Proteome profiles of two Eucalyptus species during the early stage of somatic embryogenesis

Background: Early somatic embryogenesis (SE) has been recognized as an important tool for plants to propagate in vitro . However, our knowledge about the proteins involved in early SE including the callus dedifferentiation is still limited, especially in the economic woody tree – Eucalyptus. Results: We performed the data-independent acquisition (DIA) mass-spectrometry (MS) to study the proteins involved in early SE of two Eucalyptus species - E. camaldulensis (high regeneratively potential) and E. grandis x urophylla (low regenerative potential). Initially, the data-dependent acquisition MS produced 44,451 peptides and 9,142 proteins. While the DIA MS identified 35,207 peptides and 7,077 proteins in the stem and tissue-culture induced callus of the two Eucalyptus species. MSstat identified 2,078 and 2,807 differentially expressed proteins (DEPs) in early SE of E. camaldulensis and E. grandis x urophylla , respectively. They shared 760 upregulated and 420 downregulated proteins, including 4 transcription factors, 31 ribosomal proteins, 1 histone, 3 zinc finger proteins (ZFPs), ARF19, WOX8 and PIN1. Further, 27 and 4 DEPs were found to be involved in “photosynthesis” (ko00195) and “two-component system” (ko02020), respectively. Notably, SERK, WRKY, ZFP and ABC transporter proteins were analyzed to be related with high SE potential. By combining the miRNA and RNA-Seq results, some miRNA-mRNA/protein regulation networks might be involved in early SE of Eucalyptus, like miR160~TPP2, miR164~UXS2, miR169~COX11 and miR535~ Eucgr.E01067. Conclusions: This is the first study of proteome profiles in early SE of Eucalyptus. The findings will improve our understanding of molecular changes and regulatory networks in early SE of Eucalyptus.