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Identification and characterization of PAL genes involved in the regulation of stem development in Saccharum spontaneum L.

BMC Genomic Data volume 25, Article number: 38 (2024) Cite this article

Abstract

Background

Saccharum spontaneum L. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense. However, the current knowledge about PAL genes in S. spontaneum is still limited. Thus, identification and characterization of the PAL genes by transcriptome analysis will provide a theoretical basis for further investigation of the function of PAL gene in sugarcane.

Results

In this study, 42 of PAL genes were identified, including 26 SsPAL genes from S. spontaneum, 8 ShPAL genes from sugarcane cultivar R570, and 8 SbPAL genes from sorghum. Phylogenetic analysis showed that SsPAL genes were divided into three groups, potentially influenced by long-term natural selection. Notably, 20 SsPAL genes were existed on chromosomes 4 and 5, indicating that they are highly conserved in S. spontaneum. This conservation is likely a result of the prevalence of whole-genome replications within this gene family. The upstream sequence of PAL genes were found to contain conserved cis-acting elements such as G-box and SP1, GT1-motif and CAT-box, which collectively regulate the growth and development of S. spontaneum. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that SsPAL genes of stem had a significantly upregulated than that of leaves, suggesting that they may promote the stem growth and development, particularly in the + 6 stem (The sixth cane stalk from the top to down) during the growth stage.

Conclusions

The results of this study revealed the molecular characteristics of SsPAL genes and indicated that they may play a vital role in stem growth and development of S. spontaneum. Altogether, our findings will promote the understanding of the molecular mechanism of S. spontaneum stem development, and also contribute to the sugarcane genetic improving.

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Background

Sugarcane is an important economic crop worldwide, accounting for about 75 per cent of the world’s sugar production [1]. With its high sucrose accumulation and high tillering ability, making it become the highest tonnage crop worldwide [2]. Sucrose is produced in the leaves and stored in the cane stems through the phloem [3]. Thus, the growth and development of cane stem is the main factor affecting the yield of sugarcane. Saccharum spontaneum L. is a wild germplasm resource of Saccharum genus [4]. It is notable attributes such as high fiber content, lodging resistance, and disease resistance making it become an important genetic resource in sugarcane breeding [5]. Modern sugarcane cultivars were bred through the “noble” cross between S. officinarum and S. spontaneum [6]. Furthermore, these cultivars contain 10%∼20% of S. spontaneum lineages [7, 8]. Therefore, exploring these genes involved in stem development of S. spontaneum will be beneficial for sugarcane breeding.

Phenylalanine ammonia-lyase (PAL) is a key enzyme in the phenylalanine metabolic pathway of plants [9]. It plays a crucial role in plant growth, development and resistance to biotic and abiotic stresses [10,11,12]. PAL is encoded by a small multi-gene family with various members in different species [13,14,15,16,17,18]. It is the first rate-limiting enzyme in the phenylalanine metabolic pathway and catalyze the synthesis of natural substances such as lignin, flavonoids and anthocyanin [19,20,21,22]. Specifically, lignin is the main component of the secondary cell wall and is closely associated with stem morphology and secondary wall formation [23]. It is an essential component for providing mechanical support to plants and also transporting water, mineral and photosynthetic products. In addition, it also offers protection against pathogen invasion and promote plant growth and development [24,25,26]. Therefore, PAL plays a positive key role in the growth, development and survival of vascular plants. Flavonoids, as one of the phenolic compounds, not only act as unique UV filters protecting plants from UV radiation damage [27–28], but also has roles in anti-freezing, drought resistance, heat adaptation and frost resistance [29]. Anthocyanins serves as strong antioxidants in plant cells that assisting resist biotic and abiotic stresses, and attracting insects for pollination and seed dispersal [30–31]. Responding to various stresses, PAL can rapidly induce the expression of PAL genes at the transcriptome level, thus affecting the expression levels of PAL genes and protecting plants [32].

