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Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.)
BMC Genomics volume 22, Article number: 778 (2021)
Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied.
In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions.
In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes.
Basic-helix-loop-helix (bHLH) transcription factors are widely present in eukaryotes. Although they are not unique to plants, they still form one of the largest transcription factor families in plants due to their numerous members [1, 2]. There is a bHLH domain in the bHLH transcription factor family, the domain sequence is highly conserved, with a total of approximately 50–60 amino acid residues. The domain comprises two functional regions: the basic region and the helix-loop-helix (HLH) region [3, 4]. The basic region is located at the N-terminus and contains approximately 15 amino acids. It binds to the cis-acting element E-box (5′-CANNTG-3′) and determines whether bHLH transcription factors bind to DNA [3, 4]. The HLH region is distributed at the C-terminus of the gene sequence. It comprises two α-helices connected by a relatively poorly conserved loop. This structure is essential for the formation of homo- or hetero-dimers by bHLH transcription factors [3, 5, 6]. The basic domain is located at the N-terminus of the conserved bHLH domain; its DNA-binding capacity depends on the key amino acid residues in the basic region and the number of basic amino acid residues in the basic region [5,6,7]. Pires and Dolan  used the entire genome sequence of nine terrestrial plants and algae to classify the evolutionary relationship of bHLH transcription factors in plants. The bHLH transcription factors of these different plants are divided into 26 subfamilies. Twenty of these subfamilies are present in the common ancestor of existing mosses and vascular plants, and six subfamilies continue to differentiate in vascular plants. Many bHLH genes have been identified in the plant kingdom; for example, in model plants, 147 bHLH transcription factors in Arabidopsis were divided into 21 subgroups  and 167 bHLH transcription factors of rice were divided into 22 subgroups . The bHLH family has been widely identified in many plants, including Brassica rapa ssp. pekinensis , Solanum lycopersicum , common bean , Malus pumila , Arachis hypogaea , Brachypodium distachyon , Zea mays , Triticum aestivum , Phyllostachys edulis , Carthamus tinctorius , Chinese jujube , Piper nigrum , Jilin ginseng , Ananas comosus , Fagopyrum tataricum , and sorghum . The bHLH genes have been conserved in the evolutionary history of the plant kingdom. The expansion of this family is closely related to plant evolution and diversity [1, 8] in higher plants as well as in lower plants or non-plants, such as algae, mycobacteria, lichens, and mosses . bHLH genes are mainly involved in the defence response to drought, heat, cold and high salt stresses unique to the terrestrial environment. Therefore, whole-genome analysis of the bHLH family in different species will help to understand the evolution of organisms, such as green algae, to adapt to environmental changes, along with the evolutionary origin of flowering plants.
Plant bHLH transcription factors can have biological roles as both transcriptional activators and repressors, positive and negative regulatory roles in the physiological and biochemical processes of plant light signal transduction, and influence on the development of plant tissues and organs. SPATULA is the first gene found in Arabidopsis thaliana that affects the formation of floral organs and encodes bHLH proteins. Studies on SPATULA mutants have shown that it can promote the growth of plant carpel edges and internal pollen tissues . Heisler et al. proposed that SPATULA controls the development of specific tissues of shoot apex meristems, leaves, petals, stamens, and roots . UDT1 encodes a bHLH protein, isolated from rice . UDT1 significantly affects the differentiation and microspore formation of anther wall and pollen mother cells at the meiotic stage, thereby regulating the development of rice stamens. AtSPCH plays an important regulatory role in the development of Arabidopsis stomata . The bHLH gene Tb1 cloned from maize by Doebley et al. controls the growth and development of buds, side branches, and male flowers in the leaf axils of maize . The bHLH transcription factor family has been shown to play a vital role in plant resistance to harsh environmental factors, such as drought resistance, salt tolerance, and cold tolerance. For example, ICE1 and ICE2 in Arabidopsis and their homologous genes in other species can respond to cold stress response processes [32,33,34]. Overexpression of AtbHLH92 gene in Arabidopsis can significantly enhance the tolerance of plant to salt damage and osmotic stress . In Populus euphratica, the drought resistance of plants overexpressing PebHLH35 was higher than that of the wild type . TabHLH39 has different expression levels in wheat roots, stems, leaves, glumes, pistils, and stamens, and verexpression of TabHLH39 can enhance the tolerance of Arabidopsis plants to drought, salt, and freezing stress in seedlings . FtbHLH3 is a bHLH gene isolated from tartary buckwheat that can be expressed upon exposure to polyethylene glycol (PEG) and abscisic acid (ABA) .
Foxtail millet (Setaria italica L.) is an important food and feed crop. It is one of the oldest cultivated millet crops and is widely cultivated in arid and semi-arid regions in Asia and Africa . It is a diploid C4 panicle crop with a small genome, short life cycle, strong resistance to stress, and a highly conserved genome structure relative to its ancestor, Corgi [40, 41]. Millet has been used as a model monocot crop for abiotic stress resistance research . Although the bHLH gene family may play important roles in abiotic stress resistance and plant development, this family has not been identified in millet. The main gene families identified in this plant are WD40 , MYB , AP2/ERF , ALDH , Dof , SOD , HD-Zip , SSPs , CDPK , and LIM , among others. The genomic sequence of foxtail millet has been reported, laying a foundation for studying the verify, evolution, and expression of genome-wide SibHLH genes [40, 41]. In this study, we identified 187 bHLH genes and divided them into 21 major groups and two orphan genes. In addition, the exon-intron structure, the motif compositions, chromosomal spread, gene duplications, and evolutionary relationships were analysed. The expression of SibHLH members under different tissues and abiotic stresses is discussed. These findings provide valuable clues for future functional identification and evolutionary relationship studies of foxtail millet.
