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Article

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

by
Fangyun Guo
1,2,
Wulai Xiong
1,2,
Jing Guo
1,2 and
Guibin Wang
1,2,*
1
College of Forestry, Nanjing Forestry University, Nanjing 210037, China
2
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2022, 23(12), 6754; https://doi.org/10.3390/ijms23126754
Submission received: 5 May 2022 / Revised: 4 June 2022 / Accepted: 14 June 2022 / Published: 17 June 2022
(This article belongs to the Section Molecular Plant Sciences)
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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.

1. Introduction

Auxin, the first and most abundant plant hormone discovered to be involved in growth and development, has been systematically studied in the developmental stages of different tissues and organs [1,2]. Indole-3-acetic acid (IAA) is a typical representative of auxin and is often found in rapidly developing organs, such as young stems and leaves, flowering organs, and seeds, as it mediates growth and, ultimately, determines the morphology of actively dividing and highly differentiated organs [3]. In this process, auxin response pathway regulates cell division, elongation, and differentiation, determining plants’ phenotypic characteristics and maintaining their growth [4]. Thus, auxin mediates organ differentiation, tissue development and growth rate at a macro level and contributes to their adaptation to dynamic environmental conditions [5].
The AUX/IAA protein, which encodes a primary auxin response gene, acts as a repressor of the auxin-responsive response that can be rapidly induced by auxin without generating an inducible protein that mediates the auxin signal initiation [4]. AUX/IAA acts on its own or forms a dimer with auxin response factors (ARFs) to inhibit auxin function, and this inhibition depends on the level of auxin distributed within the organ tissue [1]. ARFs constitute the foundation of auxin function, as ARFs contain a B3 domain that specifically binds to auxin-responsive elements; an ARF domain, which is related to transcriptional activation or to the repression of auxin-responsive genes; and a CTD domain that directly binds to AUX/IAA. These three domains are located in the N-terminal, the middle, and C-terminal of ARF proteins, respectively [6]. When the auxin level is high in plants, the transcriptional activity of auxin-responsive genes is activated by the ARFs, triggering an auxin response [7]. Conversely, ARFs bind directly to AUX/IAA to form dimers, which then bind to transcriptional repressors that prevent binding to the target gene, resulting in transcriptional inhibition of auxin response genes [1,8].
Arabidopsis is the most comprehensively and intensively studied model plant species with respect to the ARF family, which contains 23 members. Several of the ARF family members, such as AtARF1 and AtARF2 [9], AtARF6 and AtARF8 [10], and AtARF7 and AtARF19 [11], have been studied via mutant experiments, providing immense references for additional ARF family studies in other species. Subsequently, studies on ARFs in rice [12], tomatoes [13], and cotton [14] have advanced. However, with the exception of studies in poplar [15], apricots [16], apples [17], peaches [18], and eucalyptus [19], ARFs in woody plant species and other economically important tree species with relatively larger genomes have received less attention due to genomic resource barriers.
Ginkgo biloba is a typical gymnosperm of substantial economic value and is used for foliage, timber, and fruit production. There is only one species of Ginkgo in this Ginkgo genus, reflecting its unique botanical taxonomic status. Additionally, G. biloba is a relict plant and is dubbed as “the living fossil”, having existed for over 100 million years, which reflects its long and complex evolutionary history [20,21]. With the completion of the species genome sequence, it is no longer difficult to analyze and identify genes that play an important role in its survival, growth, development, and adaptation to dynamic environments [22]. In this study, 15 GbARF members were identified and analyzed based on the newly released Ginkgo genome, with references to other species’ sequences. The phylogenetic relationship, gene and protein structure, protein interaction networks, transcriptional and qRT-PCR profiling in tissues, and the gene ontology (GO) annotation were investigated to understand the regulatory roles of GbARFs. Through molecular cloning, relative expression analysis of the Ginkgo flower, and the test of responding to exogenous salicylic acid (SA), we identified and verified some candidate GbARFs that are involved in Gingko flower development and stimulation of SA, which provides a new foundation to further study the function of certain GbARFs in the Ginkgo flower development and in its responses to exogenous hormones.

2. Results

2.1. Identification of GbARF Proteins

A local BLAST search was performed to identify the ARF proteins in Ginkgo, and a total of 35 putative GbARF family members were identified. These 35 gene sequences were verified via the Conserved Domain Database (CDD) on the NCBI website, and 20 members without all three conserved domains (AUX_RESP, AUX/IAA andB3) were removed (Table 1). The genes were designated according to their phylogenetic relationship with Arabidopsis AtARFs (Table 1) [23]. The deduced full open reading frames (ORFs) ranged from 891 (GbARF6a) to 3834 bp (GbARF2a), with an average of 2665 bp. The putative protein sequences ranged from 296 (GbARF6a) to 1277 (GbARF2a) amino acid(aa). The predicted molecular weights (MW) varied from 33,086.80 (GbARF6a) to 141,221.98 Da (GbARF2a), and the isoelectric points (pI) varied from 5.46 (GbARF3) to 8.89 (GbARF6a). The grand average of the hydropathicity (GRAVY) values were all negative, indicating that these GbARF proteins were hydrophilic. Eleven of them were located in the nucleus, whereas GbARF2a, GbARF6a, GbARF2b, and GbARF4b were located in the plasma membrane, extracellular space, and the chloroplast, respectively.

2.2. Phylogenetic Analysis

A phylogenetic tree was constructed comprising 23 identified ARF protein sequences from Arabidopsis thaliana, 37 from Populus trichocarpa, 31 from Malus domestica, and 8 from Picea abies (Figure 1). In reference to the evolutionary classification of ARFs in Malus domestica [17] and Arabidopsis thaliana [24], the ARF members in five species were divided into five Groups. The Ginkgo ARF members were distributed in Groups I–III. Group II contained eight members, which was the largest of the three Groups, while Group I and III contained three and four members, respectively. These seven members as well as GbARF3 and GbARF4b in Group II and the eight ARFs of Picea abies were on adjacent branches, indicating that the two gymnosperms are, phylogenetically, the most closely related. Moreover, the GbARFs being concentrated in Group III, indicated that duplication events may have occurred during the expansion of the GbARFs in the evolution of the Ginkgo genome.

2.3. Domain, Motif Identification, and Gene Structure Analysis

To further verify the conserved domains of the GbARF proteins, multiple sequence alignments were performed by DNAMAN 6.0 software (Figure 2). The results showed that, similar to the ARF proteins in other species [15,16,17], all GbARFs contained two conserved domains, DBD and ARF, which comprised more than 100 amino acids, respectively. Interestingly, Group I comprised GbARF10a, GbARF10b, and GbARF10c, and all of them contained QSL-rich regions, suggesting that they might act as activators to mediate AUX/IAA expression [25]. The other proteins had GSL-rich regions, suggesting that these GbARFs have suppressive properties [25]. A CTD domain was present in the remaining proteins, except for GbARF6a and GbARF4b, which may imply that these two genes function independently of auxin-responsive genes [18]. In the motif analysis, we found that all GbARF members had motif 1 and motif 2, at the N-terminus (Figure 3b), both of which are associated with DNA binding. The remaining members contained at least ten conserved motifs, while GbARF6a and GbARF4b had eight and nine motifs, respectively.
Overall, the distribution patterns (numbers and distribution position) of the motifs, exons, and introns for all the proteins were highly similar to their corresponding phylogenetic relationships (Figure 3a). For example, GbARF1, GbARF2a, GbARF2b, and GbARF2c all belong to Group III, these GbARFs had 4–22 exons and 13–21 introns; while GbARF10b, GbARF10c, and GbARF10a all belong to Group I, they had 3–4 exons and 2–3 introns (Figure 3c). The most visible was that the GbARFs with the blue background were members of Group Ⅱ, generally, the total lengths of their introns were much longer than those of the exons (Figure 3a,c), and the exon regions tended to be distributed at the beginning and end of the exon-intron sequences. These GbARFs exon–intron lengths were larger than those of the seven genes in Group I and III. These results indicated that the GbARFs were highly conserved within a single Group, which will help to further analyze their phylogenetic relationships and their regulatory function in developmental and environmental responses [26].

