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Article

Identification and Evolution of Exon Junction Complex Core Genes and Expression Profiles in Moso Bamboo

by
Yuhua Wang
1,†,
Jun Zhang
1,†,
Mengna Zhao
1,
Xiaoyu Liu
1,
Mingzhe Wang
1,
Wenwen Zhong
1,
Jiajie Yang
1,
Tian Hua
1,
Shengcai Xiang
1,
Liangzhen Zhao
2,
Yaxin Zhang
3,* and
Lianfeng Gu
2,*
1
College of life Science, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2
Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
3
College of Landscape Architecture, Guangdong Eco-Engineering Polytechinic, Guangzhou 510520, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Forests 2025, 16(12), 1822; https://doi.org/10.3390/f16121822
Submission received: 2 November 2025 / Revised: 30 November 2025 / Accepted: 3 December 2025 / Published: 5 December 2025
(This article belongs to the Section Genetics and Molecular Biology)
Browse Figures
Versions Notes

Abstract

The exon junction complex (EJC) is a central mediator of post-transcriptional regulation in eukaryotes. A comprehensive, systematic analysis of EJC core genes has been lacking in Phyllostachys edulis (P. edulis). Here, we identified 147 EJC core genes across 17 plant species spanning the major green plant lineages. Phylogenetic analyses supported each family as a monophyletic clade consistent with established taxonomic relationships. Synteny analyses indicated that segmental duplication is the principal driver of EJC core gene expansion in P. edulis (Moso bamboo). Transcriptome profiling further showed that nearly all PedEJCs were engaged during rapid shoot growth, with PedY14b-D, PedY14c-D, and PedY14d-C displaying the most pronounced expression changes. During shoots’ post-harvest senescence process, PedEIF4A3s, PedY14s, and PedMAGOs were progressively downregulated, whereas PedBTZs were upregulated, indicating distinct module-level responses among EJC subunits. Only a small subset of PedEJCs responds to phytohormones and abiotic stresses. Furthermore, cis-regulatory element composition in promoter region likely shapes PedEJCs transcriptional regulation. Collectively, these findings lay the groundwork for in-depth functional dissection of PedEJCs in Moso bamboo.