The PAL gene family plays an irreplaceable role in plant growth and development. As an important wild species, S. spontaneum has been widely used in sugarcane breeding. Although PAL genes have been studied in various plants, limited attention has been paid to the members of the PAL enzyme family and their expression patterns in S. spontaneum. Therefore, it is necessary to understand the evolutionary mechanism and expression pattern of PAL genes in S. spontaneum. This exploration will establish foundation for identifying gene function related to stem developmental mechanisms. In the present study, based on the transcriptomic data of AP85-441, we identified 26 PAL genes of S. spontaneum and further analyzed the physicochemical properties, sequence characteristics, phylogeny, gene structure, cis-regulatory element prediction and expression pattern of PAL gene family. This comprehensive analysis will provide insights into the biological functions of PAL gene and contribute to understand the stem development in S. spontaneum.

Materials and methods

Plant materials

The experimental material is S. spontaneum SES208 (2n = 8x = 64), which grown in the greenhouse of the Sugarcane Research Institute of Guangxi University. To verify the reliability of the download transcriptome, we collected leaves at maturity and stems at internodes + 3, +6 and + 9 of S. spontaneum respectively, and then total RNA was extracted for qRT-PCR experiments.

Determination of S. Spontaneum PAL gene family members

To identify members of the PAL gene family, genomic data were collected for five species. Genomic data off S. spontaneum were downloaded from the published genome database (http://sugarcane.zhangjisenlab.cn/sgd/html/index.html) [33]. The haploid reference genome off R570 was obtained from the Sugarcane Genome Center (http://sugarcane-genome.cirad.fr/) [34]. Genomic data and protein sequences off sorghum, maize, and rice were downloaded from Phytozome (https://phytozome.jgi.doe.gov/) and EnsemblPlant (http://plants.ensembl.org/index.html) databases, respectively. The identification process involved several steps. Firstly, the Hidden Markov Model (HMM) search program [35] was used to search for protein sequences containing PAL structural domains. The HMM configuration file (PF00221) predicted by the Pfam database [36] was utilized for this purpose. Secondly, the protein sequences of four Arabidopsis thaliana PAL genes were downloaded from the Arabidopsis database (http://www.arabidopsis.org/), and using Blastp software. The PAL proteins in the three genomic databases were searched to identify candidate genes of the PAL family. Finally, the conserved domain of each candidate gene was further verified using the online tool NCBI CD-search (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi). Any genes with incomplete domain were excluded, resulting in the selection candidate genes for the PAL gene family.

Physicochemical properties and phylogenetic analysis of the PAL gene family

The physical and chemical properties of PAL family were predicted using the ExPasy online website (https://web.expasy.org/protparam). Protein sequences of PAL families from Arabidopsis, Sorghum, S. spontaneum, R570, maize, and rice were aligned using ClustalW multiplex sequence alignment with default parameters. The aim of this alignment was to investigate the phylogenetic relationships among PAL genes. The resulting alignment was then used to construct phylogenetic by the Neighbor-Joining (NJ) method of MEGA-X software. The calibration parameter bootstrap was set to 1000, while the remaining parameters were kept at their default values.

Analysis of PAL gene family gene structure and conserved motifs

The CDS and gene sequences of both PAL family members were extracted from the Sorghum genome, R570 genome and S. spontaneum genome annotation files. The gene structures were obtained using the Gene Structure Display Server 2.0 (http://gsds.gao-lab.org/) online tool. To analyze the conserve motifs of PAL family protein sequences, the MEME Suite online tool (https://meme-suite.org/meme/tools/meme) [37] was employed with the number of searches was set to 10. Finally, the results obtained from the phylogenetic tree, conserved motifs analysis and gene structure analysis were integrated and visualized by using TBtools software.

