Introduction

Colored-leaf plants played important roles in landscaping and urban beautification, which can form a nice scenery [1, 2]. Poplar is widely planted around the world due to its fast growth and better resistance to adversity, which can be used for producing timber, pulp, and paper [3]. Recently, many kinds of colored-leaf poplars have been bred, such as ‘Zhonghong polar’(ZHP), ‘Quanhong poplar’ (QHP), ‘Jinhong poplar’ (JHP) and ‘Caihong poplar’ (CHP), which also bring great economic, social and ecological benefits [4, 5]. However, the molecular mechanisms of pigment formation in colored-leaf poplar are still unclear, and needed to be exploring.

The molecular mechanisms of anthocyanins biosynthesis in many species have been well characterized, such as Arabidopsis and rice. The anthocyanin biosynthesis was regulated mainly by two kinds of genes, enzyme-coding structural genes and transcription factor genes [6, 7]. The structural genes are conserved in many kinds of species, mainly including phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), and flavonoid 3-O-glucosyltransferase (UF3GT), and the stable anthocyanins can be synthesized by various modifications, such as methylation, glycosylation and acylation [8, 9]. Several transcription factors have been reported to be involved in the anthocyanin biosynthesis, mainly including MYB, bHLH and WD40. The MYB transcription factors can regulate the anthocyanin biosynthesis independently or form MYB-bHLH-WD40 (MBW) complexes to regulate the anthocyanin biosynthesis [6, 10]. Up to now, many MYB TFs associated with anthocyanins biosynthesis has been studied in poplar, such as PtrMYB116, PtrMYB117, PtrMYB118, PtrMYB119, PtrMYB120 [11,12,13]. However, the functions of bHLH TFs in poplar have been investigated fewer compared with these of MYB TFs.

The bHLH TFs are the second largest family of plant TFs, and play a central role in anthocyanins biosynthesis [14, 15]. The conserved bHLH domain contains 50 to 60 amino acids and processes two functional regions: basic region and HLH region [16]. The basic region contained approximately 17 amino acids, which located at the N-terminus of bHLH domain and binded to a consensus hexanucleotide E-box (CANNTG) [17]. The HLH region with 50 amino acids was used to form the homodimers or heterodimers, which includes two alpha helixes separated by a variable loop [18]. bHLH TFs are involved in several plant metabolic pathways including flavonoids and anthocyanin biosynthesis [19]. The Lc protein was the first reported bHLH TFs in maize, which can be involved in the anthocyanin biosynthesis through regulating at least 2 structural genes [20]. Moreover, several bHLH TFs related to anthocyanin biosynthesis were identified and further characterized in other plants, such as Arabidopsis (AtEGL3, AtGL3, and AtTT8) [21], V. vinifera (VvMYCA1) [22], N. tabacum (NtAn1 and NtAn2) [23], M. domestica (MdbHLH3 and MdMYC2) [24, 25] and poplar (PdTT8) [26]. In poplar, PdTT8 directly interacts with PdMYB118 TF to regulate wound-induced anthocyanin biosynthesis [26]. However, several questions are still needed to be explored. Is there other bHLH TFs involved in the anthocyanin biosynthesis in poplar? What’s the difference among the different bHLH TFs associated with anthocyanin biosynthesis in different species? What’s the difference among the different bHLH TFs involving the anthocyanin biosynthesis in poplar? The genome-wide identification and characterization of bHLH gene family in poplar could give us the answer of these questions.

The genome-wide identification and characterization of bHLH gene family has been conducted in many plants [14, 27, 28]. There is 162 bHLH genes in Arabidopsis, 192 in tobacco, 159 in tomato, and 188 in apple, which can be divided into 15–26 subfamilies [28]. Among these subfamilies, members of the III subfamily have been proved to be involved in anthocyanin synthesis [29]. Therefore, bHLH TF in poplar falling into the III subfamily might also be involved in anthocyanin synthesis. In present study, the phylogenetic analysis, gene or protein structures, gene duplication, and chromosome distribution of PdbHLH transcription factors were systematically and comprehensively investigated. Moreover, the expression pattern of PdbHLH genes in green leaf poplar (L2025) and colored leaf poplar (QHP) was evaluated with the released RNA-seq data [5]. To better explore the functions of PdbHLH genes in poplar, the expression pattern of PdbHLH genes in green leaf poplar (L2025) and colored leaf poplar (JHP) was further analyzed with the released RNA-seq data [30]. Our findings should not only provide a characterization of the PdbHLH gene superfamily but also provide insight into the roles of PdbHLH genes in the regulation of anthocyanin biosynthesis in colored-leaf poplar.

