Cell wall lignification may be necessary for somatic embryogenesis of areca palm (Areca catechu)

• PER39 and PER3–1 (lignin biosynthesis) expression increased (FC ≥ 2.5) in SE. • Most up-regulated transcription factors are lignin biosynthesis regulators. • Phenolic acids (lignin precursor) were preferably accumulated in SE. • Lignin and arabinogalactan proteins (AGPs) are highly accumulated in vascular of SE. • Cell wall lignification of vascular is a critical step for somatic embryo formation. Areca palm ( Areca catechu ) is the biggest horticultural crop and the fruits are major income for more than 2 million farmers in Hainan province of China. As the increasing of areca nut prices and the threat of lethal yellowing disease, tissue culture seedlings is becoming an alternative choice for elite high yielding and disease resistant planting materials. However, relatively low somatic embryogenesis rate will limit the clonal products, while mechanisms underlying somatic embryogenesis of areca palm remains unclear so far. To this regard, we established the tissue culture system and analyzed transcrptomic changes during transition from embryogenic callus (EC) to somatic embryos (SE). Results showed that peroxidases ( PER39 and PER3–1 ), which were crucial to the last step for lignin biosynthesis in phenylpropanoid biosynthesis pathway, increased significantly (FC ≥ 2.5, p ≤ 0.001). Many hydroxyproline rich glycoproteins (HRGPs), including arabinogalactan proteins (AGPs), extensins (EXTs) and proline rich proteins (PRPs), were also highly expressed (FPKM ≥ 100) in SE. Gene co-expression network analysis showed the correlation of PERs with HRGPs and phytohormone signaling genes, of which, FLA7–1, FLA7–2 (AGPs) and EXT2–1 (EXTs) were involved in cell wall related GO process. Furthermore, mmajority of identified up-regulated transcription factors (TFs) are well-known lignin biosynthesis regulators such as basic helix-loop-helix (bHLH), and homeobox-leucine zipper (HOX) families. These TFs showed high correlations with PERs and HRGPs. Moreover, staining and microscopic observation showed that phenolic acids (precursor of lignin biosynthesis) were preferably accumulated in SE, high accumulation of lignin and AGPs was also observed in vascular of SE, suggesting that cell wall lignification of vascular may be a key step for somatic embryogenesis, and AGPs could also contribute during the process.