1. Introduction

The exon junction complex (EJC) is deposited on mRNAs during splicing, approximately 20–24 nucleotides upstream of exon–exon junctions, where it adopts a distinctive conformation that enables stable RNA binding and serves as a versatile platform for recruiting processing factors [1,2,3,4,5,6]. Acting as a central hub of post-transcriptional regulation and surveillance, the EJC coordinates pre-mRNA splicing, promotes nuclear export of mature transcripts, interfaces with nonsense-mediated mRNA decay (NMD) [4,7,8], and modulates mRNA translation, localization, and turnover [9]. In recent years, accumulating evidence has shown that the EJC suppresses N6-methyladenosine (m6A) deposition. Acting as an m6A antagonist, the EJC establishes a local protective zone near exon–exon junctions within coding regions, effectively shielding RNA in average-length internal exons from methylation [10,11,12,13]. The EJC is a multiprotein assembly composed of core and peripheral components. Its core comprises four proteins, including eIF4A3, Y14 (also known as RBM8A), MAGOH (also referred to as NASHI/MAGO), and Barentsz (BTZ; also known as MLN51/CASC3) [5]. These core subunits bind mRNAs in a sequence-independent fashion, forming an interlaced interaction network that, once the nuclear splicing machinery has specifically assembled on fully spliced mature transcripts, serves as a foundational scaffold for recruiting peripheral factors [5].
Research on the EJC has focused mainly on mammals, while plant studies began with the isolation of MAGO [14]. MAGO family genes are essential for plant growth and reproductive development, and their loss or dysfunction disrupts spermatogenesis or pollen and seed development, thereby reducing fertility [15,16,17]. Y14 and MAGO have coevolved slowly across eukaryotes to form a tight heterodimer [18,19]. In rice, simultaneous downregulation of OsMAGO1, OsMAGO2, and OsY14a exacerbates the dwarf and floral defects of OsMAGO1/OsMAGO2 double knockdowns and impairs anther development [20,21]. In Hevea brasiliensis, HbY14s and HbMAGOs are regulated by ethylene and jasmonate and may contribute to rubber particle aggregation [22].
EIF4A3 is a DEAD-box RNA helicase that engages RNA primarily through an ATP-dependent clamp formed by its two conserved RecA-like domains [23,24,25]. In Arabidopsis, EIF4A3 colocalizes with AtMAGO and AtY14 [26,27]. Loss of the two EIF4A3 homologs causes developmental and embryonic defects in rice [28], and mutation of the related EIF4A3 slows growth in Physcomitrella patens [29]. Additionally, in Arabidopsis, EIF4A3 is required for the alternative splicing of key circadian clock genes and for proper circadian rhythmicity, and eif4a3 mutants display delayed flowering under long-day conditions [30]. BTZ is a long, flexible and poorly folded protein that can bind to EIF4A3 in both the open and the closed conformation [23]. In rice, btz mutants compromise the robustness of floral development [31] and reduce salt tolerance [32].
Moso bamboo is the most widely distributed bamboo species in China and holds substantial economic value for edible shoots, construction, timber substitutes and papermaking. A hallmark of P. edulis shoots is their exceptionally rapid growth, which is of notable scientific and economic interest. However, a comprehensive, systematic investigation of EJC core genes in Moso bamboo has not been reported. The first draft genome of Moso bamboo was released in 2013 [33] and updated to a chromosome-scale assembly in 2018 [34]. Most recently, the tetraploid genome was resolved into two subgenomes (C and D) [35], providing a solid foundation for the precise identification of EJC core genes.
In this study, we performed a genome-wide survey of EIF4A3, Y14, MAGO and BTZ family members across 17 plant genomes and explored their origins and evolutionary histories. We further profiled the expression of EJC core genes across multiple tissues in Moso bamboo and evaluated whether the PedEJCs contribute to rapid shoot growth and postharvest senescence, as well as whether they exhibit differential responses across tissues and under diverse environmental stresses. This work lays the groundwork for elucidating the cellular and molecular functions of EJC core genes in Moso bamboo.

2. Methods

2.1. Genome-Wide Identification of EJC Core Genes in 17 Genomes

Genomic sequence and taxonomy relationship of 17 plants were retrieved from PHYTOZOME v.13, and other public databases with the details were listed in Table S1. To identify EJC core genes, EIF4A3, Y14, MAGO and BTZ identified in Arabidopsis were used for BLASTP v.2.12.0 as query sequences (e value < 1 × 10−5). Subsequently, the obtained sequences were manually screened according to the corresponding family characteristics. For the EIF4A3, the DEAD-like domain was required; the Y14 had to contain the RRM_RBM8 domain, the MAGO had to contain the Mago_nashi domain, and BTZ had to contain the Btz domain.

2.2. Multiple Sequence Alignment and Phylogenetic Analysis

The protein sequences identified above were aligned using MAFFT v7.455 [36] with the ‘L-INS-I’ parameter, followed by manual adjustments where necessary. A maximum likelihood phylogenetic tree was then constructed using IQ-TREE2 v2.1.4-beta [37] with the parameters ‘-m MFP -bb 3000 --bnni’; the -m MFP option automatically selects the best-fit nucleotide substitution model for the dataset. The resulting phylogenetic trees were visualized using iTOL [38] with URL: https://itol.embl.de (accessed on 2 September 2025).

2.3. Analysis of Conserved Polypeptide Motifs, Functional Domains, and Gene Structure

Gene structure data for the 17 species were obtained from the annotations listed in Table S1. The genomic data for Dendrocalamus latiflorus (D. latiflorus) was sourced from our previously assembled chromosome-scale genome with URL: https://figshare.com/articles/dataset/Allele_aware_chromosome_scale_assembly_of_theallopolyploid_genome_of_hexaploid_Ma_bamboo_Dendrocalamus_latiflorus_Munro_/24411913 (accessed on 10 August 2025).
The conserved polypeptide motifs in the EJC proteins were analyzed using MEME online software with URL: https://meme-suite.org/meme/tools/meme (accessed on 5 September 2025), parameter set a maximum motif number as 10. Conserved functional domains were identified using the NCBI CDD online tool with URL: https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi (accessed on 5 September 2025) and set default parameters. The results were then visualized using TBtools v2 software [39].