Methods

Identification of PdbHLH gene family in P. deltoids

The genome sequence and corresponding annotations of P. deltoids was downloaded from the DOE Joint Genome Institute website [31] (http://genome.jgi.doe.gov/). The hidden Markov Model profile of HLH (PF00010) domain obtained from Pfam database [32] (http://pfam.xfam.org/) was used to search candidate PdbHLH genes from P. deltoids genome using the HMMER3 software package [33]. Moreover, the physical localizations of all candidate genes and redundant sequences with the same chromosome location and short proteins (length < 100 aa) were further checked. Next, the Pfam [32] and SMART [34] (http://smart.embl-heidelberg.de/) databases was used to further verify the presence of HLH domain for all candidate protein sequences. After the above three steps, the identified protein sequences that contained the core domain (HLH) of known PdbHLH were regarded as putative homologs in the study.

Sequence analysis and structural characterization of PdbHLH genes in P. deltoids

Based on the genome sequence and annotation information, the exon-intron organization of PdbHLH genes, including intron distribution, number, and phases, was graphically displayed by the Gene Structure Display Server GSDS2.0 (http://gsds.cbi.pku.edu.cn/). The MEME suite (http://meme-suite.org/tools/meme) was used to identify the conserved motifs of PdbHLH proteins [35]. The optimized parameters were employed for the analysis as follows: maximum numbers of different motifs, 20; minimum motif width, 6 bp; maximum motif width, 50 bp.

Chromosome distribution, gene duplication, and synteny analysis of PdbHLH genes in P. deltoids

The chromosome distribution of PdbHLH genes was extracted from the genome annotation database, and the MapChart software was used to visualize the chromosomal locations of the PdbHLH gene [36]. Gene duplication analyses for P. deltoids was conducted using the Multiple Collinearity Scan Toolkit (MCScanX) [37]. To identify candidate homologous gene pairs (E < 1e− 5), BLASTp was performed to search for potential homologous gene pairs across the whole P. deltoids genome. The potential homologous gene pairs were inputted into the program MCScanX with the default parameters to identify syntenic chains. MCScanX was used to further distinguish among whole-genome duplication (WGD)/segmental, dispersed proximal, and tandem duplication events in PdbHLH gene family [37]. Gene pairs identified in the same synteny block were used to calculated Ka and Ks values using PAML package [38].

Cis-elements in the promoter regions of PdbHLH genes and GO enrichment analyses

Conserved cis-regulatory elements in the promoter region of PdbHLH genes were identified by analyzing the 2000-bp sequence upstream of the transcription start site (TSS) obtained from TBtools. Promoter sequence analysis was performed using PlantCARE [39, 40].

GOATOOLS (http://github.com/tanghaibao/GOatools) was used to perform GO annotations for PdbHLH genes. The biological function enrichment analysis for PdbHLH genes was conducted using Fisher’s exact test. Moreover, the Bonferroni multiple testing correction was used to minimize false positives, and functions were considered to be significantly enriched when their Bonferroni-corrected P-values (Padjust) were < 0.05.

Phylogenetic relationships analysis of PdbHLH gene family in P. deltoids

The bHLH protein sequences, including PdbHLH, OsbHLH, and AtbHLH proteins from poplar, rice and Arabidopsis were aligned using the Muscle algorithm with default parameters. The best-fit model of protein evolution was selected using the Model-Generator program [41]. An unrooted neighbor-joining phylogenetic tree was constructed through multiple sequence alignments of these bHLH proteins using MEGA 10.0, and these bHLH proteins were further grouped into different clades based on the topology of the phylogenetic tree. The parameters were as follows: pairwise deletion, Poisson model, and 1000 bootstrap replications.

Expression analyses of PdbHLH genes in ‘Jinghong poplar’ (JHP), ‘Quanhong poplar’ (QHP) and Populus sp. Linn. 2025 (L2025) by RNA-seq

RNA-seq data for the PdbHLH genes were obtained from previous studies of differential gene expression in colored-leaf polar (JHP and QHP) and green leaf poplar L2025 [5, 30] RNA-seq data for each PdbHLH were extracted, analyzed, normalized, and displayed in heat maps. The transcript abundance of PdbHLH genes was calculated as fragments per kilobase of exon model per million mapped reads (FPKM). The log2 (FPKM) from the RNA-seq data were subjected to hierarchical clustering with Cluster 3.0, and the results were graphically displayed using Java TreeView [35].