PAL gene family cis-acting element and covariance analysis

Based on the genome annotation information of S. spontaneum, Sorghum and R570, the CDS upstream 2000 bp transcription start site promoter sequence of each member of PAL gene family was extracted using the Gtf/Gff sequence extraction tool in TBtools software. The extracted sequences were then submitted to PlantCare [38] for cis-element prediction. This process is crucial for understanding and manipulating the regulatory mechanisms of PAL gene family members in S. spontaneum. Chromosomal location of PAL genes was obtained based on the genome annotation information. The covariance analysis software MCScanX was used to detect gene duplication events, intra- and inter-species covariance relationships in the PAL gene family [39], followed by chromosome localization [40]. Furthermore, the gene covariance analysis and visualization were conducted using the default parameters of TBtools software.

Analysis of SsPAL gene expression pattern

The transcriptome expression profiles of S. spontaneum from various tissues, growth stages, developmental leaves, and day-night rhythms were downloaded from the public sugarcane genome database (http://sugarcane.zhangjisenlab.cn/sgd/html/index.html) [41]. The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values of SsPAL genes were calculated using logarithmic function. Gene expression heatmaps were generated using TBtools software.

Total RNA extraction and qRT-PCR analysis

Mature leaves of S. spontaneum and stem sections between the + 3, +6, and + 9 stems were collected and immediately frozen in liquid nitrogen for storage at -80 °C. Total RNA was extracted using TRIZOL reagent (Takara, Japan) and reverse transcribed into cDNA using PrimeScript™ RT reagent Kit with gDNA Eraser (Perfect Real Time) (Takara, Japan). qRT-PCR was performed using primers designed from the NCBI primer database. The LightCycler® 96 instrument (Roche, Switzerland) was used to compare relative expression differences between different stem sections and leaves, thereby validating transcriptome data. The relative expression levels were calculated using the 2-ΔΔCt method with 25 S rRNA of sugarcane as reference gene. The experiment included three biological replicates [42]. qRT-PCR reaction system consisted of 1 µL cDNA, 10 µL 2×ChamQ SYBR Master Mix, 2 µL of each forward and reverse primer (10 µmol/L), and 5 µL ddH2O. The reaction profile was as follows: 95 °C for 30s, followed by 40 cycles of 95 °C for 10s, 60 °C for 30s, and 95 °C for 10s. Then results were statistically analyzed (Student’s t-test) and the data were plotted using GraphPad Prism 8.0 software.The used primers are shown in Table S1.

Results

Identification of PAL gene family members in S. bicolor, S. spontaneum, and sugarcane cultivar R570

A total of 42 PAL genes were obtained from the S. bicolor, S. spontaneum, and R570 genome databases. Among these, eight genes were identified in sorghum, 26 in S. spontaneum, and eight in R570. These 42 genes were named according to their chromosomal positions on three genomes, and the allelic genes of SsPAL were designated as a, b, c, d, following previous naming conventions (Table 1). Results showed that SsPAL4 and SsPAL15 have 4 allelic genes, while most SsPALs (15 genes) had no allele that indicated they have been lost during the evolutionary processes (Table 1). We then conducted the protein primary structure prediction on PAL genes, suggesting that its amino acid length was around 700 in sugarcane cultivar R570 and sorghum, with an isoelectric point ranging from 5.6 to 6.26, a molecular weight of 75.60-83.12 KD, protein instability coefficient ranging from 29.1 to 37.42, and average hydrophobicity ranging from − 0.138 to -0.02 (Table S2). These results implied that all PAL genes in sugarcane cultivars R570 and sorghum PAL gene families are stable acidic proteins. In S. spontaneum, the amino acid length of most PAL genes was around 700, while SsPAL5a and SsPAL16 were 1054 and 1693, respectively (Table S2). Except for SsPAL5a, the isoelectric points of other family members are between 5.69 and 7.56. Most of the molecular weights are below 100 KD, while SsPAL1 and SsPAL2 have molecular weights greater than 100 KD. Except for the protein instability coefficients SsPAL1 was 29.65, the remaining genes belong to stable acidic proteins (Table S2).