Identification of bHLH genes in S. italica
To identify all bHLH genes in the S. italica genome, two BLAST methods were used to identify all possible bHLH members (Additional file 1: Table S1). They were then renamed SibHLH1 to SibHLH187 according to their location on the S. italica chromosomes. The basic characteristics that were analysed included molecular weight (MW), isoelectric point (pI), coding sequence length (CDS), and subcellular localization (http://cello.life. nctu.edu.tw/).
Of the 187 SibHLH proteins, SibHLH111 was the smallest with 79 amino acids. The largest was SibHLH150 with 897 amino acids. The molecular weight of the proteins ranged from 9.03 kDa (SibHLH147) to 97.04 kDa (SibHLH150). The pI ranged from 4.56 (SibHLH6 and SibHLH68) to 12.03 (SibHLH46), with a mean of 6.88. Of all the SibHLH genes, five contained the bHLH-MYC domain. In the predicted subcellular localisation results, 150 SibHLHs were located in the nucleus, 16 in the chloroplast, 12 in the cytoplasm, seven in the mitochondria, one (SibHLH23) in the endoplasmic reticulum (ER), and one (SibHLH14) in the peroxisome (Table S1). The ratio of SibHLH genes to total genes in the S. italica genome was approximately 0.48%, which was less than that in Arabidopsis (0.59%)  and buckwheat (0.49%) , but higher than that in rice (0.44%) , poplar (0.40%) , and tomato (0.46%) .
Multiple sequence alignment, phylogenetic analysis, and classification of SibHLH genes
To investigate the phylogenetic relationship of the foxtail millet bHLH proteins, we constructed a phylogenetic tree of foxtail millet (187 SibHLHs) and Arabidopsis thaliana (56 AtbHLHs) using the neighbour-joining method (Fig. 1; Additional file 1: Table S1). According to the previously proposed classification method and topological structure [8, 9], 243 bHLH proteins in the phylogenetic tree were divided into 21 main clades (groups 1–21). The unclassified group (UC) contained two SibHLH genes (SibHLH153 and SibHLH176). One hundred and eighty-five SibHLH proteins were distributed unevenly in 21 subfamilies, consistent with the classification of bHLH proteins in Arabidopsis [9, 10]. These data indicate that these proteins have been maintained during the long-term evolution of S. italica. Two bHLH orphan proteins formed two different topological structures from AtbHLH proteins, which may be a new characteristics in the evolution of S. italica diversity (Fig. 1, Table S1).
Among the 21 subfamilies, subfamily 12 displayed the largest number of members (19 SibHLHs) and subfamily 20 displayed the fewest (one SibHLH protein). The phylogenetic tree results showed that some SibHLHs clustered tightly with AtbHLHs (bootstrap support ≥70), suggesting that these proteins may be orthologous and have similar functions.
The AtbHLH proteins and those from subgroups 1 to 21 were randomly selected as representative groups for further multiple sequence comparisons (Fig. 2, Table S1). The basic region was considered 17 amino acids based on previous study . The bHLH domains of S. italica span approximately 50–60 amino acids, which is different from Arabidopsis  and rice . As shown in Fig. 2, although the characteristic bHLH domain is well conserved in S. italica, it is differentiated and diversified in many SibHLH proteins [7, 10, 53]. The loop region was the most divergent region in terms of amino acid domain, especially in subfamily 1, 10, 12, and 14, which has been observed in other plant bHLH proteins, including Arabidopsis , Solanum lycopersic , and Fagopyum tataricum .
Conserved motifs and gene structure analysis of SibHLH genes
By comparing the genomic DNA sequences of SibHLH genes, we obtained the intron and exon structure of SibHLH genes to further understand the structural composition of these genes (Fig. 3, Additional files 1 and 2: Tables S1 and S2). A comparison of localization and number of the exon-intron structures revealed that the 187 SibHLH genes had different numbers of exons, varying from 1 to 13 (Fig. 3A, B). In addition, 24 (12.83%) genes contained one exon, and the remaining genes had two or more exons. The 24 genes lacking introns belonged to four subfamilies (8, 13, 14, and 19), but mainly to subfamily 8. The greatest proportion of SibHLH genes (n = 34) had two exons. Group 11 had the most exons, with 11 (SibHLH35 and SibHLH116) or 13 exons (SibHLH22). Groups 8, 10, 14, and 20 contained one or two exons. Further analyses indicated that groups 12, 15, and 21 showed more diversity in intron numbers. In general, the gene structures in the same subfamily exhibited similarities, although the locations of the exons were different.
