Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis

Abstract

Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.

Genome-wide identification and expression analysis of ARF gene family in embryonic development of Korean pine (Pinus koraiensis)

“…The ARF gene was initially identified to have 23 members in the model plant Arabidopsis and has since been identified in multiple species [ 5 ]. Rice has 25 ARF members [ 11 ], apple ( Malus domestica ) has 31 ARF members [ 55 ], silver birch ( Betula pendula ) has 17 members [ 56 ], birch ( Betula platyphylla ) has 15 members [ 57 ], Euscaphis konishii has 29 members [ 26 ], and Populus has 35 members [ 12 ]. However, the ARF gene has not yet been identified in Korean pine.…”

“…MdARF13 interacts with MdIAA121 to regulate anthocyanin biosynthesis during apple fruit ripening [ 25 ]. In addition, EkARF5.1 directly interacts with auxin response elements to regulate anthocyanin synthesis during fruit ripening in Euscaphis konishii [ 26 ]. In the case of Populus, the nuclear interaction between PtrARF23 and PtrIAA10, as well as PtrIAA28, is responsible for regulating wood formation [ 12 ].…”

Comprehensive analyses of the ARF gene family in cannabis reveals their potential roles in regulating cannabidiol biosynthesis and male flower development

“…The ARF gene family plays an important role in regulating flower development and secondary metabolite production and has been studied in many plant species, including Arabidopsis ( Okushima et al., 2005 ), rice ( Wang et al., 2007 ), Euscaphis konishii ( Liu et al., 2022 ), and maize ( Xing et al., 2011 ). However, a comprehensive investigation of the ARF gene in cannabis has not yet been conducted.…”

“…been studied in many plant species, including Arabidopsis (Okushima et al, 2005), rice (Wang et al, 2007), Euscaphis konishii (Liu et al, 2022), and maize (Xing et al, 2011). However, a comprehensive investigation of the ARF gene in cannabis has not yet been conducted.…”

Genome-Wide Identification and Expression Analysis of Auxin Response Factor (ARF) Gene Family in Panax ginseng Indicates Its Possible Roles in Root Development

“…In this study, 11 PgARF proteins do not contain CTD, namely PgARF2, PgARF6, PgARF9, PgARF15, PgARF20, PgARF32, PgARF39, PgARF46, PgARF48, PgARF52, and PgARF53, and the proportion of PgARFs (20.75%) with a CTD truncation was much lower than that of MtARFs (54%). CTD-truncated MtARFs in Medicago truncatula provide evidence for the auxin-independent regulation of ARF genes [38]. Therefore, it is speculated that these CTD-truncated PgARFs may also regulate plant life activities in an auxin-independent pathway.…”