Validation of RNA-seq reliability in the leaves of JHP, QHP and L2025

To validate the reliability of RNA-seq results, the expression levels of 9 PdbHLH genes associated with anthocyanin biosynthesis in the leaves of JHP, QHP and L2025 were evaluated by qRT-PCR using an Applied Biosystems 7500 Real-Time PCR system (Applied Biosystems, Waltham, MA, USA). Gene-specific primers were designed according to the sequence of PdbHLH genes (Table S1), and the ACTIN2 gene was used as a control gene [12]. The relative expression levels of 9 genes were analyzed using SPSS 17.0 with three biological replicates.

Protein interaction prediction

To investigate potential differential proteins that interact with PdbHLH proteins involved in anthocyanin biosynthesis, the putative PdbHLH protein sequences associated with anthocyanin biosynthesis were screened according to their phylogenetic analysis and expression pattern, and submitted to the online server STRING v10 (https://string-db.org). The PPI networks were constructed based on the active interaction sources with required confidence score > 0.4 in Arabidopsis, which included biological experiments, co-expression and databases. The PPI networks were visualized by Cytoscape software (v. 3.8.1). ClusterONE software was used to detect highly connected regions of the network, and the criteria are as follows: minimum density = 0.01, minimum size = 2 and edge weights = combined_score. The nodes and edges in the networks represent proteins and interactions, respectively. The interactions between bHLH proteins involved in anthocyanin biosynthesis and potential differential proteins in JHP and QHP were screened by STRING.

Results

Identification and chromosome distribution of the PdbHLH gene family in P. deltoids

There are 185 PdbHLH family proteins identified in P. deltoids (Table S2). The PdbHLH proteins range in size from 129 (PdbHLH72) to 943 (PdbHLH185) amino acids, with an average length of approximately 373 amino acids. The molecular weight of the identified PdbHLH proteins ranged from 14.95 kDa (PdbHLH72) to 103.49 kDa (PdbHLH185), and the predicted isoelectric points of these proteins ranged from 4.62 (PdbHLH58) to 9.46 (PdbHLH62). In addition, the subcellular localization of the identified PdbHLH proteins was also predicted, and 181 of 185 (approximately 97.8%) PdbHLH proteins were localized in the nucleus (Table S2). According to the information of gene annotation, the predicted 185 PdbHLH genes were localized on poplar chromosomes. As shown in Fig. 1, the congregate region and the number of PdbHLHs is unevenly although the PdbHLH genes distributed on all of the 19 chromosomes. Chromosome 2 possessed the largest number PdbHLH genes (19), while only four PdbHLH genes were present on chromosome 17. The percentage of PdbHLH genes per chromosome varied from 0.23% on chromosome 17 to 0.65% on chromosome 2 (Table S3).

Fig. 1
figure 1

Chromosome distribution and tandem duplication events for PdbHLH genes. The position of each PdbHLH is noted on the right side of each chromosome (Chr). The size of a chromosome is indicated by its relative length. Tandemly duplicated genes are indicated with a red bar

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Phylogenetic analysis of the PdbHLH gene family among Arabidopsis, rice, and P. deltoids

An unrooted phylogenetic tree of the bHLH family genes in P. deltoids Arabidopsis, and rice was constructed using the neighbor-joining method with the default parameters of MEGA 10.0 (Fig. 2). The PdbHLH family members of P. deltoids were divided into 15 groups (I to XV) according to the topology of the phylogenetic tree, as well as the classification and nomenclature of bHLH proteins in Arabidopsis and rice. The number of PdbHLH genes in different group was different. Group III, containing 37 PdbHLH genes, is the largest group in the 15 groups, which was further divided into 5 subgroups (subgroup a-e). Group XII and V contained 24 and 19 PdbHLH genes, respectively. Group XV only contained the bHLH genes of Aranidopsis and rice, and didn’t include the bHLH gene of P. deltoids. Apart from the groups II, IV, V, and XII, the other groups contained much more bHLH genes in P. deltoids than those in Arabidopsis and rice. In addition, some groups were further classified into two or more subgroups (Fig. 2). Subgroup VIIIa1, and IIIa-c mainly contained the bHLH gene clusters in P. deltoids, indicating that the species-specific expansion of these genes occurred in P. deltoids after the divergence of core eudicots. In addition, some subgroups just contained AtbHLH or OsbHLH genes without PdbHLH genes, suggesting that bHLH genes could have been either acquired and expanded in Arabidopsis or rice during evolution process or specially lost in P. deltoids.