The motifs of 187 SibHLH proteins were analysed online using MEME software to further study the characteristic regions of SibHLH proteins (Fig. 3C, Table S2). Ten conserved motifs were found in SibHLH proteins (Fig. 3C). As shown in Fig. 3C, the motifs 1 and 2 were widely distributed in the SibHLHs, except in SibHLH46, SibHLH62, SibHLH108, SibHLH131, and SibHLH187. The two motifs were very close to each other in SibHLH proteins. SibHLH members within the same group generally share a similar motif composition. For example, groups 4, 6, 8, 10, 11, 12, 13, 14, 19, and 21 members contained motifs 1 and 2; groups 1, 2, and 3 contained motifs 1, 2, and 3; group 5 contained motifs 1, 2, 10, and 3; group 20 contained motifs 1, 2, and 5; group 16 and 18 contained motifs 4, 1, and 2; group 17 contained motifs 4, 1, 2, and 5; and group 7 contained motifs 4, 1, 2, and 10. Some motifs were present only in specific subfamilies. In addition, motif 7 was specific to groups 3, 12, 13, and 21, whereas motif 8 was specific to groups 7, 8, 9, and 13. Further analysis showed that some motifs could only be distributed in specific locations of the pattern. Motifs 1 and 2 were always distributed at the start of the pattern in groups 1, 2, 3, 6, 10, 11, 14, and 20. Motif 4 was almost always distributed at the start of groups 16 and 18. Motif 3 was almost always distributed at the end of the pattern in groups 2 and 5. Motif 5 was distributed at the end of the pattern in group 17. The similarity of motif composition of the same subfamily indicates the conservation of the protein structure of the subfamily. The functions of these conserved motifs remain to be elucidated. Overall, the conserved motif composition and gene structure of the same subfamilies were similar, supporting the phylogenetic tree population classification.
Chromosomal spread and gene duplication of SibHLH genes
The distribution of the 187 SibHLH genes on chromosomes (Chr) 1 (I) to 9 (IX) was uneven (Fig. 4, Additional file 3: Table S3). Each SibHLH name corresponds to its physical position from the top to the bottom of S. italica Chr1 to Chr9. Chr9 contained the largest number of SibHLH genes (33 genes, ~ 17.65%), followed by Chr5 (30 genes, ~ 16.04%). Chr8 contained the lowest (5 genes, ~ 2.67%). Chr3 and Chr6 each contained 21 (~ 11.23%) SibHLH genes. Chr1, Chr2, Chr4, and Chr7 contained 25 (~ 13.37%), 20 (~ 10.70%), 9 (~ 4.81%) and 23 (~ 12.30%) SibHLH genes, respectively. Many bHLH gene duplication events were evident in S. italica. Two or more identical genomic regions were found within a 200 kb chromosomal region, which is defined as a tandem repeat event . Sixteen tandem duplication events involving 27 SibHLH genes were observed on chromosomes 1, 2, 3, 5, 6, 7, and 9 (Fig. 4). SibHLH63, SibHLH123, SibHLH124, SibHLH125, and SibHLH129 each had two tandem repeat events (SibHLH63 and SibHLH62 / SibHLH64; SibHLH123 and SibHLH122 / SibHLH124; SibHLH124 and SibHLH123 / SibHLH125; SibHLH125 and SibHLH124 / SibHLH126; SibHLH129 and SibHLH128 / SibHLH130). All SibHLH genes that formed tandem repeat events belonged to the same subfamily. For example, SibHLH164 and SibHLH165 were tandem repeat genes that were clustered together in subfamily 5 (Fig. 4, Table S3).
There were 38 pairs of segmental duplications in SibHLH genes (Fig. 5, Additional file 4: Table S4). As shown in Figs. 5, 73 (39.04%) paralogs were identified in the SibHLH genes, indicating an evolutionary relationship in these SibHLH genes. LG2 had the most SibHLH menmbers (n = 13) and LG8 had the least (n = 2). As expected, most genes were linked within their subfamily, except for SibHLH72 and SibHLH88. For all identified SibHLH genes, groups 3 and 19 had the largest number of linked genes (5 SibHLH genes). In addition, groups 12 and 18 had four genes, while groups 1, 4, 5, 14, 15, 16, and 17 had only one SibHLH gene (Table S4). These results indicate that some SibHLH genes may have been produced by gene duplication and that these tandem duplication events played a major role in the occurrence of new functions in S. italica evolution, along with the amplification of the SibHLH gene family.
Synteny analysis of SibHLH genes
To further elucidate the evolutionary relationship of bHLH proteins in several plants, six comparative synteny maps of S. italica associations with six representative species were constructed. These species included three dicotyledons (A. thaliana, S. lycopersicum, and S. tuberosum) and three monocotyledons (B. distachyon, O. sativa, and Zea mays) (Fig. 6, Additional file 5: Table S5). A total of 153 SibHLH genes displayed syntenic relationships with those in A. thaliana (n = 17), S. lycopersicum (n = 39), S. tuberosum (n = 44), O. sativa (n = 137), B. distachyon (n = 137), and Z. mays (n = 145) (Table S5). The number of orthologous pairs between the other six species (A. thaliana, S. lycopersicum, S. tuberosum, O. sativa, B. distachyon, and Z. mays) were 20, 53, 53, 211, 196, and 268, respectively. Some SibHLH genes were associated with at least three syntenic gene pairs (particularly between S. italica and Z. mays bHLH). These genes included SibHLH32, SibHLH37, SibHLH38, SibHLH107, SibHLH112, SibHLH119, SibHLH149, and SibHLH150, suggesting their important roles during evolution.