Table 1 The members of PAL gene family in S. spontaneum
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Construction of a phylogenetic tree of PAL gene family in S. spontaneum

To explore the evolutionary relationship of PAL family members, we screened the PAL protein sequences of Z. mays, O. sativa, S. spontaneum, S. bicolor, sugarcane cultivar R570 and A. tricolor. Then, a phylogenetic tree was constructed using MEGA-X. Phylogenetic analysis indicated that PALs of different plants could be divided into 3 groups, Group A, Group B, and Group C (Fig. 1). Of these, Group C further divided into two subgroups, C1 and C2-1/2 branches. Group C1 has one SbPAL1, suggesting that this gene had diverged from other genes in S. bicolor (Fig. 1). Group A only contained AtPALs, indicating that the significant differences of PALs between monocotyledonous and dicotyledonous (Fig. 1). SsPAL genes were unevenly distributed among Group B and Group C2-1/2, where Group C2-2 contained the highest number of SsPAL family members (contained 18 SsPAL genes). Furthermore, these results showed that SsPALs were closest to ShPALs, followed by SbPALs, ZmPALs and OsPALs (Fig. 1).

Fig. 1
figure 1

Phylogenetic tree of PAL genes family among different species. Ss: S. spontaneum, At: A. tricolor, Os: O. sativa, Zm: Z. mays, Sb: S. bicolor, Sh: sugarcane cultivar R570. The different colors indicated different groups of PAL genes in various species

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Analysis of the gene structure and conserved structural domains of S. spontaneum PAL gene family

Conservative gene structures may provide insights to the key events in the evolution of genes. We predicted the exon-intron and conserved motifs of SsPAL, SbPAL and ShPAL genes. The conserved motif composition and number analysis of the genes were done by using MEME software, and 10 conserved motifs were identified (named motif 1–10) (Fig. 2). Results showed that all PAL proteins contained motif 1–10 in these three species. In most proteins, motif 4, 5 and 8 are always closely linked to motif 1, 2, 3, 6, 7, 9 and 10, indicating that they were conserved in the majority of members (Fig. 2). All PALs contained exons, mostly have 1 to 2, while a few have 3 or 5 exons. In contrast, introns of PAL gene family members are more stable. ShPAL family does not contain introns, while SbPAL1, SbPAL2, SbPAL3, SbPAL5, SbPAL7, SbPAL8, SsPAL5a, SsPAL11 and SsPAL15b have 1-2 introns. This indicated that the structural differences among members of SbPAL gene family are not significant, and only a few members exhibit variation in intron-exon organization. The original gene structures are less complex than those of SsPAL gene family.

Fig. 2
figure 2

Analysis of conserved motifs and gene structure of PAL gene family in S. spontaneum. The different colored modules represent different motifs of PAL genes. CDS stands for exon. UTR stands for intron

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Analysis of promoter cis-acting elements

The cis-acting elements in the promoter region play a critical role in controlling gene transcription and expression. Analyzing promoter cis-acting elements can improve the understanding of gene function. In this study, we predicted 2,000 bp sequences upstream of PAL gene family members using the PlantCARE online website, and a total of 18 cis-acting elements were identified (Fig. 3). These different cis-acting elements could be functionally classified into four major categories: light-responsive elements, hormone-responsive elements, stress-responsive elements and plant growth metabolism-responsive elements. The analysis of cis-acting element showed that the promoter motifs of S. spontaneum PAL gene are involved in a variety of biological processes. All SsPAL genes contained light-responsive elements, with the conserved G-Box being the most prevalent element (100%), followed by sp1 (69.2%), meristematic tissue expression element (CAT-box) (61.5%) and GT1-motif (46.2%) (Fig. 4). Among the hormone response elements, abscisic acid response elements (ABRE) involved in abscisic acid response were found abundance across the three gene families. With some genes containing a high number of ABRE elements, such as SbPAL3 was up to 10 elements. Among the stress response elements, low temperature response elements (LTR) were relatively abundant, suggesting their potential involvement in stress regulation. These results indicated that SsPAL genes are not only widely involved in the growth and development of sugarcane, but also regulate various stress responses.