Fig. 2
figure 2

Phylogenetic analysis of bHLH gene family in Arabidopsis, rice and P. deltoids. An un-rooted phylogenetic tree of bHLH gene family among Arabidopsis, rice and P. deltoids was constructed using the neighbor-joining method in MEGA 10.0 software with a bootstrap test (replicated 1000 times). The bHLH gene families in Arabidopsis, rice and P. deltoids were marked black, dark green and red, respectively

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Gene structure and protein motif analysis of the PdbHLH gene family in P. deltoids

To better analyze the structural diversity and motif composition of PdbHLH genes, the investigation of intron and exon distribution profile was conducted and visualized using the Gene Structure Display Server 2.0 (GSDS, Fig. 3). A total of 185 PdbHLH genes possessed exons varying from 1 to 12. Fourteen PdbHLH genes lacked introns and had only one exon, including PdbHLH43, PdbHLH48, PdbHLH53, PdbHLH54, PdbHLH55, PdbHLH56, PdbHLH85, PdbHLH117, PdbHLH118, PdbHLH132, PdbHLH144, PdbHLH152, PdbHLH176, PdbHLH179. The majority (171 of 185) of the PdbHLH genes have 2 to 8 introns, and PdbHLH19 contained 12 exons and 11 introns, which was the greatest number of exons in the total PdbHLH genes. As expected, gene structure analysis showed that most members in the same group had similar intron/exon compositions, including the numbers and length of exons. For example, all the members of subfamily XV have more than 5 exons, and all the members of group X have 3 exons. Thus, our results indicate that PdbHLH genes in the same group or subgroup had similar gene structures, further verify the phylogenetic relationship of these PdbHLH genes (Fig. 2).

Fig. 3
figure 3

Schematic diagram of exon/intron distribution and amino acid motifs of PdbHLH family genes in P. deltoids. a Exon/intron distribution of of PdbHLH genes in P. deltoids. The exons are represented by orange round-cornered rectangles. The black lines connecting two exons represent introns. b Distribution of conserved motifs in each PdbHLH proteins. Schematic diagram of motif structure in P. deltoids PdbHLH gene family using MEME. The relative positions of each conserved motif within the PdbHLH proteins are shown in color. The black lines represent the non-conserved sequences

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There were 15 putative conserved protein motifs identified in the PdbHLH proteins through MEME analysis (Motifs 1–15, Fig. 3, Fig. S1). Motifs 1 the basic region and the first helix, and Motif 2 contained the second helix, both of which correspond to the bHLH domain. The bHLH domain has been identified in all PdbHLH proteins. Seven PdbHLH genes, including PdbHLH38, PdbHLH39, PdbHLH175, PdbHLH176, PdbHLH166, PdbHLH127 and PdbHLH108, only contained the Motifs 1 and Motif 2. In each group, the components of the conserved motifs for most of the proteins were similar (Fig. 3b). For example, Motif 11, Motif 9, and Motif 15 were specifically distributed in the groups V, X, and XII, respectively. Motifs 6-8, 10-14 were commonly identified in all members of group IX.

Pivotal cis-elements in the promoter of PdbHLH genes in P. deltoids

Cis-regulatory elements, which are usually restricted to 5′ upstream areas of genes, are the binding sites of TFs, and are responsible for transcriptional regulation. Thus, the 2000 bp upstream of the transcription start site (TSS) of PdbHLH genes were used to explore gene regulation patterns with PlantCARE (Fig. S2). There were 23 functionally annotated cis-elements in the promoter of most PdbHLH genes, which were roughly divided into three categories: light-responsive elements (GT1-motif, I-box, AT1-motif, G-box, GATA-motif, GA-motif, Box II, Gap-box, L-box, CGTCA-motif, CAG-motif, AAAC-motif, and GTGGC-motif), stress-responsive elements [MYB-recognizing element (MRE), MYB-binding site (MBS), GC-motif, TC-rich repeats, LTR, and CCAAT-box]; and hormone-responsive elements (TCA-element, P-box, ABRE, TGACG-motif, TGA-element, GARE-motif, TATC-box, and SARE). The presence of MRE and MBS cis-elements in the PdbHLH gene promoter suggests that bHLH proteins might be transcriptional regulated by MYB TFs in P. deltoids to modulate the expression of downstream targets.

