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Background  Viruses in the genus  Begomovirus  (Family  Geminiviridae ) include many important economic plant viruses transmitted by whiteflies of the  Bemisia tabaci  species complex. In general, different begomoviruses may be acquired and transmitted by the same whitefly species with different efficiencies. For example, the species Mediterranean (MED) in this whitefly species complex transmits tomato yellow leaf curl virus (TYLCV) at a higher efficiency than papaya leaf curl China virus (PaLCuCNV). However, the proteomic responses of whitefly to the infection of different begomoviruses remain largely unknown.    Methods  We used iTRAQ-based proteomics coupled with RT-qPCR to investigate and compare responses of the MED whitefly to the infection of TYLCV and PaLCuCNV.    Results  Totally, 259, 395 and 74 differently expressed proteins (DEPs) were identified in the comparisons of TYLCV-infected vs. un-infected, PaLCuCNV-infected vs. un-infected, and TYLCV-infected vs. PaLCuCNV-infected whiteflies, respectively. These proteins appear associated with catabolic process, metabolic process, transport, defense response, cell cycle, and receptor. The comparisons of TYLCV-infected vs. un-infected and PaLCuCNV-infected vs. un-infected shared some similar DEPs, indicating possible involvement of laminin subunit alpha, dystroglycan, integrin alpha-PS2 and cuticle proteins in viral transport as well as the role of putative defense proteins 3 and PITH in anti-viral response. However, 20S proteasome subunits associated with regulation of virus degradation and accumulation were up-regulated in PaLCuCNV-infected but not in TYLCV-infected whiteflies, which may be related to the constraints of PaLCuCNV accumulation in MED.    Conclusions  These findings provide valuable clues for unravelling the roles of some whitefly proteins in begomovirus transmission.    Electronic supplementary material  The online version of this article (10.1186/s12985-019-1138-4) contains supplementary material, which is available to authorized users.

Comparative proteomic analysis provides new insight into differential transmission of two begomoviruses by a whitefly