AUTHOR=Liu Bobin , Zhu Juanli , Lin Lina , Yang Qixin , Hu Bangping , Wang Qingying , Zou Xiao-Xing , Zou Shuang-Quan 

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

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.737293

DOI=10.3389/fgene.2021.737293

ISSN=1664-8021

ABSTRACT=<p><italic>Euscaphis konishii</italic> is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving <italic>E</italic>. <italic>konishii</italic> 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. <italic>Aux/IAA</italic> and <italic>ARF</italic> genes have been described in many plants but have not yet been described in <italic>E. konishii</italic>. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the <italic>E. konishii</italic> genome through database searching using HMMER. We also performed a bioinformatic characterization of <italic>EkIAA</italic> and <italic>EkARF</italic> genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and <italic>cis</italic>-element analysis, as well as conserved motifs in the proteins. Our results suggest that <italic>EkIAA</italic> and <italic>EkARF</italic> genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of <italic>EkIAA</italic> and <italic>EkARF</italic> genes in leaves, branches, and fruits, which identified a subset of seven <italic>EkARF</italic> 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 <italic>EkIAA</italic> and <italic>EkARF</italic> gene families in <italic>E. konishii</italic>, laying a foundation for further research on high-yielding industrial products and <italic>E. konishii</italic> breeding.</p>