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

Abstract BackgroundEarly 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.ResultsWe 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.ConclusionsThis 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.