2.4. Analysis of cis-Elements in the Promoter of GbARFs

To better understand GbARFs functions and the probable regulatory pathways among them, an analysis of cis-acting elements in the promoters was conducted. The results showed that GbARFs contained a total of 33 cis-acting elements, all of them could be broadly clustered into the following three categories: biotic and abiotic stress response, plant development and promoter binding, and response to hormone induction (Figure 3d).
Among these elements, CAAT-box and TATA-box, two elements that bind to proteins, accounted for the highest proportion of all the elements in GbARFs. Except for GbARF6a and GbARF8, all the remaining genes in this family contained anaerobic-response elements (AREs), suggesting that most genes might play a role in the oxygen deprivation signaling response. Notably, 13 elements related to drought response, namely, MBSs, can bind with MYBs in response to the drought stress [27] and were present in the GbARF19b promoter, suggesting that GbARF19b might play a specific role in drought response. There were also elements identified that were related to meristem expression, and CAT-boxes were present in eleven of GbARFs’ promoters. Moreover, with the exception of GbARF6a, all the remaining genes contained TGACG or CGTCA motifs, showing a certain MeJA response for most genes. Abscisic acid response elements (ABREs) were present in 11 genes’ promoters, excluding GbARF2b, GbARF6a, GbARF19b, and GbARF4b, and this was the second most abundant element involved in hormone responses in the GbARFs.

2.5. Protein Tertiary Structure and Interaction Network Analysis

The GbARF proteins tertiary structures were predicted using sequences with more than 45% identity as templates, the results showed that all of the proteins mainly contained random coils (48.31–60.65%), alpha helixes (17.06–35.04%) and extended strands (13.89–23.50%) as part of their secondary structure (Table S3). The tertiary structures of GbARF10b, GbARF10c, and GbARF10a (belonging to Group I) were similar, as were those of GbARF1, GbARF2a, GbARF2b, and GbARF2c (belonging to Group III), while little consistency was found among the Group II members. These similarities and differences may imply the functional redundancy and divergence of GbARFs (Figure S1).
After the protein structure analysis, the orthologous ARF proteins in Arabidopsis were selected to further analyze the possible interaction networks to infer the biological function of the GbARFs in auxin signaling (Table S4). ARF4 (ortholog of GbARF4a), ARF6 (ortholog of GbARF19a), and ARF10 (ortholog of GbARF10a) all interact with MP and NPH4 (orthologs of GbARF19b) by encoding transcriptional receptors. These genes jointly participate in the modulation of auxin-dependent differential growth in Arabidopsis [28]. ARF10 is also involved in root cap development [29] and TIR1 has been shown to mediate the degradation of Aux/IAA transcriptional repressor proteins and regulate the development of leaves [29]. ARF8 (GbARF6a and GbARF8 orthologue) is a transcriptional activator of auxin gene expression that regulates stamen and gynoecium maturation by sensing auxin concentration [10] and interacts with BPEp and SHY2. BPEp is involved in the regulation of petal development, SHY2 functions as a repressor of early auxin response genes at a slow synthesis rate of IAA and is involved in root growth [10,29]. ARF2 (GbARF4b and GbARF4a orthologue) controls leaf senescence and floral organ abscission in Arabidopsis [9] (Figure 4c). Therefore, these GbARFs might function as their orthologs do in Aux/IAA transcription (Figure S2).

2.6. Chromosomal Location and Collinearity Analysis

The 15 GbARFs were unevenly distributed across 9 of the 12 Ginkgo chromosomes (Figure 4a). Three genes were located on chromosomes 5 and 10, separately, and only one was located on each of chromosomes 1, 3, 4, 6, and 7, respectively. A collinearity analysis showed a total of 7 fragmental duplication gene pairs were present on seven chromosomes (Figure 4b), among which, chromosomes 4 and 8 contained the most abundant duplicated pairs. The nonsynonymous substitution and the synonymous substitution (Ka/Ks) ratio of the GbARF pairs showed that only GbARF3 and GbARF1 were >1 (Table 2), while the remaining gene pairs were < 1, implying that segmental duplication is the main reason for the GbARF family’s expansion and that GbARF3 and GbARF1 have been subjected to positive selection pressure during the GbARFs evolution. These two genes may contribute to Ginkgo’s adaptation to various environmental conditions [30,31]. Additionally, the Ka/Ks values of four paralogous pairs (GbARF1 and GbARF2a; GbARF2a and GbARF19b; GbARF2c and GbARF19b; GbARF3 and GbARF10c) were >0.3, suggesting the possibility of functional divergence through duplication events [32]. Two paralogous pairs (GbARF2a and GbARF2c; GbARF10b and GbARF10a) had Ka/Ks values of <0.3, suggesting that their functions are conserved among paralogs [32]. Overall, those paralogous pairs whose Ka/Ks values were <1 reflect a stable evolutionary process because of the effect of the purifying selection.

2.7. GO Annotation of GbARF Family

GO enrichment showed that all GbARFs were annotated to three broad term categories, including biological process, molecular function, and cellular component (Table S6). Each gene was annotated to the auxin-activated signaling pathway term in the biological process (Figure 5), demonstrating the accuracy of our GbARF family identification. Six genes (GbARF10b, 10c, 10a, 6b, 2a, and 2b), were annotated to be involved in floral organ development (sepal, petal, and ovule), and GbARF10a, 10b, 10c were also annotated to the abscisic acid-activated signaling and the leaf development pathway, respectively (Figure 5). Molecular function mainly reflected the function of the GbARF products with DNA, protein and miRNA binding, and oxidoreductase activity. The cellular component explained that GbARFs were present in the nucleus.

2.8. GbARF Family Transcriptional Profiles

According to the expression pattern heatmap, we found most of the GbARF genes (GbARF4a, GbARF19a, GbARF19b, GbARF2c, GbARF2a, GbARF2b, GbARF6a, GbARF3) were specifically expressed in the stems, cambium, buds (both female and male) and immature fruits (Figure 6a). Moreover, the transcript levels of another class of members (GbARF4a, GbARF19a, GbARF19b, GbARF10b, GbARF10c, GbARF2c, GbARF2a, GbARF2b, GbARF6a, and GbARF6b) were gradually down-regulated with the tissue development. This was most notable in the leaves, as the levels reached their lowest at the yellow-leaf stage. Across the five stages of kernel development, with the exception of GbARF2c, the expressions of all the genes were distinctly up-regulated. These results suggested that certain GbARFs might play crucial roles in highly differentiated tissues, as well as in Ginkgo’s mature organs. Moreover, those genes that belonged to the same group, such as GbARF10b, GbARF10c, and GbARF10a (Group I); and GbARF2a, GbARF2b, and GbARF2c (Group III), exhibited similar expression patterns, which corroborated the conservative function of GbARF10b, GbARF10a and GbARF2a, GbARF2c in syntenic analysis. In contrast, most Group II members showed a varied main expression, such as GbARF4a, GbARF19a, GbARF6b, GbARF8, and GbARF3.
Under MeJA and SA induction, the GbARFs were not responsive (Figure 6b). There were no visible expression differences between the treatments and the controls (CKs). However, the expressions of GbARF3, GbARF8, GbARF10a, and GbARF4b were increased after UV-B exposure, reflecting a certain functional activity in response to light signals. After PEG-6000 treatment, GbARF6a and GbARF19a were downregulated, compared with their CKs at 12 h, respectively, after which they gradually recovered over a period of 48 h. In contrast, GbARF10b, GbARF10a, and GbARF4b were upregulated at 12 h, while their levels were consistent with those of the CK, up to 24 h. GbARF10b was upregulated again at 48 h, while GbARF10a and GbARF4b were continuously downregulated. Taken together, the results suggest that these five GbARFs may be involved in temporal, dynamic biological response process to drought.