GO enrichment analysis of the PdbHLH genes in P. deltoids

The bHLH proteins play a central role in a wide range of metabolic, hysiological, and developmental processes in higher plants. To further investigate the biological functions of the PdbHLH genes in P. deltoids, gene ontology (GO) annotation and enrichment analysis of the 185 PdbHLH genes were performed in present study (Fig. 4 and Table S4). Six molecular functions, two cellular components, and fifty-two biological processes in GO terms were enriched in the PdbHLH genes relative to the complete GO database. In the biological process category, PdbHLH genes were mainly enriched in flower development (n = 10), plant epidermis development (n = 10), floral organ development (9), floral whorl development (9), plant organ morphogenesis (7), response to red or far red light (7) and so on. In the cellular component category, the genes were enriched in RNA polymerase II transcription (5) and transcription regulator complex (5). In the molecular function category, the genes were enriched in DNA-binding transcription activator activity (14), DNA-binding transcription activator activity and RNA polymerase II-specific (13), DNA-binding transcription factor activity and RNA polymerase II-specific (13), RNA polymerase II transcription regulatory region sequence-specific DNA binding (7), identical protein binding (7) and transcription factor binding (5). GO enrichment results suggested that PdbHLH TFs mainly involved in nucleic acid-binding TF activity, catalytic activity, developmental processes of cellular and multi-organism.

Fig. 4
figure 4

GO enrichment analysis of the PdbHLH proteins relative to the GO database. The vertical axis indicates the enrichment factor, and the size of the circle indicates the number of genes annotated with a given GO term. GOATOOLS (http://github.com/tanghaibao/GOatools) was used to assign GO annotations to PdbHLHs, and Fisher’s exact test was used to identify biological functions enriched in the PdbHLHs relative to the full GO database. Visualization was performed using the Majorbio online platform (https://cloud.majorbio.com)

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Gene duplication events of the PdbHLH gene family in P. deltoids

Several gene duplication events, including WGD or segmental duplication, tandem duplication, dispersed gene duplication and others, promote the evolution of protein-coding gene families [42]. In the present study, the origins of duplicate genes for the PdbHLH gene family in P. deltoids genome was detected with MCScanX package. Each member of PdbHLH gene family was assigned to one of five different categories: singleton, WGD/segment duplication, tandem, proximal and dispersed. Remarkably, 31 (16.7%), 57 (30.8%) and 57 (30.8%) of the PdbHLH family genes in P. deltoids were duplicated and retained from singleton, proximal, and whole genome duplication (WGD)/segmental duplication, respectively (Fig. S3). Only five PdbHLH genes originated from tandem duplication. However, there was no PdbHLH genes originated from proximal in our results (Fig. S3).

To further explore the potential evolutionary mechanisms of PdbHLH gene family, the collinearity analysis of the PdbHLH gene family in P. deltoids genome was performed using the all-vs.-all local BLASTP and MCScan methods (Fig. 5). A total of 33 segmental duplication events with 52 PdbHLH genes were identified in the P. deltoids genome, which accounted for 91.2% of WGD-type PdbHLH genes (Fig. 5 and Table S5). PdbHLH genes were located within synteny blocks on all chromosomes. Subsequently, non-synonymous to synonymous substitution ratio (Ka/Ks) was calculated using the pairwise model by maximum likelihood (PAML v8.0, Table S5). Ka/Ks < 1 indicates purifying selection, whereas Ka/Ks > 1 is the signature of positive selection (Hurst, 2002). In the present study, the Ka/Ks ratios of 32 PdbHLH gene pairs were less than one, implying that these genes are under negative purifying selection, which maintained the functions of the PdbHLH gene family in P. deltoids. Moreover, Ks was usually used to estimate the evolutionary dates of genome or gene duplication events. The WGD/segmental duplicated events in P. deltoids occurred from 6.42 (Ks = 0.1927) to 90.14 mya (Ks = 2.8244).

Fig. 5
figure 5

Genomic locations of PdbHLH genes and segmentally duplicated gene pairs in the P. deltoids genome (a) and the orthologous relationships of PdbHLH TFs with Arabidopsis (b) and rice (c). The black lines in a indicated 33 segmentally duplicated PdbHLH gene pairs. The chromosome number is indicated at the top of each chromosome. Ka (d), Ks (e), and Ka/Ks (f) ratio of segmental duplicate genes and orthologous genes among rice, Arabidopsis, and P. deltoids. The box plots are exhibiting the distributions of Ka, Ks, and Ka/Ks values among paralogs and orthologs. The small square and the line in the box represent average and median values of the Ka, Ks, and Ka/Ks values, respectively. Pd: P. deltoids; At: Arabidopsis; Os: Rice

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The orthologous relationships of the PdbHLH family genes among Arabidopsis, Rice and P. deltoids were also investigated by collinearity analysis (Fig. 5, Table S6 and Table S7). There were 56 orthologous bHLH gene pairs between P. deltoids and Arabidopsis and 20 orthologs between P. deltoids and rice (Fig. 5). The number of orthologous events of PdbHLH-AtbHLH was much greater than that of PdbHLH-OsbHLH. The details of the collinear bHLH gene pairs were provided in Table S6 and S7.