In addition, many collinear gene pairs (with 99 SibHLH genes) identified between S. italica and B. distachyon, O. sativa, and Z. mays were not identified in S. italica, A. thaliana, S. tuberosum, and S. lycopersicum. These included SibHLH2 with BGIOSGA006833 / KQJ94140 / Zm00001d016257 and SibHLH6 with BGIOSGA007229 / PNT65750 / Zm00001d053895. Similar patterns were also found among S. italica with O. sativa/ B. distachyon / Z. mays, which indicated that these paralogous genes may be gradually formed after the independent differentiation of monocotyledons (Table S5). In addition, some SibHLH genes were associated with at least one paralogous pair among in six plants (especially between S. italica and Z. mays). These genes included SibHLH1, SibHLH23, SibHLH79, SibHLH87, SibHLH114, SibHLH117, SibHLH11, and SibHLH181, suggesting that these homologous genes already existed before the ancestral divergence. To better observe the evolutionary constraints of the 187 SibHLH genes, the SibHLH genes were subjected to the Tajima D neutrality test. The calculated D of 7.05 deviated markedly from 0, suggesting that the SibHLH gene family might have been involved in the purification and selection pressure during evolution process.
Evolutionary analysis of SibHLH and bHLH genes of several different species
To analyse the evolutionary relationship of the trihelix family of bHLH proteins in S. italica and six other plants (A. thaliana, S. tuberosum, S. lycopersicum, O. sativa, B. distachyon, and Z. mays), an unrooted NJ tree was constructed. The tree contained ten conserved motifs according to the MEME web server relative to the protein sequences of 298 bHLH proteins (Fig. 7, Additional file 2: Table S2). The detailed genetic correspondence was shown in Additional files 1 and 2 . These bHLH proteins in the phylogenetic tree were divided into 21 clades (groups 1–-21). Except for a few SibHLH proteins, such as SibHLH42, SibHLH61, and SibHLH131, all other SibHLH proteins contained motif 2. In addition, many motifs existed only in a few specific SibHLH branches, such as the motifs 8 and 10. In general, the bHLH proteins of O. sativa, Z. mays, and S. italica on the same branch had similar motif compositions. Similar motifs compositions tend to be distributed in some specific bHLH protein subfamilies. For example, serial motifs 10, 1, 2, 4, and 5 tended to gather within the group 7, and serial motifs 3, 1, 2, and 8 tended to gather within group 17.
Expression patterns of SibHLHs in several plant organs
To investigate the potential roles of the SibHLH genes, real-time PCR was used to detect the expression of 15 individual members from different subfamilies. As far as possible, these subfamilies have distant clustering relationships and significant differences in their amino acid structures. The accumulation of the transcriptional products of 15 SibHLH genes from different subfamilies in five organs (third leaf, flag leaves, stems, roots, and fruits) was evaluated (Fig. 8A). Some genes were preferentially expressed in some tissues of S. italica. Most genes were expressed in all the organs. Four genes (SibHLH7, SibHLH8, SibHLH10, and SibHLH32) displayed highest expression in the flag leaves; the expression of two genes (SibHLH29 and SibHLH36) was highest in the fruits, whereas the expression of SibHLH16 and SibHLH22 was highest in the roots, and SibHLH7 and SibHLH22 were highly expressed in the stem.
Some SibHLHs may regulate the fruit development of S. italica, thus affecting its nutritional composition and the development rate. This was assessed by studying the expression of 15 SibHLH genes at 18 (early filling stage), 25 (middle filling stage), and 32 (initial maturity stage) days post-anthesis (DPA) to identify the genes that may regulate the development of fruits of S. italica . The expression levels of most SibHLH genes were different in fruits and glumes during the three fruit development stages. In the fruits of foxtail millet, the expression of three genes (SibHLH1, SibHLH25, and SibHLH46) increased with fruit development, whereas the expression levels of five SibHLH genes (SibHLH22, SibHLH29, SibHLH30, SibHLH47, and SibHLH176) decreased with fruit development. The expression levels of two genes (SibHLH11 and SibHLH36) were highest at DPA 25, whereas the expression levels of four genes (SibHLH7, SibHLH10, SibHLH16, and SibHLH32) were lowest at 18 DPA (Fig. 8B). The expression levels of most genes (SibHLH1, SibHLH7, SibHLH16, SibHLH22, SibHLH25, SibHLH32, SibHLH36, SibHLH46, and SibHLH176) decreased with fruit development, whereas the expression of SibHLH10 increased.