2.9. Quantitative Real-Time PCR(qRT-PCR) Verification of Tissue-Specific Expression

To verify the expression patterns and potential regulatory roles of the GbARF family in different tissues, 10 genes that had been previously predicted for biological functions were selected for qRT-PCR assays. In general, the expression levels of 10 genes were consistent with the fragments per kilobase per million (FPKM) values, except for the levels of the mature leaves and fruits(Figure 7), this inconsistency was probably due to the different materials used in this test and the transcriptome sequencing test. The expression of GbARF2b and GbARF2c in male and female buds, mature leaves, and fruits were significantly higher than in other tissues, supporting the GO prediction that GbARF2b is involved in fruit dehiscence and the positive regulation of flower development. GbARF2a, GbARF2b and GbARF2c showed priority expression in mature leaves in a relative level; considering that PtARF2.1, as a GbARF2 homolog, has been reported to be involved in leaf developmental regulation and lignin biosynthesis in poplar, it was mainly expressed in leaves [26]. Therefore, here, the expression patterns of three GbARF2s might indicate that these GbARF2s were involved in the consistent developmental regulation as PtrARF2.1. The high expression of GbARF10b in staminate strobilus was in agreement with its predicted function in the biological process, it was allocated to the term of petal and calyx development. In addition, GbARF4a, GbARF6b, and GbARF8 were not only highly expressed in mature leaves, fruits, and kernels, but were also significantly up-regulated in cambium, compared to other tissues. This phenomenon was different from the other genes and supported the transcriptional profile above.

2.10. GbARF6a, GbARF10b, and GbARF10a Cloning and Expression Profiles of GbARFs in Flower Development

GbARF6a, GbARF10b and GbARF10a were used as candidates for molecular cloning to validate the putative protein-coding regions. According to the GO functional annotation and the tissue-specific expression, cDNA from early developmental staminate strobilus (collected on 26 March 2022) were used as templates to amplify the full-length ORFs of three genes. The amplified products are shown in Figure 8a–c, sequencing results suggested that the protein coding regions of the three genes were fully consistent with the previous genomic identification, and the nucleic acid coding region of GbARF6a was only 860 bp, without CTD domain, reflecting that it is not dependent on the Aux/IAA for its function. The ARF domain ends of GbARF10b and GbARF10a contained more Q than the other members (Figure 8d), revealing their transcriptional activation in auxin signaling [25].
We further selected nine GbARFs to analyze their possible roles in Ginkgo flower development by comparing the expression profiles during three development stages of staminate strobilus and four development stages of ovulate strobilus (Figure 8e). GbARF2b was involved in ovule development and its comparative expression in ovulate strobilus was at least nine-fold higher than in male flowers (staminate strobilus), which reached the highest on 20 April (Figure 8f). Meanwhile, GbARF10b, GbARF10c and GbARF10a were all assigned to the term petal and sepal development. They had higher expression at two later stages (15 and 20 April) of ovule development than staminate strobilus. This indicates that these three genes play an integral role in female flowers’ maturation. Notably, the expression variation of GbARF2a in staminate strobilus was consistent with that of GbARF2c, as also GbARF10b, GbARF4a, GbARF10a, and GbARF6b.The latter four genes had the highest expression at the early stage of male flower development (26 March), and their expression gradually decreased on 2 April and 9 April. Overall, nine selected GbARFs were preferentially expressed in female flowers rather than the male flowers, especially in the latter two stages of development.

2.11. Expression of GbARFs in Response to Exogenous Salicylic Acid (SA)

In the exogenous SA treatment assay, with the exception of GbARF6a and GbARF4a, the remaining genes all showed significant response (Figure 9a). Among them, members containing more SA cis-elements showed the following two expression trends overall: (1) GbARF1, GbARF2a, and GbARF10a were significantly up-regulated than the CK, and (2) GbARF2c, GbARF19b and GbARF8 were down-regulated. In addition, GbARF6b had a significant correlation in expression level with GbARF2b and GbARF10b, respectively, as was also the case between GbARF4b, GbARF19b and GbARF8, and between GbARF2b and GbARF10b, respectively. More interestingly, the expression of GbARF1, GbARF10b, GbARF10c and GbARF10a were positively correlated with the IAA concentration under SA stimulation (Figure 9c), which verified our earlier identification of them as activators. GbARF10b, GbARF10c and GbARF10a mediated the expression of IAA-related genes, and might be involved in the transportation of endogenous IAA induced by exogenous SA, resulting in new growth and development [33].

3. Discussion

Auxin is an essential hormone for plant development, from influencing embryonic differentiation to causing organ abscission and even the survival of the entire plant. These biology processes cannot be initiated without auxin induction. ARFs constitute a class of transcription factors that are associated with growth and stress responses and mediate the development of various tissues in plants [9,10,11,12]. Previous studies have suggested that the number of ARFs in different plants is not directly related to their genome size, which varies widely among species. For instance, there are 50 ARF genes in Osmanthus fragrans [34], 17 in physic nut [35], 31 in apple [17], 26 in Brachypodium distachyon [36], 17 in melon [37], 17 in peach [18], 19 in Vitis vinifera [38], 51 in soybean [25], and 28 in chickpea [32]. Ginkgo biloba, is the only broad-leaved gymnosperm that exists, the members and biological features of GbARF family still remain unknown.
In this study, based on the recent release of more than nine Gb Ginkgo genomes, a total of 15 GbARF members were identified. The CTD domain for two members (GbARF6a and GbARF4b) was truncated, which accounted for 13.3% of all the genes, this percentage was lower than that in Osmanthus fragrans (18%) [34], maize (30.6%) [39], melon (23.5%) [37] and Medicago (54.2%) [40], suggesting that CTD is a key region for the function of GbARFs. The 15 members were grouped into three groups according to their homology with the ARFs in Arabidopsis, Populus, Malus domestica and Picea abies: Groups I-III. Of which, GbARF6a, GbARF6b and GbARF8(that belong to Group II) were identified as homologs of ARF6/8-like in Ginkgo, which was previously reported in other study [23]. The protein sequence identity of these three members and of ARF6/8-like were 100%, 70.2% and 84.9%, respectively. GbARF6b and GbARF8, as two new ARF6/8-like homologs, were recognized in Ginkgo, which will facilitate the study of their regulatory functions. Overall, the identifications of motifs, intron–exons, cis-acting elements, and protein tertiary structures indicated that the organization of the GbARFs were fairly conserved within a given group, supporting their classification and evolutionary relationships among the members and implying that they have a redundant function in each subgroup. Subsequently, GbARF10b, GbARF10a and GbARF10c, as the members of Group I, were verified as transcriptional activators due to the Q enrichment at the end of the ARF domain by gene cloning and sequence alignment [25]. Furthermore, GbARF10a and GbARF8 were as the orthologs of AtARF10 and AtARF8, respectively. GbARF10a exhibited predominant expression in yellow leaves and GbARF8 was highly expressed in flowers and fruits in transcriptional and relative expression profiles. Studies have shown that together with TIR1, AtARF10 coregulates leaf development and root cap formation [41], and that AtARF8 interacts with BIGPETALp (BPEp) to regulate flower fertilization and fruit development in Arabidopsis [10]. Therefore, these predominant expressions may suggest the putative functions of GbARF10a and GbARF8 in organs’ development.
It has been considered that the cis-acting elements positively correlate with the regulatory functions of genes [42,43]. In our work, eight GbARFs had AuxRR core or TGA elements that specifically bind to downstream target Aux/IAA [29]. GbARF10b was found to have four of these elements in its promoter, as the most among the eight genes. GbARF10b and GbARF10a contained more elements associated with light response than those of the remaining GbARFs. The transcript abundance and relative expression were analyzed to further recognize these genes’ roles. GbARF10a was confirmed to have more sensitive transcript abundance after UV-B and PEG-6000 treatment, and members of Group I and III showed the same pattern in their tissue-specific expressions, demonstrating previous prediction that they share consistent a function in tissue development. In Ginkgo flowers, GbARF10b, GbARF4a, GbARF10a, and GbARF6b showed the highest expression in the early stages of staminate strobilus development (26 March), and then gradually decreased to the lowest level after 2 weeks. This suggests that these minimum expressions of the four genes were related to the late development of the staminate strobilus, the typical developmental phenotype for which is that after the pollen sacs are opened to release mature pollens, the staminate strobilus are close to wilting. This result is in line with down-regulated LcARFs in the treatment of litchi fruit abscission [44]. On the other hand, the high expression level of nine genes at the latter two stages of ovule verified their biological functional predictions, which stated that they were involved in ovule development and fertilization. Thus, we can speculate that most of the GbARFs play important mediating roles in the IAA-induced initial development of male flowers and, later, of female flowers. However, further experimentation is needed to verify our hypothesis.
Under exogenous SA treatment, GbARF1, GbARF10c and GbARF10a were positively correlated with the IAA concentration, respectively. These results were in agreement with those reported for ARF in Osmanthus fragrans [34] and tomatoes [45], suggesting that three GbARFs are positively involved in IAA signaling under exogenous SA stimulation. At the same time, the expression of GbARF10c was also positively correlated with GbARF6a and GbARF10b.This finding is also in agreement with that of soybean [25], chickpea [32], and maize [39], respectively, where some ARFs functional redundancy may be due to segmental duplication. Overall, most of the GbARFs showed a down-regulation expression under T1 treatment, followed by up-regulation in higher concentrations of exogenous SA. This can be explained that slight SA stimulation weakened the IAA action because of co-regulation among endogenous phytohormones [45], while the stronger induction of exogenous SA in T2 and T3 groups activated the IAA metabolic pathway [45].