Fig. 3
figure 3

Distribution of cis-acting elements of the PAL family in S. spontaneum. Cis-elements with similar functions are displayed in the same color boxes. The grey line indicates the promoter region length of the PAL genes

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Fig. 4
figure 4

Heat map of the distribution and number of cis-acting elements of the PAL promoter in S. spontaneum. The number of cis-elements from the PAL genes were shown in heatmap boxes. Blank box means no corresponding cis-elements

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Collinearity analysis reveals pervasive gene duplications

To further infer the phylogenetic mechanism of the PAL gene family, the collinearity of SsPAL gene family was analyzed using McScanX software. Results showed that 34 pairs of homologous genes were existing among members of SsPAL gene family, including 26 pairs occurred in alleles and 8 pairs occurred in non-alleles, and 26 pairs (76.47%) within homologous chromosome groups (Fig. 5, Table S3). It was found that whole genome replication or segmental replication (84.62%) was the main replication type of SsPAL genes, which was the main way of SsPAL gene family expansion that accord with the characteristics of gene family expansion in polyploid species (Table S3). Therefore, the mainly reason for the significantly higher number of SsPAL genes family than other crops such as Arabidopsis and rice is the polyploid nature of S. spontaneum resulting from the whole genome duplication and chromosome doubling events. Similarly, collinearity analysis of SbPAL genes family revealed that only one pair of homologous genes were distributed in chromosomes4 and 6, respectively. These non-allelic genes may have originated from segmental duplication events.

Fig. 5
figure 5

Distribution and collinearity analysis of SsPAL genes in S. spontaneum and Sorghum bicolor. The inner line indicates the covariance within the SsPAL and SbPAL genes

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Analysis of the spatio-temporal expression pattern of SsPAL genes

The temporal and spatio-temporal expression pattern of PAL genes in S. spontaneum were investigated using transcriptomic data from different tissues and leaf developmental gradients. Five genes (SsPAL1, SsPAL18, SsPAL14, SsPAL17 and SsPAL16) exhibited low or no expression in both stem and leaves across the developmental stages of S. spontaneum (Fig. 6). In addition to these 5 genes, most other SsPAL genes showed higher expression in the stem than that of the leaves, indicating their important role in the growth and elongation of stalks. The expression leaves of + 6 stems were more significant compared to + 9 and + 3 stems, indicating higher expression during both pre-mature and mature stages. This suggests that these genes may have a stronger biosynthetic function during the vigorous growth stage, contributing to the synthesis of compounds such as lignin.

To elucidate the functional differentiation of S. spontaneum PAL gene family in photosynthetic tissues, expression analysis was performed on a continuous gradient model of S. spontaneum development. SsPAL16, SsPAL18 and SsPAL7 were not expressed in leaves with different developmental gradients, indicating their very limited role in leaf development of S. spontaneum. Most other SsPAL genes exhibited a relatively high level of expression in the base, transition zone, and the first half of mature zone 1 of leaves (Fig. 7). High level of expression at the base of the leaf may be due to its role as a source pool transition zone, which is closer to the stalk and contains higher lignin content compared to other parts. The above results suggest that these genes also have an effect on the growth of specific regions during the leaf development.