Expression profile of the PdbHLH genes in colored-leaf poplar JHP and green-leaf poplar L2025

To evaluate the expression pattern of PdbHLH genes in colored-leaf poplar, the expression profiles of PdbHLH genes in the leaves of JHP and L2025 was evaluated using the previous RNA-seq data (Fig. 6, S4 and Table S8). The expression level of candidate PdbHLH genes in the leaves of JHP was more than 10 times that these in L2025, including 1 PdbHLH gene from Group I, 10 PdbHLH genes from Group III, 4 PdbHLH genes from Group IV, 4 PdbHLH genes from Group V, 5 PdbHLH genes from Group VII, 3 PdbHLH genes from Group IX, 2 PdbHLH genes from Group XI, 9 PdbHLH genes from Group XII, and 1 PdbHLH gene from Group XIII. These candidate PdbHLH genes are shown in Table S8. Among them, the expression levels of 12 PdbHLH genes (PdbHLH141, PdbHLH95, PdbHLH140, PdbHLH57, PdbHLH136, PdbHLH91, PdbHLH94, PdbHLH156, PdbHLH1, PdbHLH173, PdbHLH148, and PdbHLH143) were more than 100 times than that in L2025. In addition, the expression level of 23 PdbHLH genes in the leaves of L2025 was more than 10 times that these in JHP (Table S8). Among them, the expression level of 2 genes (PdbHLH4 and PdbHLH 36) in the leaves of L2025 was more than 40 times that these in JHP. These results suggested that these genes might be involved in regulating the anthocyanin biosynthesis.

Fig. 6
figure 6

Gene expression pattern of PdbHLHs in the leaves of JHP and L2025 by RNA-seq. The scale bars represent the log2 transformations of the RPKM values

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Expression profile of the PdbHLH genes in colored-leaf poplar QHP and green-leaf poplar L2025

To further verify the expression pattern of PdbHLH genes, the expression level of PdbHLH genes in the leaves and buds of QHP and L2025 was evaluated using the previous RNA-seq data. A total of 102 PdbHLH genes were detected based on the RNA-seq analysis in leaves and buds of QHP and L2025 (Fig. 7, S5 and Table S9). Among them, the expression levels of 21 PdbHLH genes in the leaves and buds of QHP were significantly higher than that of L2025, and 2 genes (PdbHLH143 and PdbHLH9) were specifically expressed in the leaves and buds of QHP, indicating that these 2 genes might be involved in the positive regulation of anthocyanin biosynthesis. PdPdbHLH123 gene was specifically expressed in the buds of poplar, and the expression level of this gene in the buds of QHP was more than 16 times than that of L2025. Moreover, the expression level of 20 PdbHLH genes in buds and leaves of L2025 were higher than those in QHP (Table S9). Among them, the expression level of 3 PdbHLH genes (PdbHLH183, PdbHLH73, and PdbHLH85) in leaves of L2025 were more than 5 times than those in QHP, and 2 genes (PdbHLH67 and PdbHLH74) were specifically expressed in the leaves of L2025.

Fig. 7
figure 7

Expression profle of PdbHLH genes in the leaves and buds of the QHP and L2025. QHP-L, QHP leaf; L2025-L, L2025 leaf; QHP-B, QHP bud; L2025-B, L2025 bud

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Combined with the comparative transcriptome data between the green leaf poplar and colored-leaf poplar (JHP and QHP), the candidate genes associated with leaf coloration were further screened (Table S10). The expression level of 12 PdbHLH genes (PdbHLH12, PdbHLH131, PdbHLH143, PdbHLH156, PdbHLH160, PdbHLH173, PdbHLH20, PdbHLH57, PdbHLH7, PdbHLH82, PdbHLH91, and PdbHLH95) in leaves of JHP was more than eight times than those in L2025, and their expression in leaves of QHP was different from those in L2025, suggesting that these genes may be involved in positively regulating the anthocyanin biosynthesis. In addition, the expression level 4 PdbHLH genes (PdbHLH4, PdbHLH1, PdbHLH18, and PdbHLH164) in leaves of L2025 was more than 10 times than those in JHP, and its expression in leaves of L2025 was slightly higher than those in QHP, suggesting that these genes may be involved in negatively regulating the anthocyanin biosynthesis. Therefore, these 16 PdbHLH genes might be involved in the anthocyanin biosynthesis in leaf coloration in poplar.

Validation of RNA-Seq-based gene expression

To validate the reliability of RNA-seq results, RT-PCR was performed on 9 genes associated with anthocyanin biosynthesis selected at random with high or low expression levels. Expression comparisons were performed in the leaves of L2025, QHP and JHP, and the expression trends in RT-PCR results were in agreement with the RNA-Seq data (Fig. S6).