4. Materials and Methods

4.1. Identification and Sequence Analysis of GbARFs

The recent Ginkgo genome-wide data were obtained from Liu H.L. [20]. The published full-length ARF protein sequences of Arabidopsis thaliana [24], Populus trichocarpa [15], Picea abies and Malus domestica [17] were obtained from the Plant Transcription Factor Database (PTFD) (http://planttfdb.gao-lab.org/, accessed on 10 December 2021). First, the ARF protein sequences of the above four species were used as query sequences to search for ARF members in Ginkgo biloba, via local BLASTP (https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/, accessed on 20 December 2021), with an E-value ≤ 10 − 5. Second, the sequences of all putative members were merged from four searches, and the repetitive sequences were removed. The online Conserved Domains Database (CDD: https://www.ncbi.nlm.nih.gov/cdd, accessed on 23 December 2021) was used to detect AUX_RESP, AUX/IAA, and B3 conserved domains, members lacking more than two of these domains were deleted [24]. The physicochemical properties of GbARFs were subsequently predicted using ExPASy (http://web.expasy.org/protparam/, accessed on 28 December 2021), and subcellular localization of each GbARF was determined using WoLF PSORT (http://psort.hgc.jp/, accessed on 1 January 2022).

4.2. Phylogenesis, Protein Conserved Domain, Motif and Gene Structure Analysis

ARF protein sequences from Arabidopsis thaliana, Populus trichocarpa, Picea abies, Malus domestica and Ginkgo biloba were used to construct a phylogenetic tree via MEGA 7.0 software (https://www.megasoftware.net/, accessed on 6 January 2022) based on the maximum likelihood method, with 1000 bootstrap replications [46]. Multiple sequence alignment was performed using the ClustalW program of MEGA 7.0. The tree was then visualized using the online tool EvolView (http://www.evolgenius, accessed on 10 January 2022).
To confirm the highly conserved domains among GbARF members, sequence alignments were conducted by DNAMAN software [46]. Twelve conserved motifs were searched with the default parameters to distinguish the organization of GbARFs using the online website, Multiple Em for Motif Elicitation (http://meme.nbcr.net/meme/intro.html, accessed on 13 January 2022). The genome annotation gff3 file was used to extract exon-intron sequences from the GbARF genes, after which TBtools [47] analyzed their structure and constructed diagrams.

4.3. Protein Tertiary Structure, Cis-Acting Element and Interaction Network Analysis

The tertiary structures of the GbARFs were predicted using SWISS-MODEL (https://swissmodel.expasy.org/, accessed on 13 January 2022), based on template sequences that had more than 45% identity with GbARFs. We submitted the 2000 bp sequence upstream of the start codon of GbARF genes in the Ginkgo genome to PlantCARE (http://bioinformatics.psb.ugent be/webtools/plantcare/html/, accessed on 14 January 2022) to predict their cis-regulatory elements and then displayed the element locations by TBtools for subsequent analysis [47]. The GbARF protein interaction network was analyzed using String (https://string-db.org/, accessed on 15 January 2022) based on the highest-scoring proteins identified via BLAST of TBtools.

4.4. Chromosomal Location and Synteny Analysis

All GbARF genes were mapped to the Ginkgo chromosomes according to the data in the gff3 file, and gene duplication analysis of the paralogous genes was performed using TBtools [47]. Briefly, the “Gene Location Visualize” component of the GFF tool was used to construct a diagram of the physical location of the genes on the chromosomes. The protein sequences were matched using the subroutine “Two Sequence Files” of BLAST to perform pairwise alignment of the GbARFs. The E-value was set as 1 × 10−5. Both NumOfHits and NumOfAligns were set to 5, and the output file was obtained for further analysis. Finally, the gff3 and alignment files were utilized to analyze the collinear relationship using the Quick MCScanX Wrapper program [47,48]. The advanced Circos tool was subsequently used to display pairwise relationships. The DnaSP 6.0 (http://www.ub.edu/dnasp/, accessed on 17 January 2022) software was used to calculate nonsynonymous substitution/synonymous substitution (Ka/Ks) ratios for GbARF paralogous pairs.

4.5. GO Annotation Analysis

The online tool Protein ANNotation with the Z-scoRE server (PANNZER) (http://ekhidna2.biocenter.helsinki.fi/sanspanz, accessed on 21 March 2022) was utilized to describe comprehensive annotation of gene function and gene products for all GbARF members.

4.6. Transcription Analysis of GbARF Family Genes

The publicly available RNA raw sequencing (RNA-seq) data in the European Nucleotide Archive (ENA) database (https://www.ebi.ac.uk/ena/browser/view/,accessed on 20 October 2021) were downloaded (Table 3), including from strobilus, buds, roots, stems, cambium, leaves, and fruits in different development stages as well as the kernels. Additionally, the transcriptional profiles also contained data in response to induction of methyl jasmonate (MeJA), salicylic acid (SA), UV-B and simulated drought stress caused by polyethylene glycol (PEG)-6000. We also conducted a trial of exogenous SA spraying on the leaves of Ginkgo seedlings, 12 samples from which were sequenced by Shanghai Majorbio Bio Co., Ltd. (Shanghai, China) using Illumina NovaSeq 6000. After evaluating the raw data by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc, accessed on 30 October 2021), the low-quality reads and adapter sequences were removed by Trimmomatic [49]. The clean reads were mapped to the newest Ginkgo genome by STAR [50], and the fragments per kilobase per million mapped reads (FPKM) values were then calculated by RSEM [51]. Finally, the transcript abundance of GbARFs were converted to log2(FPKM + 1) values, and an expression heatmap was constructed with GraphPad Prism 8.0.

4.7. GbARF6a, GbARF10b, and GbARF10a Cloning

Total RNA from young staminate strobilus (collected on 26 March) were used to obtain cDNA using a reverse transcription kit (Monad Biotech Co., Ltd., Nanjing, China). The full length CDS was amplified with three pairs of specific primers (Table S7). The PCR procedure was as follows: 95 °C for 3 min, followed by 35 cycles of 95 °C for 15 s, 60 °C for 15 s, 72 °C for 52 s in GbARF6a and for 130 s in GbARF10b and GbARF10a, finally at 72 °C for 5 min. The amplified products were injected in 1% agarose gel to move the positive side of the gel bath with voltage of 120 V and the quality of products were observed on a gel imager. The gel blocks containing the target genes were purified using FastPure® Gel DNA Extraction Mini Kit (Vazyme Biotech Co., Ltd., Nanjing, China), then ligated into the clone vector pClone007 Blunt Simple Vector (Tsingke, Nanjing, China), and transferred into DH5α strain (Tsingke, Nanjing, China). The resuscitation solution was spread on LB solid medium, then put in 37 °C incubator to dark culture for 16 h, the positive clones were identified and sequenced to verify their genomic sequences.

