Nups, we measured their stage-specific expression levels. Our tests revealed these proteins were differentially expressed among diverse tissues. We analyzed the expression levels of seven apple Nups in response to an indole-3-acetic acid (IAA) treatment. The phytohormone treatment significantly inhibited apple flowering. A qRT-PCR analysis proved that an IAA treatment significantly inhibited the expression of these seven genes. A preliminary study regarding two members of the  Nup62  subcomplex,  MdNup54  and  MdNup62 , confirmed these two proteins can interact with each other. A yeast two-hybrid assay verified that  MdNup54  can interact with  MdKNAT4  and  MdKNAT6 . On the basis of the study results, we identified apple NPC and predicted its structure and function. The data generated in this investigation provide important reference material for follow-up research.

Genomic identification and expression analysis of nuclear pore proteins in Malus domestica