Protein interaction prediction

Different bHLH proteins can form homodimers or heterodimers to bind DNA and regulate the transcription of downstream targets, which can interact with MYB and WD40 TFs to form a ternary complex (MBW) that regulates the expression of anthocyanin biosynthesis and structural genes [43, 44]. Thus, to further investigate the interaction networks of candidate PdbHLH TFs, protein interaction networks of sixteen PdbHLH proteins associated with anthocyanin biosynthesis were conducted. In our study, 16 candidate PdbHLH genes associated with leaf coloration were used to perform protein interaction networks, and 11 of them interacted with more than one protein (Fig. 8 and Table S11). In particular, two PdbHLH proteins (PdbHLH131, PdbHLH156) can interact with three kinds of PdMYBs, PdWDs and PdbHLHs (Fig. 8). PdbHLH20, PdbHLH173 and PdbHLH57 can interact with two kinds of PdMYBs, PdWDs and PdbHLHs, and the left ones can only interact with one kind of PdMYBs, PdWDs and PdbHLHs. However, most of them interact with PdMYBs. Interestingly, PdbHLH57, corresponding to PdTT8 associated with anthocyanin biosynthesis, can interact with many kinds of PdMYBs (such as PdMYB117, PdMYB112) and PdWDR6. It is very interesting to explore the regulation of MYB-bHLH-WDR40 model in the anthocyanin biosynthesis in poplar.

Fig. 8
figure 8

Protein interaction network analysis for the candidate PdbHLHs associated with anthocyanin biosynthesis. The online tool STRING was used to predict the network

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Discussion

The bHLH transcription factors comprise a large family in higher plants, and numerous studies have shown that bHLH transcription factors are involved in diverse biological processes in plant growth, development, and stress responses [45]. However, a systematic characterization of bHLH genes in P. deltoids has not been performed. In this study, the genome-wide identification and characterization of bHLH family genes in P. deltoids were carried out. A total of 185 PdbHLH genes have been identified and divided into 15 groups based on phylogeny, gene structure and protein motif analyses.

Moreover, the number of bHLH family genes from lower plants (Volvox carteri, Chlamydomonas reinhardtii) to higher plants (Oryza sativa, Solanum lycopersicum, Vitis vinifera, Fragaria vesca, Arabidopsis thaliana, Brassica rapa, P. deltoids, and Malus domestica) were further investigated. There are a large number of bHLH family genes in higher plants, while a little number of bHLH family genes in lower plants. There was/were only one or few bHLH family gene (s) in each lower plants [17, 46]. The above results indicated that the expansion of bHLH gene family occurred in higher plants. Gene duplication events, including five types of gene duplication events, namely WGD (whole-genome duplication), dispersed, tandem, proximal and singleton duplications, contribute to the expansion of protein-coding gene families in plants [47,48,49]. Some large transcription factor gene families, such as APETALA2/ethylene-responsive factor (AP2/ERF) and WRKY, most likely expanded through WGD/segmental duplication and tandem duplication [40,41,42,43,44,45,46,47,48,49,50,51,52]. Conversely, the expansion of some other transcription factor gene families, such as MADS (Minichromosome Maintenance1 Agamous Deficiens Serum response factor) box gene family and NBS-LRR (nucleotide-binding site–leucine-rich repeat) gene family, are derived from the transposed duplication [44]. In our results, above 60% of the PdbHLH family genes in P. deltoids were duplicated and retained from proximal and whole genome duplication (WGD)/segmental duplication, respectively, suggesting that the WGD/segmental and proximal duplication contributed to the expansion of PdbHLH family genes. Gene expansion is accompanied by subfunctionalization and neofunctionalization, as well as gene expression patterns and protein-protein interactions. PdbHLH143 and PdbHLH148 were derived and retained from WGD/segmental duplication events. PdbHLH143 was highly expressed in the leaves and buds of QHP, while the expression of PdbHLH148 was not detected in the leaves and buds of QHP, which indicated that PdbHLH143 might be involved in the anthocyanin biosynthesis in the color-leaf poplar.

The promoter of a gene contains cis-regulatory elements that can potentially reveal gene function [53]. Our result showed that the upstream promoter of bHLH genes in P. deltoids contained three types of cis-elements, including light-, stress-, and hormone-responsive elements (Fig. S2). Moreover, the promoters of PdbHLH genes contained the bHLH binding site (G-box), MYB-recognizing element (MRE), MYB-binding site (MBS), indicating that PdbHLH TFs can interact with each other or with MYB TFs or WDR40 TFs in the regulation of the growth and development in P. deltoids, including the anthocyanin biosynthesis, which was confirmed by the PPI network in our study (Fig. 8).