4.8. qRT-PCR Expression of GbARFs

Staminate strobili, ovulate strobili, and buds at different developmental stages were harvested from ten Ginkgo trees (five females and five males) that were approximately 20 years old, located in the Nanjing Forestry University campus. Specifically, the female and male buds, as well as the young staminate strobilus were separately harvested on 26 March 2022. After this the middle and late developmental staminate strobili were taken after 1 week (2 April) and 2 weeks (9 April), respectively. The ovulate strobili were harvested on 2 April, 9 April, 15 April, and 20 April 2022, respectively. Other tissues were all collected from female Ginkgo trees. The immature leaves were harvested in June 2021, and the mature leaves, cambium and xylem, fruits, and kernels were harvested in October 2021. Three biological replicates of each tissue from five females/males were rapidly frozen in liquid nitrogen for total RNA extraction. The extraction procedure was performed according to the instructions of the E.Z.N.A.® Plant RNA Kit (Omega, Nanjing, China). After the total RNA was tested for concentration and purity, the cDNA was synthesized using MonScript™ RTIII All-in-One Mix with dsDNase (Monad, Nanjing, China), and 1ul of cDNA was used in MonAmp™ SYBR® Green qPCR Mix (Monad, Nanjing, China) to react PCR with an Applied Biosystems® 7500 Real Time PCR System (Thermo Fisher Scientific Inc., Waltham, MA, USA). PCR program was set as 30 s at 95 °C, 40 cycles of 95 °C for 10 s, and 60 °C for 15 s, and the parameters of melting curves were default by instrument that were collected before. The GAPDH gene was used as an internal control to analyze the relative expression level for GbARF members by the 2–ΔΔCt method [62].

4.9. Plant Materials and Exogenous SA Treatments

Two-year-old Ginkgo seedlings provided the materials for this experiment, and three treatments of exogenous SA gradient concentration were set as follows: 1 mmol/L (T1), 2 mmol/L (T2) and 3 mmol/L (T3), with 0 mmol/L concentration as the control (CK). A total of 25 seedlings were sprayed for each treatment. The spraying trials were conducted four times:1 June, 8 June, 22 June, and 29 June 2019, Twenty days after completion of the 4 spray times, the mature leaves were collected for transcriptome sequencing and IAA concentration determination. The raw sequencing data have been deposited in the China National Center for Bioinformation (CNCB) database (accession no. PRJCA009411). One biological replicate of each treatment was obtained from eight seedlings, for a total of three replicates. IAA concentration was determined using an enzyme-linked immunoassay kit from the Institute of Hormone Research, China Agricultural University, and the test procedure was referenced to Sheng et al. [33].

4.10. Statistical Analysis

All samples used in this experiment were three biological replicates, the correlation and one-way analysis of variance (ANOVA) (Duncan’s test) were analyzed using GraphPad Prism 8.0 software (https://www.graphpad.com/, accessed on 1 August 2021).

5. Conclusions

In summary, we recognized 15 GbARF members by genome-wide identification in Ginkgo biloba and grouped them into Groups I–III based on phylogenetic analysis. Multiple analyses including sequence alignment, structure characteristics, and GO annotation, all suggested that the GbARFs that were part of the same Group were highly conserved in structure and biological function. Subsequently, transcriptome, gene cloning, and qRT-PCR were conducted to investigate their possible regulatory roles in responding to flower development and to the stimulation of exogenous SA. GbARF10b and GbARF10a were verified as candidate genes that acted as transcriptional activators of the IAA signaling involved in Ginkgo male floral organ development and in the response of exogenous SA. This study provides insight into the regulatory functions of certain GbARFs associated with Ginkgo floral organ development and exogenous hormones, which will contribute to further research on the mechanisms of regulatory functions for GbARFs in Ginkgo.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms23126754/s1.

