AUTHOR=Zhao Mingqi , Haxim Yakupjan , Liang Yuqing , Qiao Siqi , Gao Bei , Zhang Daoyuan , Li Xiaoshuang 

TITLE=Genome-wide investigation of AP2/ERF gene family in the desert legume Eremosparton songoricum: Identification, classification, evolution, and expression profiling under drought stress

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.885694

DOI=10.3389/fpls.2022.885694

ISSN=1664-462X

ABSTRACT=<p><italic>Eremosparton songoricum</italic> (Litv.) Vass. is a rare leafless legume shrub endemic to central Asia which grows on bare sand. It shows extreme drought tolerance and is being developed as a model organism for investigating morphological, physiological, and molecular adaptations to harsh desert environments. APETALA2/Ethylene Responsive Factor (AP2/ERF) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, our knowledge on the AP2/ERF family in legume species is limited, and no respective study was conducted so far on the desert shrubby legume <italic>E. songoricum</italic>. Here, 153 <italic>AP2/ERF</italic> genes were identified based on the <italic>E. songoricum</italic> genome data. <italic>EsAP2/ERFs</italic> covered <italic>AP2</italic> (24 genes), <italic>DREB</italic> (59 genes), <italic>ERF</italic> (68 genes), and <italic>Soloist</italic> (2 genes) subfamilies, and lacked canonical <italic>RAV</italic> subfamily genes based on the widely used classification method. The <italic>DREB</italic> and <italic>ERF</italic> subfamilies were further divided into A1–A6 and B1–B6 groups, respectively. Protein motifs and exon-intron structures of <italic>EsAP2/ERFs</italic> were also examined, which matched the subfamily/group classification. <italic>Cis</italic>-acting element analysis suggested that <italic>EsAP2/ERF</italic> genes shared many stress- and hormone-related <italic>cis</italic>-regulatory elements. Moreover, the gene numbers and the ratio of each subfamily and the intron-exon structures were systematically compared with other model plants ranging from algae to angiosperms, including ten legumes. Our results supported the view that <italic>AP2</italic> and <italic>ERF</italic> evolved early and already existed in algae, whereas <italic>RAV</italic> and <italic>DREB</italic> began to appear in moss species. Almost all plant <italic>AP2</italic> and <italic>Soloist</italic> genes contained introns, whereas most <italic>DREB</italic> and <italic>ERF</italic> genes did not. The majority of <italic>EsAP2/ERFs</italic> were induced by drought stress based on RNA-seq data, <italic>EsDREBs</italic> were highly induced and had the largest number of differentially expressed genes in response to drought. Eight out of twelve representative <italic>EsAP2/ERFs</italic> were significantly up-regulated as assessed by RT-qPCR. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of <italic>AP2/ERF</italic> genes in <italic>E. songoricum</italic> and lays a foundation for better understanding of drought stress tolerance mechanisms in legume plants. Moreover, candidate genes for drought-resistant plant breeding are proposed.</p>