The expression patterns of SibHLH members have shown many coordinated expressions in several plant organs (Fig. S1). Most bHLH genes showed significant positive correlations; for example, five genes SibHLH8, SibHLH32, SibHLH46, SibHLH47, and SibHLH176 were significantly positively correlated, and SibHLH11, SibHLH29, and SibHLH30 were significantly positively correlated. On the other hand, some pairs of SibHLH genes (SibHLH25 and SibHLH29 / SibHLH30; SibHLH10 and SibHLH36; SibHLH1 and SibHLH29) were significantly negatively correlated.
Expression patterns of SibHLH genes in response to different treatments
To further determine whether the expression of SibHLH genes was influenced by different abiotic stresses, the expression of 15 SibHLH members was examined under eight abiotic stresses: acid (0.1 M), alkali (0.2 M), PEG (10%), NaCl (5%), heat (40 °C), cold (4 °C), flooding, and darkness. qRT-PCR analysis was performed to analyse the expression patterns of the 15 SibHLH genes in the roots, leaves, and stems to response the different abiotic stresses (Fig. 9). Some SibHLH genes were significantly upregulated or inhibited under different stresses. Interestingly, the expression levels of SibHLHs showed changes over time or in different organs, depending on the specific treatments. For example, under heat stress, SibHLH29 and SibHLH36 were significantly upregulated and then downregulated. SibHLH16 expression was significantly upregulated in the roots at 24 h, whereas it was significantly downregulated in the leaves. Under acid stress, SibHLH25 was significantly downregulated in the roots and leaves, but SibHLH16 was significantly upregulated. Several genes showed opposing expression patterns during different treatments. Transcript levels of many SibHLH genes, such as SibHLH16 was upregulated in stems and downregulated in leaves by heat stress treatment, whereas its expression pattern was reversed by cold stress. The expression of some genes showed similar patterns under different stress treatments. For example, SibHLH16 expression was unchanged first and then significantly upregulated in the roots by the different treatments. Other genes showed changes in specific organs. For instance, SibHLH7 responded significantly to acid and alkali treatment in the leaves and stems, and SibHLH22 responded significantly to cold treatment in the roots. Furthermore, correlations between SibHLH gene expression patterns were observed (Fig. S2). Negative correlations were observed among the most SibHLH genes. However, a few SibHLH genes were significantly positively correlated, such as SibHLH29 with SibHLH30 / SibHLH46, as well as SibHLH10 with SibHLH16 / SibHLH32 (P < 0.05).
SibHLH gene structure and evolutionary analyses
The encoded proteins of 187 SibHLH genes were structurally distinct, suggesting the complexity of their possible functions (Figs. 1 and 2, Additional file 1: Table S1). The DNA-binding properties were determined by the conserved amino acids in the DNA-binding domain of transcription factors. Similar transcription factors were bound to the same cis-acting elements. The DNA-binding ability of the basic region of SibHLHs was analysed [4, 9] (Table S1). Atchley et al.  identified that Glu-9 and Arg-13 in the basic region are essential amino acid residues for binding to the E- and G-box in the H / K5-E9-R13 mode. A total of 132 SibHLHs (70.6%) were classified as E-box binding proteins, 95 SibHLHs (50.8%) were classified as G-box binding proteins, and 37 SibHLHs (19.8%) were classified as non-G-box binding proteins. In addition, there were 30 non-E-box-binding genes (16.0%). The remaining 25 members (13.4%) were not considered capable of binding to DNA because of a lack of Glu-13 or Arg-16 in the alkaline region (Fig. 2, Attachment 1: Table S1). The highest proportion of SibHLH was G-box binding protein, but the value was lower than that of O. sativa (n = 95, 56.9%) and A. thaliana (n = 89, 60.5%) . Previous studies have found that some key amino acid residues can bind DNA, bHLHs, and other transcription factors to form homo- or hetero-dimers, which can change the interaction between molecules to generate new DNA-binding sites and further generate new functions [9, 56]. For example, His-5, Glu-9, and Arg-13 are closely related to DNA-binding activity, whereas Leu-27 and Leu-57 determine whether bHLH transcription factors can form dimers, which is related to the regulatory function of the bHLH protein. There are two connected helical structures in most SibHLH genes composed of hydrophobic amino acids, including leucine at positions 23 and 64 (Leu23 / 64), leucine or isoleucine at position 54 (Leu / Iso54), and valine (Val61) at position 61. Leu23 and Leu52 residues in the HLH region are necessary for dimer formation [1, 57]. In the present study, the retention rates of Leu-25 and Leu-57 of SibHLHs were 97 and 91%, respectively (Fig. 2), which were lower than those of S. lycopersicum (99 and 97%, respectively)  and Citrus reticulata (both 100%) . Notably, all SibHLH proteins of subfamily 1 lacked Leu-57. We also observed this in sorghum, where none of the proteins had the ability to form dimers in subfamily 1 . However, whether this is related to the independent differentiation of C4 plants requires further investigation.
