Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L.

Abstract

Auxin participates in various physiological and molecular response-related developmental processes and is a pivotal hormone that regulates phenotypic formation in plants. Auxin response factors (ARFs) are vital transcription factors that mediate downstream auxin signaling by explicitly binding to auxin-responsive genes’ promoters. Here, to investigate the possible developmental regulatory functions of ARFs in Ginkgo biloba, through employing comprehensive bioinformatics, we recognized 15 putative GbARF members. Conserved domains and motifs, gene and protein structure, gene duplication, GO enrichment, transcriptome expression profiles, and qRT-PCR all showed that Group I and III members were highly conserved. Among them, GbARF10b and GbARF10a were revealed as transcriptional activators in the auxin response for the development of Ginkgo male flowers through sequences alignment, cis-elements analysis and GO annotation；the results were corroborated for the treatment of exogenous SA. Moreover, the GbARFs expansion occurred predominantly by segmental duplication, and most GbARFs have undergone purifying selection. The Ka/Ks ratio test identified the functional consistence of GbARF2a and GbARF2c, GbARF10b, and GbARF10a in tissue expression profiles and male flower development. In summary, our study established a new research basis for exploring Ginkgo GbARF members’ roles in floral organ development and hormone response.

Protoplast isolation and transient transformation system for Ginkgo biloba L.

“…Many omics studies have been conducted to better understand this species; however, the extensive amount of genetic information generated through these efforts has not yet been deeply explored and verified, mainly because a transformation system for this species has not been developed. Although many researchers have carried out studies on callus culture (Zhang, 2003) and embryoid induction (Guo, 2004) in ginkgo, there has still been no effective transformation technology developed for the functional verification of ginkgo genes. As a result, the current genetic research on ginkgo relies on the transformation of heterologous plants (Su et al, 2020;Xin et al, 2021), thereby posing many limitations in interpretation and practice due to the unreliability of distant kin.…”

“…First, the unique evolutionary status of ginkgo augments the difficulty of bioinformatics prediction. Second, despite many generations of research, there is still no effective stable genetic transformation system for ginkgo (Dupréet al, 2000;Zhang, 2003;Guo, 2004). To date, ginkgo gene research has mainly been carried out based on heterologous transformation, limiting the depth and accuracy of gene function studies (Wu et al, 2020;Xin et al, 2021).…”

Genome-Wide Identification of Expansin Gene Family and Their Response under Hormone Exposure in Ginkgo biloba L.

“…Fastq files of RNA-sequencing (RNA-seq) in different tissues, including buds, staminate, and ovulate strobili (PRJNA289172); root (PRJNA373812); stem (PRJNA473396); cambium (PRJNA488475); developing leaves (PRJNA473396, PRJNA517218, and PRJNA578374); fruits (PRJNA473396); and developing kernels (PRJNA292849), were searched with the accession numbers and downloaded from the EMBL-EBI ( , accessed on 18 October 2021) database, as well as the data under treatments of exogenous methyl jasmonate (MeJA) (PRJNA553587), salicylic acid (SA) (PRJNA598887), UV-B (PRJNA595103), and drought exposure (PRJNA604486) from a published study [ 55 ]. Raw data were filtered using Trimmomatic [ 56 ], and then FastQC evaluation was conducted for high-quality data [ 57 ], clean reads were mapped to genome with STAR [ 58 ], the transcript abundance was calculated as transcripts per million (TPM) value with RSEM [ 59 ], and TPM was converted into log2(TPM + 1) values with Micosoft excel 2010 (accessed on 20 April 2020) to draw heatmaps by TBtools [ 54 ].…”

“…PRJCA010326). The RNA-seq data of spraying exogenous salicylic acid (SA) were obtained from our previous study [ 55 ].…”

Identification of ARF genes in Cucurbita pepo L and analysis of expression patterns, and functional analysis of CpARF22 under drought, salt stress

“…Maize has 35 gene members and 23 of 35 ZmARF proteins containing domains III and IV, also observed at the C-terminus of Aux/IAA [ 8 ]. There are 15 GbARF members in Ginkgo biloba , of which GbARF10b and GbARF10a revealed transcriptional activators in auxin responses in male flower development [ 9 ]. 22 members of the gene family were identified in tomato, and eight SlARF genes were identified as repressors, five of which were activators [ 10 ].…”