Author Contributions

Conceptualization, F.G.; methodology, F.G. and J.G.; software, F.G.; validation, W.X. and G.W. formal analysis, W.X.; data curation, F.G.; writing—original draft preparation, F.G.; writing—review and editing, F.G.; W.X. and G.W.; visualization, F.G.; supervision, J.G.; project administration, G.W.; funding acquisition, G.W. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Agricultural Science and Technology Independent Innovation Funds of Jiangsu Province (CX(20)3145, National Natural Science Foundation of China (31971689), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The data presented in this study are available upon request from the corresponding author and the public pomegranate transcriptomes presented in this study are available in the insert article.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Teale, W.D.; Paponov, I.A.; Palme, K. Auxin in action: Signaling, transport and the control of plant growth and development. Nat. Rev. Mol. Cell Biol. 2006, 7, 847–859. [Google Scholar] [CrossRef]
  2. Tiwari, S.B.; Hagen, G.; Guilfoyle, T. The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell. 2003, 15, 533–543. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  3. Schuetz, M.; Fidanza, M.; Mattsson, J. Identification of auxin response factor-encoding genes expressed in distinct phases of leaf vein development and with overlapping functions in leaf formation. Plants 2019, 8, 242. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  4. Tan, S. Repressors for auxin responsive transcriptional activators. Mol. Plant. 2020, 14, 6–8. [Google Scholar] [CrossRef]
  5. Krogan, N.T.; Berleth, T. The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development. Plant Signal. Behav. 2015, 10, e992748. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  6. Guilfoyle, T.J.; Hagen, G. Auxin response factors. Curr. Opin. Plant Biol. 2007, 10, 453–460. [Google Scholar] [CrossRef] [PubMed]
  7. Krogan, N.T.; Berleth, T. Auxin-responsive gene expression: Genes, promoters and regulatory factors. Plant Mol. Biol. 2002, 49, 373–385. [Google Scholar] [CrossRef]
  8. Freire-Rios, A.; Tanaka, K.; Crespo, I.; Wijk, E.; Levitsky, V.; Sizentsova, Y. Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis. Proc. Natl. Acad. Sci. USA 2020, 117, 24557–24566. [Google Scholar] [CrossRef]
  9. Ellis, C.M.; Nagpal, P.; Young, J.C.; Hagen, G.; Guilfoyle, T.J.; Reed, J.W. AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana. Development 2005, 132, 4563–4574. [Google Scholar] [CrossRef] [Green Version]
  10. Ryo, T.; Masaya, I.; Takahiro, F.; Aida, M.; Tian, C.; Ueno, Y.; Yamamoto, K. Arabidopsis AUXIN RESPONSE FACTOR6 and 8 regulate jasmonic acid biosynthesis and floral organ development via repression of class 1 KNOX genes. Plant Cell Physiol. 2010, 51, 164–175. [Google Scholar] [CrossRef] [Green Version]
  11. Okushima, Y.; Overvoorde, P.J.; Arima, K.; Alonso, J.M.; Chan, A.; Chang, C.; Ecker, J.R.; Hughes, B.; Lui, A.; Nguyen, D.; et al. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thalian: Unique and overlapping functions of ARF7 and ARF19. Plant Cell. 2005, 17, 444–463. [Google Scholar] [CrossRef] [Green Version]
  12. Zhang, S.Z.; Wu, T.; Liu, S.J.; Liu, X.; Jiang, L.; Wan, J.M. Disruption of OsARF19 is critical for floral organ development and plant architecture in rice (Oryza sativa L.). Plant Mol. Biol. Rep. 2016, 34, 748–760. [Google Scholar] [CrossRef]
  13. Zouine, M.; Fu, Y.Y.; Chateigner-Boutin, A.L.; Mila, I.; Frasse, P.; Wang, H.; Audran, C. Characterization of the tomato ARF gene family uncovers a multi-levels post-transcriptional regulation including alternative splicing. PLoS ONE 2014, 9, e84203. [Google Scholar] [CrossRef]
  14. Zhang, X.F.; Cao, J.F.; Huang, C.C.; Zheng, Z.S. Characterization of cotton ARF factors and the role of GhARF2b in fiber development. BMC Genom. 2021, 22, 202. [Google Scholar] [CrossRef]
  15. Yang, C.X.; Xu, M.; Xuan, L.; Jiang, X.M.; Huang, M.R. Identification and expression analysis of twenty ARF genes in Populus. Gene 2014, 544, 134–144. [Google Scholar] [CrossRef]
  16. Niu, J.; Bi, Q.; Deng, S.; Chen, H.; Yu, H.; Wang, L.; Lin, S. Identification of AUXIN RESPONSE FACTOR gene family from Prunus sibirica and its expression analysis during mesocarp and kernel development. BMC Plant Biol. 2018, 18, 21. [Google Scholar] [CrossRef] [Green Version]
  17. Luo, X.C.; Sun, M.H.; Xu, R.R.; Shu, H.R.; Wang, J.W.; Zhang, S.Z. Genome-wide identification and expression analysis of the ARF gene family in apple. J. Genet. 2014, 93, 785–797. [Google Scholar] [CrossRef]
  18. Diao, D.; Hu, X.; Guan, D.; Wang, W.; Yang, H.; Liu, Y. Genome-wide identification of the ARF (auxin response factor) gene family in peach and their expression analysis. Mol. Biol. Rep. 2020, 47, 4331–4344. [Google Scholar] [CrossRef]
  19. Yu, H.; Soler, M.; Mila, I.; Clemente, H.S.; Savelli, B.; Dunand, C.; Paiva, J.A.P.; Myburg, A.A.; Bouzayen, M.; Grima-Pettenati, J.; et al. Genome-wide characterization and expression profiling of the AUXIN RESPONSE FACTOR (ARF) gene family in Eucalyptus grandis. PLoS ONE 2014, 9, e10890. [Google Scholar] [CrossRef] [Green Version]
  20. Liu, H.L.; Wang, X.B.; Wang, G.B.; Cui, P.; Wu, S.G.; Ai, C.; Hu, N.; Li, A.; He, B.; Shao, X.J.; et al. The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution. Nat. Plants 2021, 7, 748–756. [Google Scholar] [CrossRef]
  21. Crane, P.R. An evolutionary and cultural biography of ginkgo. Plants People Planet. 2019, 1, 32–37. [Google Scholar] [CrossRef]
  22. Zheng, J.; Liao, Y.; Xu, F.; Zhou, X.; Ye, J.; Fu, M.; Liu, X.; Cao, Z.; Zhang, W. Genome-wide identification of WD40 superfamily genes and prediction of WD40 gene of flavonoid-related genes in Ginkgo biloba. Not. Bot. Horti. Agrobo. 2021, 49, 12086. [Google Scholar] [CrossRef]
  23. Zhang, R.; Min, Y.; Holappa, L.D.; Walcher-Chevillet, C.L.; Duan, X.S.; Donaldson, E.; Kong, H.Z.; Kramer, E.M. A role for the Auxin Response Factors ARF6 and ARF8 homologs in petal spur elongation and nectary maturation in Aquilegia. New Phytol. 2020, 227, 1392–1405. [Google Scholar] [CrossRef] [PubMed]
  24. Li, S.B.; Xie, Z.Z.; Hu, C.G.; Zhang, J.Z. A review of auxin response factors (ARFs) in plants. Front. Plant Sci. 2016, 7, 47. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  25. Ha, C.V.; Le, D.T.; Nishiyama, R.; Watanabe, Y.; Sulieman, S.; Tran, U.T.; Mochida, K.; Dong, N.V.; Yamaguchi-Shinozaki, K.; Shinozaki, K.; et al. The auxin response factor transcription factor family in soybean: Genome-wide identification and expression analyses during development and water stress. DNA Res. 2013, 20, 511–524. [Google Scholar] [CrossRef] [PubMed]
  26. Fu, Y.Y.; Win, P.P.; Zhang, H.J.; Li, C.F.; Shen, Y.; He, F.; Luo, K.M. PtrARF2.1 is involved in regulation of leaf development and lignin biosynthesis in poplar trees. Int. J. Mol. Sci. 2019, 20, 4141. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  27. Krogan, N.T.; Yin, X.; Ckurshumova, W.; Berleth, T. Distinct subclades of Aux/IAA genes are direct targets of ARF5/MP transcriptional regulation. New Phytol. 2014, 204, 474–483. [Google Scholar] [CrossRef] [PubMed]
  28. Wang, J.W.; Wang, L.J.; Mao, Y.B.; Cai, W.J.; Xue, H.W.; Chen, X.Y. Control of Root Cap Formation by MicroRNA-Targeted Auxin Response Factors in Arabidopsis. Plant Cell. 2005, 17, 2204–2216. [Google Scholar] [CrossRef] [Green Version]
  29. Chapman, E.J.; Estelle, M. Mechanism of auxin-regulated gene expression in plants. Annu. Rev. Genet. 2009, 43, 265–285. [Google Scholar] [CrossRef] [Green Version]
  30. Gidhi, A.; Kumar, M.; Mukhopadhyay, K. The auxin response factor gene family in wheat (Triticum aestivum L.): Genome-wide identification, characterization and expression analyses in response to leaf rust. S. Afr. J. Bot. 2021, 140, 312–325. [Google Scholar] [CrossRef]
  31. Roth, C.; Liberles, D.A. A systematic search for positive selection in higher plants (Embryophytes). BMC Plant Biol. 2006, 6, 12. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  32. Singh, V.K.; Rajkumar, M.S.; Garg, R.; Jain, M. Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea. Sci. Rep. 2017, 7, 10895. [Google Scholar] [CrossRef] [PubMed]
  33. Sheng, J.Y.; Li, X.; Zhang, D. Gibberellins, brassinolide, and ethylene signaling were involved in flower differentiation and development in Nelumbo nucifera. Hortic. Plant J. 2022, 8, 243–250. [Google Scholar] [CrossRef]