A total of 185 SibHLH genes were identified and classified into 21 subfamilies according to their phylogenetic relationships with known bHLH genes from Arabidopsis (Fig. 1) [9, 10]. These results indicate their indispensable role in the evolution and development of S. italica. Compared with A. thaliana, these subfamily genes were not lost in S. italica, despite its status as a monocotyledonous C4 plant, suggesting that the diversity of most of the bHLH proteins may have been established in early land plants. In addition, further differentiation of bHLH genes in monocotyledonous plants was supported by the presence of two orphan genes (SibHLH153 and SibHLH176). Our findings support the view that the bHLH family of plants evolved in a highly monophyletic manner , rather than the absence of several types of parallel evolution. Based on the evolutionary tree, the number of members was greater in S. italica group 15 (n = 17, 9.8%) and group 18 (n = 15, 8.6%), similar to that of A. thaliana and rice, suggesting that these bHLH gene groups may have experienced stronger expansion in the long evolutionary process under the characteristics of monocotyledons. The number and proportion of members in groups 5, 12, and 21 were significantly higher than those in Arabidopsis  and similar to those in rice . Whether this differentiation is beneficial for herbaceous and woody plants has not yet been determined.
Significant intron loss or expansion was evident in some SibHLH member domains. These may lead to family expansion and the generation of new functions. Genes with few or no introns are generally expressed at low levels in plants . However, genes with a compact structure may facilitate rapid gene expression in response to plant development or abiotic stress . For example, the expression of SibHLH8 increases rapidly under acid, alkali, and cold stress and may be in response to these abiotic stresses. The extension of gene families and the mechanism of genomic evolution are mainly dependent on tandem repetition and fragment replication [60,61,62,63]. We identified 16 tandem repeat events involving 27 SibHLH genes (Fig. 4, Table S3), especially on chromosomes 3, 6, and 7. In addition, SibHLH genes had 38 pairs of segment duplications (Fig. 5, Table S4). As expected, almost all the expanded genes were mainly within the subfamily, except for SibHLH72 (subfamily 3) and SibHLH88 (subfamily 12), similar to A. thaliana , rice , and Tartary buckwheat . Therefore, segment duplication of SibHLH genes may make a higher contribution to the amplification in the bHLH family in foxtail millet. There were many duplication events in S. italica, nevertheless,,it was still lower than that of the dicotyledonous plants Solanum lycopersicum and S. tuberosum [64, 65].
Expression patterns and function prediction of SibHLHs
The pattern of gene expression is an important factor in determining the function and characteristics of bHLH genes . In this study, the expression patterns of 15 SibHLH genes with significant differences in phylogenetic trees in different organs and different developmental stages of fruits were studied (Fig. 8A, B). Almost all bHLH-TFs were significantly differentially expressed (more than 2-fold differences). SibHLH22 is classified in subfamily 9 and has the highest expression levels in roots and stems. This is similar to the expression pattern of the homologous gene AtbHLH46, which regulates the development of roots and stems in Arabidopsis . In addition, the expression of SibHLH8, SibHLH10, and SibHLH32 in flag leaves of millet was significantly higher than that in the roots, stems, and fruits. Therefore, the possible relationship between these genes and leaf development could be experimentally verified. In addition, SibHLH8 and SibHLH11 were highly correlated (Fig. 8A, Fig. S1). SibHLH8 and SibHLH11 were highly expressed, not only in the evolutionary relationships in the flag leaves of S. italica, but also in fruits and glumes at the middle filling stage (Fig. 8B). The exploration of the evolutionary relationship between SibHLH genes and bHLHs in other plants revealed a similar evolutionary relationship and function. For example, SibHLH30 and AtbHLH30 both belong to subgroup 10 and have similar motif components (Fig. 3, Fig. 7). SibHLH30 is highly expressed in leaves, including flag leaves and the third leaf. Its expression pattern was similar to that of AtbHLH30. Overexpression of AtbHLH30 can alter auxin balance and vein development in A. thaliana, thereby regulating leaf epidermal morphology . AtbHLH42, which is classified under subfamily 7, is expressed much more in fruits than in roots , similar to the expression pattern of SibHLH29. These findings provide a direction for further validation of its function. AtbHLH18 (At2g22750) and AtbHLH20 (At2g22770) were identified in A. thaliana and were highly expressed in the roots. They negatively regulate root development and iron uptake by promoting JA-induced FIT protein degradation . AtbHLH18, AtbHLH20, and SibHLH47 are closely related, and their tissue-specific expression patterns are similar. Therefore, it is necessary to further validate the regulation of root development by SibHLH47. As a typical C4 plant, the development of spikelets and fruits is very important for S. italica. Therefore, to identify the bHLH genes that may regulate the development of foxtail millet fruits, the expression levels of 15 bHLH genes in the pericarp and grain of S. italica during the grain-filling stage were investigated in this study. SibHLH36 displayed high expression levels in all tissues, with the highest expression observed in fruits. Moreover, SibHLH36 expression was the highest in the middle filling stage (green fruit stage). We attempted to further verify the role of SibHLH36 in plant growth and fruit development.
