Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites

Abstract

Background: ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relatively high economic and nutritional value, and they are specifically found in Capsicum. However, there is little understanding of how ERFs participate in the regulatory networks of capsorubin and capsaicinoids biosynthesis. Results: In this study, a total of 142 ERFs were identified in the Capsicum annuum genome. Subsequent phylogenetic analysis allowed us to divide ERFs into DREB (dehydration responsive element binding proteins) and ERF subfamilies, and further classify them into 11 groups with several subgroups. Expression analysis of biosynthetic pathway genes and CaERFs facilitated the identification of candidate genes related to the regulation of capsorubin and capsaicinoids biosynthesis; the candidates were focused in cluster C9 and cluster C10, as well as cluster L3 and cluster L4, respectively. The expression patterns of CaERF82, CaERF97, CaERF66, CaERF107 and CaERF101, which were found in cluster C9 and cluster C10, were consistent with those of accumulating of carotenoids (β-carotene, zeaxanthin and capsorubin) in the pericarp. In cluster L3 and cluster L4, the expression patterns of CaERF102, CaERF53, CaERF111 and CaERF92 were similar to those of the accumulating capsaicinoids. Furthermore, CaERF92, CaERF102 and CaERF111 were found to be potentially involved in temperature-mediated capsaicinoids biosynthesis. Conclusion: This study will provide an extremely useful foundation for the study of candidate ERFs in the regulation of carotenoids and capsaicinoids biosynthesis in peppers.

Genome-wide identification of the Capsicum bHLH transcription factor family: discovery of a candidate regulator involved in the regulation of species-specific bioactive metabolites

“…Phenotypes and the contents of β-carotene, zeaxanthin. lutein and capsorubin at four developmental pericarp stages, namely, the mature green (MG), breaker (B), breaker plus 7 days (B + 7) and breaker plus 14 days (B + 14) stages [ 34 ]. b .…”

“…a . Phenotypes (up) and the content of capsaicin and dihydrocapsaicin (down) at seven developmental placental stages, including 10, 13, 16, 25, 33, 39 and 45 DPA stages [ 34 ]. b .…”

“…a . The content of capsaicin and dihydrocapsaicin in response to different temperatures [ 34 ]. b .…”

“…4 ). Numerous studies have reported that MYC2 typically regulated alkaloid biosynthesis by interacting with ERF TFs [ 41 – 43 ], and ERF TFs were associated with capsaicinoid biosynthesis in Capsicum [ 34 , 71 ]. MYC2 was mapped to two homologous genes CabHLH006 and CabHLH018 that were classified into clusters L8 and L7, respectively.…”

“…The bHLH TFs have been identified in the majority of plants, including Arabidopsis thaliana , rice, and potato [ 15 , 21 – 30 ]. WRKY, NAC and APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) TF families have been analysed systematically in peppers [ 31 – 34 ]. The bHLH TFs are closely related to the primary and specialized metabolites of the plant.…”