Aquaporins (AQPs), a type of intrinsic membrane proteins that transport water and small solutes across biological membranes, play crucial roles in plant growth and development. This study presents a first genome-wide identification and comparative analysis of the AQP gene family in papaya (Carica papaya L.), an economically and nutritionally important fruit tree of tropical and subtropical regions. A total of 29 CpAQP genes were identified, which represent five subfamilies, i.e., nine plasma intrinsic membrane proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), seven NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). Although the family is smaller than the 35 members reported in Arabidopsis, it is highly diverse, and the presence of CpXIP genes as well as orthologs in Moringa oleifera and Bretschneidera sinensis implies that the complete loss of the XIP subfamily in Arabidopsis is lineage-specific, sometime after its split with papaya but before Brassicaceae–Cleomaceae divergence. Reciprocal best hit-based sequence comparison of 530 AQPs and synteny analyses revealed that CpAQP genes belong to 29 out of 61 identified orthogroups, and lineage-specific evolution was frequently observed in Brassicales. Significantly, the well-characterized NIP3 group was completely lost; lineage-specific loss of the NIP8 group in Brassicaceae occurred sometime before the divergence with Cleomaceae, and lineage-specific loss of NIP2 and SIP3 groups in Brassicaceae occurred sometime after the split with Cleomaceae. In contrast to a predominant role of recent whole-genome duplications (WGDs) on the family expansion in B. sinensis, Tarenaya hassleriana, and Brassicaceae plants, no recent AQP repeats were identified in papaya, and ancient WGD repeats are mainly confined to the PIP subfamily. Subfamily even group-specific evolution was uncovered via comparing exon–intron structures, conserved motifs, the aromatic/arginine selectivity filter, and gene expression profiles. Moreover, down-regulation during fruit ripening and expression divergence of duplicated CpAQP genes were frequently observed in papaya. These findings will not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further studies of AQP genes in papaya and species beyond.

Pearl bodies are small, pearl-like structures found on the surfaces of many tropical and subtropical plant species, including Carica papaya L., that serve as a nutritious food source for arthropods, helping plants defend against herbivores. This study investigated the role of pearl bodies in viral accumulation and transmission, focusing on papaya plants infected with papaya leaf distortion mosaic virus (PLDMV), a destructive pathogen threatening papaya production. Viral analysis of pearl bodies from PLDMV-infected plants confirmed the presence of viral particles, genomic RNA, and coat protein, with quantitative real-time reverse transcriptase PCR showing significant viral RNA accumulation. These findings suggest that pearl bodies act as reservoirs for PLDMV. Infectivity tests demonstrated that ruptured pearl bodies from infected plants effectively transmitted PLDMV to healthy plants via mechanical inoculation. The fragility of stalks and cell surfaces of pearl bodies facilitates their detachment or rupture during mechanical activities, potentially releasing virus-laden contents into the environment. This poses a significant risk of contamination for agricultural tools, equipment, and personnel, contributing to secondary transmission. This study emphasizes the importance of recognizing pearl bodies as an overlooked source of viral spread, highlighting the need for careful handling and targeted management strategies to reduce virus transmission risks in papaya cultivation. This is the first report of pearl bodies’ involvement in virus transmission, which provides novel insights into virus epidemiology and disease management in papaya cultivation and other crops with pearl bodies.