Genome-wide identification and characterization of bHLH family genes in many plants revealed that members of the III (f) subfamily have been proved to be involved in anthocyanin biosynthesis [28, 29, 54]. The FabHLH29 gene of white-flesh strawberry mutant, a member of the III (f) subfamily in bHLH TFs, has been reported to be involved in the anthocyanin biosynthesis [28]. In Freesia hybrida, two members of III (f) subfamily in bHLH TFs, FhGL3L and FhTT8L, contributed to the biosynthesis of flavonoids and anthocyanin [55]. Moreover, bHLH proteins of III (f) subfamily were involved in regulating the anthocyanin biosynthesis by interacting with MYB and WDR. In chrysanthemums, CmbHLH2 gene of III (f) subfamily regulates the anthocyanin biosynthesis by interacting with CmMYB6 to generate CmbHLH2-CmMYB6 complex, which can bind to the promoter of CmDFR gene [28]. VvMYC1, the first bHLH TF described in the grapevine, can control anthocyanin and proanthocyanidin biosynthesis through interacting with MYB5a, MYB5b, MYBA1/A2 and MYBPA1 [56]. In strawberry fruits, FvbHLH9 could form a HY5–bHLH9 complex with HY5 TF, which can positively regulate the anthocyanin biosynthesis [57]. PdTT8, one of bHLH transcription factors in poplar, physically interacted with PdMYB118 could form the PdMYB118-PdTT8 complex, which can regulate wound-induced the anthocyanin biosynthesis [26]. The PdbHLH57 in our study corresponding to previous PdTT8 belonged to the III (f) subfamily, and PdbHLH57 can interact with many kinds of PdMYBs, including PdMYB117 similar with PdMYB118, which is consistent with previous results. PdbHLH57 can also interact with PdWDR6, which can form PdMYB- PdbHLH57- PdWDR6 complex to regulate the anthocyanin biosynthesis. However, the detailed functions are still needed to be explored. In addition, the expression level of PdbHLH57 in the leaves of JHP is much higher than that in the leaves of L2025, and there is a slightly higher expression level than that in the leaves of L2025, which indicated that PdbHLH57 might play important roles in the leaf coloration of JHP. Another two PdbHLH genes PdbHLH143 and PdbHLH173, belonging to the III (f) subfamily, the expression level of which in colored-leaf of polar was higher than these in green-leaf of poplar, indicating that these two genes might also be involved in the anthocyanin biosynthesis in poplar. In addition, nine PdbHLH genes (PdbHLH20, PdbHLH7, PdbHLH12, PdbHLH91, PdbHLH95, PdbHLH82, PdbHLH156, PdbHLH160, and PdbHLH13) did not include into the III (f) subfamily, however, the expression level of which in colored-leaf of polar was also higher than these in green-leaf of poplar, suggesting that these genes may be used as the candidate gens to regulate the anthocyanin biosynthesis. CpbHLH1 is a transcription factor from Chimonanthus praecox. Overexpression of CpbHLH1 in Arabidopsis and tobacco resulted in a dramatic decrease in anthocyanin accumulation by repressing the expression of late biosynthesis genes in the flavonoid biosynthesis pathway [58]. In our study, four genes (PdbHLH4, PdbHLH1, PdbHLH18, and PdbHLH164) displayed higher expression in the leaves of L2025 than those in colored-leaf poplar (JHP and QHP), which indicated that these genes might be involved in reducing the anthocyanin accumulation.

Conclusions

In this study, 185 PdbHLH genes were identified in the Populus deltoids genome and were classified into 15 groups based on the sequence similarity and phylogenetic relationships. Conserved domain, gene structure, and evolutionary relationships of PdbHLH genes were also established and analyzed. Investigation of cis-regulatory elements of PdbHLH genes indicated that many PdbHLH genes are involved in the regulation of anthocyanin biosynthesis. Comprehensive analysis revealed that 12 candidate genes, including 3 genes (PdbHLH57, PdbHLH143, and PdbHLH173) from the subgroup III(f) and 9 gene from other groups, were positively associated with anthocyanin biosynthesis. In addition, 4 genes (PdbHLH4, PdbHLH1, PdbHLH18, and PdbHLH164) may be involved in negatively regulating the anthocyanin biosynthesis. The above results could provide a basis for the functional characterization of bHLH genes, and also provide candidate genes for the future improvement of leaf colorization in Populus deltoids.