2.4. Physicochemical Property Analysis and Protein Subcellular Localization Prediction

The sequences of the identified PedEJC proteins were submitted to the ExPASy online platform (https://www.expasy.org), where the ProtParam tool (https://web.expasy.org/protparam) was used to analyze Physicochemical property such as amino acid composition, isoelectric point (PI), molecular weight (MW), and grand average of hydropathy (GRAVY). The subcellular localization was predicted using the Plant-mPLoc tool with URL: http://www.csbio.sjtu.edu.cn/bioinf/plant-multi (accessed on 10 September 2025).

2.5. Structure Prediction

The secondary structure of the proteins was predicted using the NPS program with URL: https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_server.html (accessed on 18 September 2025) with the SOPMA method. The tertiary structures were predicted using the AlphaFold3 web service (https://alphafoldserver.com). Four representative proteins (PedEIF4A3a-D, PedY14a-D, PedMAGO1-D, PedBTZ1-C) were selected for the prediction of the EJC structure. The resulting tertiary structures were visualized using PyMOL v3.1.0 software.

2.6. Chromosomal Distribution and Gene Duplication Analysis

MCScanX [40] was employed to analyze intra-species gene duplication events within PedEJCs and inter-species synteny with other species, including Chlamydomonas reinhardtii, Physcomitrium patens, Cunninghamia lanceolata, Nymphaea colorata, Arabidopsis thaliana, Oryza sativa, and D. latiflorus, using default parameters. To visualize the syntenic relationships between paralogous and orthologous PedEJCs, a figure was generated using TBtools software [39]. The non-synonymous (Ka) and synonymous (Ks) substitutions for each duplicated PedEJC pair were calculated using the KaKs Calculator 3.0 [41]. The evolutionary divergence time among the EJC core genes was inferred by applying the bamboo-specific formula T = Ks/2λ(λ = 6.5 × 10−9) [33].

2.7. Gene Expression Analysis

To characterize tissue-specific expression patterns of PedEJCs, evaluate their potential roles in rapid shoot growth and postharvest senescence, and assess whether they exhibit hormone- and stress-dependent responses, we compiled relevant RNA-seq datasets from the NCBI Sequence Read Archive (SRA). Detailed metadata and accession information are provided in Table S2. Raw sequencing data were first quality-controlled using fastp with default parameters [42]. Adapter sequences were removed, and the cleaned FASTQ files were subsequently aligned to the Moso bamboo reference genomes [35], using HISAT2 [43]. The resulting BAM files were filtered to retain only those reads that aligned to a unique region of the genome, and read counts were generated using featureCounts [44]. Gene expression levels were normalized in Transcripts per Kilobase per Million mapped reads (TPM) with formula: TPM = RPK/ΣRPK × 106; RPK = gene counts/gene length (kb).

2.8. Upstream Promoter Region Cis-Acting Element

The 2000 bp region upstream of the start codon of each EJC core gene was defined as the proximal promoter region and submitted to the PlantCARE database [45] with URL: http://bioinformatics.psb.ugent.be/webtools/plantcare/html (accessed on 30 September 2025) to predict cis-acting elements. The identified cis-acting elements were then counted and used to construct a heatmap.

3. Results

3.1. Identification of EJC Core Gene Family Members in Plant Kingdom

To systematically identify the family members of EJC core genes (EIF4A3, Y14, MAGO, and BTZ) across plants, we selected 17 species representing a diverse range of plant groups, including 1 chlorophyte, 2 bryophytes, 1 gymnosperm, 1 basal angiosperm, 4 monocots, and 8 eudicots (Figure S1; Table S1). Through homology searches and domain predictions, we identified a total of 147 candidate EJC core gene protein sequences from these species, consisting of 30 EIF4A3s, 41 Y14s, 34 MAGOs, and 42 BTZs (Figure 1; Table S3). Each component of the EJC core gene had copy numbers in each lineage studied in this article and the copy number of EJC core genes was conserved among different land plant lineages (Figure 1), suggesting that the EJC-mediated post-transcriptional regulatory system in land plants might be conserved. Notably, polyploid species, such as Brassica rapa, Glycine max, Zea mays, D. latiflorus and P. edulis, were found to have higher copy numbers of EJC core genes (Figure 1).