Fig. 6
figure 6

Expression pattern of SsPAL gene in different period and stages of S. spontaneum. Seeding refers to seedling stage, Pre-mature refers to the elongating stage, Mature refers to maturity stage

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Fig. 7
figure 7

Expression of SsPAL gene in different leaf development gradients of S. spontaneum L. 1 ∼ 15 refers to different locations of leaf segment parts around 1 cm length. Basal refers to leaf base. Transitional refers to source bank transition region. Maturing refers to mid maturity. Mature refers to maturity stage

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Validation of relative expression levels of SsPAL gene family by qRT-PCR

In order to compare the expression levels between different tissues of S. spontaneum and to validate the results of the expression pattern analysis described above. We chose the first leaf and the +3, +6 and +9 stems of S. spontaneum as the experimental materials. Three SsPAL genes were randomly selected for qRT-PCR validation. Results of gene expression showed that in the stems and leaves of mature S. spontaneum SES208, the expression levels of these three genes in the stem sections between the +3, +6, and +9 stem were higher than that of the leaves. In particularly, the mean expression levels of SsPAL gene in + 3, +6 and + 9 stems were about 7.72, 10.68 and 3.65 times higher than that of + 1 leaves, respectively. This result suggests that the SsPAL gene plays an important role in stem development. The differences in expression levels were found to be extremely significant, which is consistent with the expression pattern in the transcriptome data. Moreover, all three genes exhibited higher expression levels in the + 6 stem compared to + 3 stem, which aligns with the previous hypothesis (Fig. 8).

Fig. 8
figure 8

qRT-PCR validation of the relative expression of SsPAL gene in S. spontaneum leaves and stems. Leave: S. spontaneum leaves at maturity; Stem 3: the 3rd stem node of S. spontaneum at maturity; Stem 6: the 6th stem node of S. spontaneum at maturity; Stem 9: the 9th stem node of S. spontaneum at maturity

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Discussion

Phenylalanine ammonia-lyase (PAL) plays an important role in plants as a link between primary and secondary metabolism. As a key enzyme in the metabolic pathway of phenylpropane, PAL plays an important role in plant growth, development and resistance in a widely species [11–12, 43,44,45,46]. The yielding of S. spontaneum depends on the growth and development of its stems. However, there are few studies on the PAL gene family of S. spontaneum involved in stem growth and development. Therefore, exploring the molecular characteristics of PAL genes in S. spontaneum is important for further improving the sugarcane agronomic trait. PAL is a conserved multigene family, while contains various gene number in different species. For example, Arabidopsis [47] and tobacco [48] both contain 4 PALs, sorghum [49] contains 8 PALs, potato [16] contains 14 PALs, rice [50] contains 9 PALs, and cucumber [51] contains 13 PALs. In this study, we identified 26 S. spontaneum PAL genes, suggesting the number of S. spontaneum PAL genes was significantly higher than that of rice, Arabidopsis and maize [52], but lower than that of wheat. This indicates that the number of PAL genes is stochastic among species, which is consistent with the results of previous studies [53].

In contrast to the results of previous studies, S. spontaneum PAL genes were distributed on only two chromosomes, and in combination with the type of replication of this gene family. Whole-genome replication led to a more conservative evolutionary and expansion of S. spontaneum PAL gene family, which resulting in a restricted distribution region. It was also one of the main reasons for the larger number of S. spontaneum PAL genes than that of Arabidopsis and other crops. Previous studies have shown a link between whole-genome duplication and plant morphological evolution. Whole-genome duplication can break the limits of purifying selection on gene evolution and allow genes to assume new functions [54]. Therefore, the genome-wide replication type of the PAL gene in S. spontaneum may be able to play a role in sugarcane breeding, such as thecontrol offlowering time, alteration of stem length and stem diameter size, and thus the variation of its sugar content.