To further explore the physiological role of the bHLH family in environmental adaptation, we systematically analysed the expression of 15 SibHLHs in foxtail millet seedlings under different stressors (Fig. 9). Under drought stress, the expression levels of 13 SibHLH genes in the roots, 11 genes in the leaves, and 10 genes in the stems were significantly upregulated. These responses may help foxtail millet adapt to drought conditions. This is consistent with the nature of millet as a drought-tolerant crop. Similar conclusions have been reached for poplar  and Tartary buckwheat . AtbHLH20 (At2g22770) is preferentially expressed in root epidermal non-hair cells in subfamily 5 of A. thaliana . Similarly, SibHLH47 responded significantly to eight stresses in roots. Its expression was increased during seven stresses (acid, alkali, NaCl, heat, cold, flooding, and dark) but decreased significantly during PEG stress. AtbHLH34, which belongs to the same subfamily 6 as SibHLH7 and has a similar motif composition, can interact with 5′-GAGA-3′ cis regulatory elements in vitro, and activates the transcription of planar AtPGR . This enhances the resistance to abiotic stress. Similarly, the expression of SibHLH7 was significantly upregulated in almost all abiotic stresses, which may enhance the adaptability of foxtail millet to the environment in a similar manner. In addition, AtbHLH45 (At3g06120), AtbHLH97 (At3g24140), and AtbHLH98 (At5g53210) belong to three subfamilies related to stomatal development in leaves [71, 72]. Under drought conditions, SibHLH1 expression was rapidly and significantly upregulated in leaves and stems, which may help regulate stomatal action to reduce water loss. This function is consistent with the physiological characteristics of foxtail millet, which is a drought-tolerant plant. As expected, SibHLH1 expression levels gradually decreased in the dark, which may contribute to stomatal dilation and increased respiration. These expression pattern results suggest that bHLH-TFs are involved in a complex cross-regulatory network. For example, SibHLH29 and SibHLH30 showed a significant positive correlation, and they had a strong response to alkali, NaCl, and dark exposure, suggesting that they have a synergistic regulatory effect under various adverse conditions.
We first identified and analysed the genome-wide SibHLH family in S. italica. These 187 genes were divided into 21 groups and one UC group. Segment and tandem duplications contributed to the expansion of the SibHLH family, and segment duplication may have a more important contribution. We analysed the expression of these genes in different tissues and different fruit development stages during the filling period, in addition to their response to eight abiotic stresses. Based on the above analyses of genetic structures and functional speculation in the SibHLH family, some key candidate genes were preliminarily screened out, such as SibHLH7, SibHLH22, and SibHLH36. These results indicated that the bHLH transcription factors in S. italica may be involved in various physiological processes of plant growth and development. The collective data provides a reference for future studies of bHLH genes on foxtail millet.
We downloaded the entire foxtail millet genome from the Ensembl Genomes website (http://ensemblgenomes.org/). Based on two BLASTp methods [73, 74], bHLH family members were identified. First, the candidate bHLH proteins of foxtail millet were authenticated by a BLASTp search. Second, the hidden Markov model (HMM) file corresponding to the bHLH domain (PF00011) was downloaded from the Pfam protein family database (http://pfam.sanger.ac.uk/). The bHLH protein sequences of foxtail millet were aligned using the HMM model in HMMER3.0, with a cut-off of 0.01 (http://plants.ensembl. org/hmmer/index.html) . The existence of bHLH core sequences was verified using the PFAM and SMART programs (http://smart.embl-heidelberg.de/) [76, 77]. The 187 SibHLH genes were identified in the foxtail millet genome. Then, 187 SibHLH proteins were used as initial queries in the NCBI protein database (https://blast.ncbi.nlm.nih.gov/Blast.cgi? PROGRAM = blastp&PAGE_TYPE = BlastSearch&LINK_LOC = blasthome) using BLASTp to verify bHLH proteins. Finally, the basic features of the trihelix proteins of the bHLH genes of S. italica (sequence length, MW, pI, subcellular localisation) were identified using the ExPasy (http://web.expasy.org/protparam/).
bHLH gene structure and conserved motif analysis
ClustalW was used to create a multi-sequence alignment project with default parameters to further analyse the characteristic domain of the SibHLH proteins . Mega software (version 7.0) and GeneDoc2.7 (http://genedoc.software.informer.com/2.7/) were then used to manually adjust the bHLH structure domain using the deduced amino acid sequences. The gene structure display server (GSDS; http://gsds.cbi.pku.edu.cn) online program  was used to analyse the exon-intron structures of the SibHLH genes. The conserved motifs in the encoded bHLH proteins were studied, to investigate their structural differences. The MEME online program (http://meme.nbcr. net/meme/intro. html) was used to analyse the motifs of the SibHLH proteins [80, 81]. The optimised parameters included a maximum number of motifs of 10 and an optimum width of 6 to 200 residues [81, 82].
Chromosomal distribution and gene duplication
All SibHLH genes were mapped to locations on the S. italica chromosomes based on physical location information. The Circos program was used to process the chromosomal location information of the SibHLH genes . Analysis of SibHLH gene replication events were analysed using multiple collinear scanning toolkits (MCScanX). The homology of the bHLH genes between S. italica and six other plants (A. thaliana, S. lycopersicum, S. tuberosum, B. distachyon, O. sativa subsp. indica, and Z. mays) was analysed using the dual synteny plotter (https://github.com/CJ-Chen/TBtools).