  34. Chen, G.; Yue, Y.; Li, L.; Li, Y.; Wang, L. Genome-wide identification of the auxin response factor (ARF) gene family and their expression analysis during flower development of Osmanthus fragrans. Forests 2020, 11, 245. [Google Scholar] [CrossRef] [Green Version]
  35. Tang, Y.; Bao, X.; Liu, K.; Wang, J.; Zhang, J.; Feng, Y.; Wang, Y.; Lin, L.; Feng, J.; Li, C. Genome-wide identification and expression profiling of the auxin response factor (ARF) gene family in physic nut. PLoS ONE 2018, 13, e0201024. [Google Scholar] [CrossRef] [Green Version]
  36. Zhou, X.; Wu, X.; Li, T.; Jia, M.; Liu, X.; Zou, Y.; Liu, Z.; Wen, F. Identification, characterization, and expression analysis of auxin response factor (ARF) gene family in Brachypodium distachyon. Funct. Integr. Genom. 2018, 18, 709–724. [Google Scholar] [CrossRef] [PubMed]
  37. Wu, B.; Wang, L.; Pan, G.; Li, T.; Li, X.; Hao, J. Genome-wide characterization and expression analysis of the auxin response factor (ARF) gene family during melon (Cucumis melo L.) fruit development. Protoplasma 2020, 257, 20. [Google Scholar] [CrossRef] [Green Version]
  38. Wan, S.; Li, W.; Zhu, Y.; Liu, Z.; Huang, W.; Zhan, J. Genome-wide identification, characterization and expression analysis of the auxin response factor gene family in Vitis vinifera. Plant Cell Rep. 2014, 33, 1365–1375. [Google Scholar] [CrossRef]
  39. Xing, H.; Pudake, R.N.; Guo, G.; Xing, G.; Hu, Z.; Zhang, Y.; Sun, Q.; Ni, Z. Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize. BMC Genom. 2011, 12, 178. [Google Scholar] [CrossRef] [Green Version]
  40. Shen, C.; Yue, R.; Sun, T.; Zhang, L.; Xu, L.; Tie, S.; Wang, H.; Yang, Y. Genome-wide identification and expression analysis of auxin response factor gene family in Medicago truncatula. Front. Plant Sci. 2015, 6, 73. [Google Scholar] [CrossRef] [Green Version]
  41. Trenner, J.; Poeschl, Y.; Grau, J.; Gogol, A.; Quint, M.; Delker, C. Auxin-induced expression divergence between Arabidopsis species may originate within the TIR1/AFB-AUX/IAA-ARF module. J. Exp. Bot. 2016, 3, 539. [Google Scholar] [CrossRef] [Green Version]
  42. Bansal, M.; Kumar, A.; Yella, R.V. Role of DNA sequence based structural features of promoters in transcription initiation and gene expression. Curr. Opin. Struct. Biol. 2014, 25, 77–85. [Google Scholar] [CrossRef]
  43. Zhang, H.X.; Cao, N.; Dong, C.J.; Shang, Q.M. Genome-wide identification and expression of ARF gene family during adventitious root development in Hot Pepper (Capsicum annuum). Hortic. Plant J. 2017, 3, 151–164. [Google Scholar] [CrossRef]
  44. Zhang, Y.Q.; Zeng, Z.H.; Chen, C.J.; Li, C.Q.; Xia, R.; Li, J.G. Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): Phylogenetic analysis, miRNA regulation and expression changes during fruit abscission. PeerJ. 2019, 4, e6677. [Google Scholar] [CrossRef] [Green Version]
  45. Zhang, S.L.; Gu, X.; Shao, J.C.; Hu, Z.; Yang, W.; Wang, L.; Su, H.; Zhu, L. Auxin metabolism is involved in fruit set and early fruit development in the parthenocarpic tomato “R35-P”. Front. Plant Sci. 2021, 12, 671713. [Google Scholar] [CrossRef]
  46. Zhao, X.; Yang, J.; Li, G.; Sun, Z.; Hu, S.; Chen, Y.; Guo, W.; Hou, H. Genome-wide identification and comparative analysis of the WRKY gene family in aquatic plants and their response to abiotic stresses in giant duckweed (Spirodela polyrhiz). Genomics 2021, 113, 1761–1777. [Google Scholar] [CrossRef]
  47. Chen, C.J.; Chen, H.; Zhang, Y.; Thomas, H. TBtools-an integrative toolkit developed for interactive analyses of big biological data. Nat. Plant. 2020, 13, 8. [Google Scholar] [CrossRef] [Green Version]
  48. Zhi, C.; Ali, M.M.; Alam, S.M.; Gull, S.; Ali, S.; Yousef, A.F.; Ahmed, M.A.A.; Ma, S.; Chen, F. Genome-wide in silico analysis and expression profiling of phosphoenolpyruvate carboxylase genes in loquat, apple, peach, strawberry and pear. Agronomy 2022, 12, 25. [Google Scholar] [CrossRef]
  49. Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30, 2114–2120. [Google Scholar] [CrossRef] [Green Version]
  50. Dobin, A.; Davis, C.A.; Schlesinger, F.; Drenkow, J.; Zaleski, C.; Jha, S.; Batut, P.; Chaisson, M.; Gingeras, T.R. STAR: Ultrafast universial RNA-seq aligner. Bioinformatics 2013, 29, 15–21. [Google Scholar] [CrossRef]
  51. Raghupathy, N.; Choi, K.; Vincent, M.J.; Beane, G.L.; Sheppard, K.S.; Munger, S.C.; Korstanje, R.; De Villena, F.P.-M.; Churchill, G.A. Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression. Bioinformatics 2018, 34, 2177–2184. [Google Scholar] [CrossRef] [PubMed]
  52. Liu, X.J.; Sun, L.M.; Wu, Q.K.; Men, X.Y.; Yao, L.M.; Xing, S.Y. Transcriptome profile analysis reveals the ontogenesis of rooted chichi in Ginkgo biloba L. Gene 2018, 669, 8–14. [Google Scholar] [CrossRef]
  53. Du, S.H.; Sang, Y.L.; Liu, X.J.; Xing, S.Y.; Li, J.H.; Tang, H.X.; Sun, L.M. Transcriptome profile analysis from different sex types of Ginkgo biloba L. Front. Plant Sci. 2016, 7, 871. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  54. Ye, J.B.; Cheng, S.Y.; Zhou, X.; Chen, Z.X.; Kim, S.U.; Tan, J.P.; Zheng, J.R.; Xu, F.; Zhang, W.; Liao, Y.; et al. A global survey of full-length transcriptome of Ginkgo biloba reveals transcript variants involved in flavonoid biosynthesis. Ind. Crops Prod. 2019, 139, 111547. [Google Scholar] [CrossRef]
  55. Wang, L.; Cui, J.W.; Jin, B.; Zhao, J.G.; Xu, H.M.; Lu, Z.G.; Li, W.X. Multifeature analyses of vascular cambial cells reveal longevity mechanisms in old Ginkgo biloba trees. Proc. Natl. Acad. Sci. USA 2020, 117, 2201–2210. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  56. Wu, Y.Q.; Guo, J.; Wang, T.L.; Cao, F.L.; Wang, G.B. Metabolomic and transcriptomic analyses of mutant yellow leaves provide insights into pigment synthesis and metabolism in Ginkgo biloba. BMC Genom. 2020, 21, 858. [Google Scholar] [CrossRef] [PubMed]
  57. Li, W.X.; Wang, L.; He, Z.C.; Lu, Z.G.; Cui, J.W.; Xu, N.T.; Jin, B. Physiological and transcriptomic changes during autumn coloration and senescence in Ginkgo biloba leaves. Hortic. Plant J. 2020, 6, 396–408. [Google Scholar] [CrossRef]
  58. He, B.; Gu, Y.C.; Xu, M.; Wang, J.W.; Cao, F.L.; Xu, L.A. Transcriptome analysis of Ginkgo biloba kernels. Front. Plant Sci. 2015, 6, 819. [Google Scholar] [CrossRef]
  59. Ye, J.B.; Mao, D.; Cheng, S.Y.; Zhang, X.; Tan, J.P.; Zheng, J.R.; Xu, F. Comparative transcriptome analysis reveals the potential stimulatory mechanism of terpene trilactone biosynthesis by exogenous salicylic acid in Ginkgo biloba. Ind. Crops Prod. 2020, 145, 112104. [Google Scholar] [CrossRef]
  60. Zhao, B.B.; Wang, L.; Pang, S.Y.; Cui, J.Z.; Wang, L.; Li, W.X.; Jin, B. UV-B promotes flavonoid synthesis in Ginkgo biloba leaves. Ind. Crops Prod. 2020, 151, 112483. [Google Scholar] [CrossRef]
  61. Zhu, Z.B.; Yu, W.W.; Cao, F.L.; Wang, G.B. Transcriptome Analysis of Ginkgo biloba Leaves under PEG6000 simulated drought stress. Mol. Plant Breed. 2020, 18, 8061–8069. [Google Scholar] [CrossRef]
  62. Pfaffl, M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001, 29, 9. [Google Scholar] [CrossRef]
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Figure 1. Phylogenetic tree of the ARF gene family in Ginkgo biloba, Populus trichocarpa, Malus domestica, Picea abies, and Arabidopsis thaliana. GbARF members of five species marked with different colored stars.
Figure 1. Phylogenetic tree of the ARF gene family in Ginkgo biloba, Populus trichocarpa, Malus domestica, Picea abies, and Arabidopsis thaliana. GbARF members of five species marked with different colored stars.
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Figure 2. Multiple sequence alignment of GbARFs. Dark blue, light red, and light blue background indicates protein identity in 100%, 75%, and 50%, respectively. The DNA binding domain (DBD), auxin response factor (ARF) and C-terminal dimerization (CTD) domain regions were marked with black line boxes.
Figure 2. Multiple sequence alignment of GbARFs. Dark blue, light red, and light blue background indicates protein identity in 100%, 75%, and 50%, respectively. The DNA binding domain (DBD), auxin response factor (ARF) and C-terminal dimerization (CTD) domain regions were marked with black line boxes.
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Figure 3. Phylogenetic tree, conserved motifs, gene structures, and regulatory elements of GbARF family. (a) Phylogenetic tree of GbARFs. (b) Conserved motifs in GbARFs. Different conserved motifs, numbers 1–12, are displayed in different colored boxes. (c) Exon-intron regions of GBARFs. (d) Numbers of cis-elements in GbARFs. Each gray box means that the gene does not contain following cis-element.