The obvious difference between the genes of monocotyledonous and dicotyledonous plants resulted in S. spontaneum PAL gene being more closely homologous to graminaceous plants and more distantly homologous to Amaranth. PAL, the first key enzyme of the phenylpropane metabolic pathway, has maintained stability and convergence during genetic evolution. This is consistent with the results of previous studies [55, 56]. Except for SsPAL18, all the PALs proteins identified in this study have complete conserved structural domains and exhibit very similar alignments. However, there are also some unique motifs such as SsPAL9, SsPAL5c and SsPAL16, indicating the entire conserved structural domain facilitates the functional diversity of SsPAL genes in addition to performing the conserved biological functions of S. spontaneum PAL family members [47]. PAL is considered to be a master regulator of various abiotic stress responses and is involved in plant growth and development. The results of this study showed that the conserved light element G-box (100%), which is correspondingly associated with light, as well as sp1 (69.2%), GT1-motif (46.2%) and CAT-box (61.5%) are widely present in the upstream sequences of genes. This suggests that these genes regulate plant seed growth and meristematic tissue development, thus affecting plant growth metabolism, which is consistent with the above findings. These functional differences confirm that PAL is a multifunctional gene family.

The growth and development of stem is a critical factor affecting the yields of S. spontaneum. Our qRT-PCR results revealed that the expression of PAL gene was higher in stems than that of leaves, which was similar to the expression pattern of other plants [50, 57–58]. The expression of PAL genes in + 6 stem was higher than that of  + 3 and + 9 stems, which may be due to the fact that the growth and development of S. spontaneum is mainly depended on internode elongation. In the tissue closest to the S. spontaneum stalk, SsPAL was highly expressed in the base of the leaf with more lignin content than the other leaf parts. This suggests that PAL is controlled by a family of genes with different expression properties in different tissues and involved in different metabolic pathways [59]. The results of this experiment not only proved the reliability of the transcriptome data analysis of S. spontaneum, but also indicated that the SsPAL gene family might play an important function in stem development.

Conclusions

In this study, a total of 26 SsPAL family members were identified in S. spontaneum, along with 8 SbPAL family members in sorghum and 8 ShPAL family members in modern sugarcane cultivars. Analysis of the physicochemical properties, gene structure, protein conserved structural domains, phylogeny, collinearity, and expression heat map of these members revealed that the S. spontaneum PAL family genes likely play a critical role in plant growth and development, especially in stem nodes. The findings suggest that these SsPAL genes could serves as potential genetic resources for sugarcane breeding, and provide basic information for further studies on the biological functions of SsPAL and promoting breeding efforts to enhance important traits in sugarcane.

Data availability

Data is provided within the manuscript or supplementary information files.

Abbreviations

PAL:

Phenylalanine ammonia-lyase

ABRE:

Abscisic acid responsiveness element

qRT-PCR:

Quantitative reverse transcription polymerase chain reaction

HMM:

Hidden Markov Model

NJ:

Neighbor-Joining

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Acknowledgements

We are grateful to the reviewers for their helpful comments on the original manuscript. We would like to thank editors for their efficient works.

Funding

This work was supported by the Sugarcane Research Foundation of Guangxi University (No. 2022GZB006), an independent fund of Guangxi Key Laboratory of sugarcane biology, academy of Sugarcane and Sugar Industry (ASSI-2023009) and the China Agricultural Research System funded by MFA and MARA (CARS170109).

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  1. Xiaoqing Wu and Zetian Cui contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory for Sugarcane Biology, Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530004, China

    Xiaoqing Wu, Zetian Cui, Xinyi Li, Zehuai Yu, Pingping Lin, Li Xue, Abdullah Khan, Cailan Ou, Zuhu Deng, Muqing Zhang, Wei Yao & Fan Yu

  2. National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

    Zuhu Deng

  3. Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Zuhu Deng

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  1. Xiaoqing Wu
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Contributions

WY and FY designed the research. XQW and ZTC performed the experiments. XYL, ZTC and ZHY analyzed the results. LX, CLO and XQW assisted with some experiments. ZHD, MQZ, WY, FY, PPL and AK assisted in writing the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Wei Yao or Fan Yu.

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Wu, X., Cui, Z., Li, X. et al. Identification and characterization of PAL genes involved in the regulation of stem development in Saccharum spontaneum L.. BMC Genom Data 25, 38 (2024). https://doi.org/10.1186/s12863-024-01219-9

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