Phylogenetic analysis and classification of SibHLH family
According to the classification of bHLH proteins of Arabidopsis, 187 bHLH proteins of S. italica were divided into several groups. In MEGA 7.0, the NJ tree was constructed used the Jukes–Cantor model. The phylogenetic tree was constructed with a bootstrap value of 1000 and assigned with Geneious R11 with BLOSUM62 cost matrix. In addition, a multi-species phylogenetic evolutionary tree was constructed that included SibHLH proteins and bHLH protein sequences of six plants (A. thaliana, S. lycopersicum, S. tuberosum, B. distachyon, O. sativa subsp. indica, and Z. mays), downloaded from the UniProt database (UniProt: https://www.uniprot.org/).
Plant materials, growth conditions, and abiotic stress in S. italica
S. italica cv. Yugu 1, a typical cultivated variety in northern China, was used throughout the study. Since 2020, ‘Yugu 1’ has grown in the greenhouse of the experimental base located at the Guizhou University farm. In the appropriate development stages of foxtail millet, we obtained the flag leaves, third leaves, roots, stems, fruits, and three developmental stages of fruits and glumes at 18 (green fruit stage), 25 (discolouration stage), and 32 (initial maturity stage) DPA in the laboratory. All organ samples were taken from five plants under the same growth conditions, quickly placed in liquid nitrogen, and stored at − 80 °C until further use. In addition, the expression patterns of SibHLH genes under different stresses were studied, and the expression levels of 15 SibHLH genes were analysed. All seedlings of S. italica were planted in seedling trays, and 50 mL of solution was poured into each independent tray to fully immerse the root system. At the seedling stage (28 days), the plant seedlings of S. italica were subjected to eight different abiotic treatments: acid (HCl 0.1 M), alkali (NaOH 0.2 M), salt (5% NaCl), flooding (whole plant), drought (30% PEG6000), darkness (complete shading), heat (40 °C), and cold (4 °C). Each stress treatment was performed with five replicates, and the leaves, roots, and stems were taken at 0, 2, and 24 h for qRT-PCR analysis.
Total RNA extraction, cDNA reverse transcription, and qRT-PCR analysis
Total RNA was extracted using the plant RNA extraction kit (TaKaRa Bio) and treated with RNase-free DNase I to remove trace amounts of DNA. The qRT-PCR primers were designed using Primer 5.0 software (Additional file 6: Table S6). Using ACTIN (Si001873m.g) as an internal control, standard RT-qPCR with SYBR Premix Ex Taq II (TaKaRa Bio) was repeated at least three times on a CFX96 Real-Time System (Bio-Rad). The total reaction system was 20 μL, contains 1 μL cDNA (100 ng/μL− 1), 10 μL SYBR Green Realtime PCR Master Mix, 0.5 μL forward and reverse primers, 8 μL rnase-free water, respectively. The reaction procedures for real-time quantitative PCR detection were as follows: pre-denaturation at 95 °C for 30s, denaturation at 95 °C for 5 s, annealing at 60 °C for 20s, and extension at 72 °C for 20s, with a total of 40 cycles. All primers were validated by melting curve analysis. The experimental data was calculated using the 2− (ΔΔCt) method .
We processed and analysed all the above data via variance analysis using JMP6.0 software (SAS Institute). The means were compared using the least significant difference test at significance levels of 0.05 and 0.01. The histogram was drawn using Origin 8.0 software .
Availability of data and materials
The entire Setaria italica genome sequence information was obtained from the Ensembl Genomes website (http://ensemblgenomes.org/). S. italica materials (Yugu 1) used in the experiment were supplied by Prof. Cheng Jianping of Guizhou University. The datasets supporting the conclusions of this study are included in the article and its additional files.
- bHLH :
- SibHLH :
Setaria italica bHLH
Quantitative real-time polymerase chain reaction
- AtbHLH :
Arabidopsis thaliana bHLH
Hidden Markov Model
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We thank all our colleagues for providing useful discussions and technical assistance. We are very grateful to the editor and reviewers for critically evaluating the manuscript and providing constructive comments for its improvement.
This research was supported by the National Science Foundation of China (31560578, Cheng JP, http://www.nsfc.gov.cn), the Sichuan International Science and Technology Cooperation and Exchange Research and Development Project (2018HH0116, Yan J, http://kjt.sc.gov.cn), and the Guizhou Science and Technology Support Project (No. 20201Y125).
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This article does not contain any studies involving human participants or animals performed by the authors. These methods were carried out in accordance with relevant guidelines and regulations. All experimental protocols were approved by the Guizhou University.
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List of 187 S. italica bHLH genes identified in this study.
Analysis and distribution of conserved motifs in S. italica bHLH proteins.
Tandem duplication events in S. italica bHLH genes.
The 38 pairs of segmental duplications in S. italica bHLH genes.
One-to-one orthologous genes relationships between S. italica and other plants.
Primer sequences for qRT-PCR.
The correlations 15 S. italica bHLH genes in several plant organs. Positive number: positively correlated; negative number: negatively correlated. Red numbers indicate a significant correlation at the level of 0.05.
The correlations 15 S. italica bHLH genes in several abiotic stresses.
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Fan, Y., Lai, D., Yang, H. et al. Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.). BMC Genomics 22, 778 (2021). https://doi.org/10.1186/s12864-021-08095-y
- Foxtail millet
- bHLH gene family
- Genome-wide analysis
- Abiotic stress