Figure 3. Phylogenetic tree, conserved motifs, gene structures, and regulatory elements of GbARF family. (a) Phylogenetic tree of GbARFs. (b) Conserved motifs in GbARFs. Different conserved motifs, numbers 1–12, are displayed in different colored boxes. (c) Exon-intron regions of GBARFs. (d) Numbers of cis-elements in GbARFs. Each gray box means that the gene does not contain following cis-element.
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Figure 4. Physical chromosomal location, collinearity analysis and protein interaction of GbARFs. (a) Physical chromosomal location of GbARFs. (b) Duplicated relationship of GbARF genes. (c) A putative protein interaction network of GbARF4b and GbARF4a.
Figure 4. Physical chromosomal location, collinearity analysis and protein interaction of GbARFs. (a) Physical chromosomal location of GbARFs. (b) Duplicated relationship of GbARF genes. (c) A putative protein interaction network of GbARF4b and GbARF4a.
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Figure 5. Annotation of biology process of GO analysis for GbARFs.
Figure 5. Annotation of biology process of GO analysis for GbARFs.
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Figure 6. Expression profiles of GbARFs in different tissues, hormone induction and abiotic stress. (a) Tissue-specific expression of GbARFs. (b) Expression of GbARFs under hormone induction and abiotic stress. The FPKM, transcript abundance was converted to log2(FPKM+1) to construct heatmaps.
Figure 6. Expression profiles of GbARFs in different tissues, hormone induction and abiotic stress. (a) Tissue-specific expression of GbARFs. (b) Expression of GbARFs under hormone induction and abiotic stress. The FPKM, transcript abundance was converted to log2(FPKM+1) to construct heatmaps.
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Figure 7. qRT-PCR validation for 10 selected genes. The colored vertical bars of each gene represent relative expression level in qRT-PCR and the black folds show FPKM value in transcript level. Relative expression was indicated as means ± standard deviation (SD). Different letters denote significant differences at 0.05 level by Duncan’s multiple range test.
Figure 7. qRT-PCR validation for 10 selected genes. The colored vertical bars of each gene represent relative expression level in qRT-PCR and the black folds show FPKM value in transcript level. Relative expression was indicated as means ± standard deviation (SD). Different letters denote significant differences at 0.05 level by Duncan’s multiple range test.
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Figure 8. PCR amplification of GbARF6a (a), GbARF10b (b), GbARF10a (c) and identification of ARF domain (d). (e) Developmental stages of staminate strobilus and ovulate strobilus. (f) Relative expression of 9 GbARFs during male and female flower development in Ginkgo. Orange and blue vertical bars represent staminate strobilus and ovulate strobilus, respectively, expression levels were indicated as means ± standard deviation (SD), different letters denote a significant difference of 0.05 in Duncan’s multiple range test.
Figure 8. PCR amplification of GbARF6a (a), GbARF10b (b), GbARF10a (c) and identification of ARF domain (d). (e) Developmental stages of staminate strobilus and ovulate strobilus. (f) Relative expression of 9 GbARFs during male and female flower development in Ginkgo. Orange and blue vertical bars represent staminate strobilus and ovulate strobilus, respectively, expression levels were indicated as means ± standard deviation (SD), different letters denote a significant difference of 0.05 in Duncan’s multiple range test.
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Figure 9. Expression profiles of GbARFs and the correlation with IAA concentration under SA treatment. (a) FPKM values of GbARFs (b) IAA Concentration. (c) Correlation heat map in GbARFs expression level and IAA response to SA. FPKM values were showed as mean means ± standard error (SE). CK, T1, T2 and T3 in (a) represent exogenous SA concentration of 0, 1, 2 and 3 mmol/L, respectively. Letters in Figure (a,b) represent significant differences at the 0.05 level, and * in Figure (c) means the 0.05 significant level, ** means the 0.01 level, and *** means the 0.001 level.
Figure 9. Expression profiles of GbARFs and the correlation with IAA concentration under SA treatment. (a) FPKM values of GbARFs (b) IAA Concentration. (c) Correlation heat map in GbARFs expression level and IAA response to SA. FPKM values were showed as mean means ± standard error (SE). CK, T1, T2 and T3 in (a) represent exogenous SA concentration of 0, 1, 2 and 3 mmol/L, respectively. Letters in Figure (a,b) represent significant differences at the 0.05 level, and * in Figure (c) means the 0.05 significant level, ** means the 0.01 level, and *** means the 0.001 level.
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Table
Table 1. The protein characteristics of GbARFs in Ginkgo.
Table 1. The protein characteristics of GbARFs in Ginkgo.
Gene NameGene IDORFAAMW (Da)pIGRAVYSubcellular
Localization
GbARF3evm.model.chr1.30002922973108,130.405.46−0.458Nuclear
GbARF1evm.model.chr3.203630091002110,896.656.63−0.530Nuclear
GbARF2aevm.model.chr4.67738341277141,221.986.5−0.335Plasma membrane
GbARF2bevm.model.chr5.14562982993109,968.786.62−0.516Chloroplast
GbARF6aevm.model.chr5.146286028533,086.808.89−0.242Extracellular
GbARF10bevm.model.chr5.854225074982,844.926.64−0.476Nuclear
GbARF19aevm.model.chr6.9333841127126,560.126.06−0.516Nuclear
GbARF2cevm.model.chr7.1996264087997,850.615.59−0.615Nuclear
GbARF19bevm.model.chr8.179032221073121,038.596.36−0.692Nuclear
GbARF10cevm.model.chr8.618235278386,475.317.60−0.447Nuclear
GbARF4aevm.model.chr10.1507264988297,626.735.83−0.469Nuclear
GbARF10aevm.model.chr10.178241280388,729.166.44−0.512Nuclear
GbARF6bevm.model.chr10.8102790929103,431.846.13−0.506Nuclear
GbARF8evm.model.chr11.85133451114123,501.217.34−0.482Nuclear
GbARF4bevm.model.chr11.970129042948,215.218.70−0.209Chloroplast
Table
Table 2. Ka (nonsynonymous), Ks(synonymous), and Ka/Ks ratio of duplicated GbARF genes.
Table 2. Ka (nonsynonymous), Ks(synonymous), and Ka/Ks ratio of duplicated GbARF genes.
Gene 1Gene 2KaKsKa/Ks(ω)SelectionDuplication Mode
GbARF3GbARF13.182372.304241.38109PositiveSegmental
GbARF1GbARF2a0.280250.893120.31379PurifyingSegmental
GbARF2aGbARF2c0.189700.862080.22005PurifyingSegmental
GbARF2aGbARF19b0.938541.341060.69985PurifyingSegmental
GbARF10bGbARF10a0.149410.962580.15522PurifyingSegmental
GbARF2cGbARF19b0.729790.895790.81469PurifyingSegmental
GbARF3GbARF10c0.842951.161640.72566PurifyingSegmental
Table
Table 3. List of RNA-Seq data in GBARF family of Ginkgo.
Table 3. List of RNA-Seq data in GBARF family of Ginkgo.
Project NumberSample TypeLibraryPlatformReference
PRJNA289172Ovulate strobilusPaired endIllumina HiSeq 2500[52]
PRJNA289172Staminate strobilusPaired endIllumina HiSeq 2500[52]
PRJNA289172Female and male budsPaired endIllumina HiSeq 2500[52]
PRJNA373812RootsPaired endIllumina HiSeq 4000[53]
PRJNA473396StemsPaired endIllumina HiSeq 4000[54]
PRJNA488475CambiumPaired endIllumina HiSeq 2000[55]
PRJNA473396Immature leavePaired endIllumina HiSeq 4000[54]
PRJNA517218Mature leavePaired endHiSeq X Ten[56]
PRJNA578374Turning stage and yellow leavePaired endIllumina HiSeq 4000[57]
PRJNA473396Immature and mature fruitsPaired endIllumina HiSeq 4000[54]
PRJNA292849Kernel1–5Paired endIllumina HiSeq 2000[58]
PRJNA553587Treatment of MEJPaired endHiSeq X Ten[59]
PRJNA598887Treatment of SAPaired endHiSeq X Ten[59]
PRJNA595103Treatment of UV-BPaired endIllumina HiSeq 4000[60]
PRJNA604486Treatment of PEG-6000Paired endIllumina NovaSeq 6000[61]
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Guo, F.; Xiong, W.; Guo, J.; Wang, G. Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L. Int. J. Mol. Sci. 2022, 23, 6754. https://doi.org/10.3390/ijms23126754

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Guo F, Xiong W, Guo J, Wang G. Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L. International Journal of Molecular Sciences. 2022; 23(12):6754. https://doi.org/10.3390/ijms23126754

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Guo, Fangyun, Wulai Xiong, Jing Guo, and Guibin Wang. 2022. "Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L." International Journal of Molecular Sciences 23, no. 12: 6754. https://doi.org/10.3390/ijms23126754

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