3.2. Multiple Alignment and Phylogenetic Analysis of the EJC Core Protein Families

We performed multiple sequence alignment (MSA) of four types of EJC components from 17 species mentioned above respectively (Figures S1–S4). The DExD/H helicase family, which includes the DEAD-, DEAH-, DExH-, and DExD-box subfamilies, belongs to the SF2 superfamily and shares eight conserved motifs: I, Ia, Ib, II, III, IV, V, and VI [46]. EIF4A3 as a member of the DEAD-box family which is characterized by the conserved Asp–Glu–Ala–Asp (DEAD) motif and an additional Q motif [46]. Our results showed that plants EIF4A3 also had nine highly conserved motifs along with an N-terminal flanking sequence (Figure S1). While these nine signature motifs were highly conserved across plant species, some variations were observed. For instance, EIF4A3 in bryophytes, gymnosperms, basal angiosperms, and eudicots exhibited a conserved DESD motif instead of the DEAD motif found in chlorophytes and monocots (Figure S1). As observed in animals [47,48], the RNA recognition motif (RRM) of the plant Y14 protein contained two highly conserved motifs (RNP1 and RNP2) at its middle, and is flanked by more divergent N-terminal and C-terminal regions (Figure S2). Four conserved leucine residues of MAGO in animals form a hypothetical leucine zipper motif in the C-terminal region [49,50]. In this study, we also observed these four leucine residues in plants, with the third “L” being more substituted as “F” (Figure S3). Additionally, a conserved sequence termed SELOR, about 80 amino acids in length, was observed in the BTZ family of plants [51] (Figure S4).
To understand the evolutionary relationship of EJC core genes, the sequences for each type of EJC core genes in the 17 species were used to construct phylogenetic trees. Our results showed that EIF4A3, Y14, MAGO, and BTZ each formed a monophyletic clade (Figure 2). In each tree, sequences clustered into six clades corresponding to the major plant lineages: chlorophytes, bryophytes, gymnosperms, basal angiosperms, monocots, and eudicots (Figure 2).

3.3. Conserved Motifs, Functional Domains, and Gene Structure Determination of the EJC Core Protein Families

The conserved motifs of the 147 EJC core genes from 17 species were analyzed using the MEME program, and the top 10 conserved motifs were identified and named motif1–motif10 (Figure 3 left). For EIF4A3, motifs 1–10 were widely distributed across all surveyed taxa and together constitute the conserved DEAD-like_helicase_N domain, except for Brassica rapa (BnaC03T0369500WE), which lacked motifs1 and 9 (Figure 3A left and middle). For Y14, motifs 4, 1, and 2 occurred within the RRM_RBM8 domain and were present in all species (Figure 3B left and middle). Additionally, motifs 3, 6, 5, 8, and 7 were more frequently observed in eudicots, basal angiosperms, gymnosperms, and bryophytes, while motifs 3, 9, and 7 appeared in some monocots (Figure 3B left). Algal lineages lacked motifs 3, 6, 8, and 7 (Figure 3B left). For MAGO, aside from a few exceptions, such as Physcomitrium patens (PAC:32970857), which lacked motif 3, motifs 1, 3, 2, and 4 were widely distributed across species and constituted the conserved Mago_nashi domain in that order (Figure 3C left and middle). For BTZ, motifs 1 and 2 formed the conserved Btz domain (Figure 3D left and middle). Notably, in algae, only motifs 8 and 1 were detected, showing a distinct shift in motif composition (Figure 3D left).
To compare the similarities and differences in the composition of gene structures among different species, we further presented the exon-intron structures of 147 EJC core genes from 17 species (Figure 3 right). The results showed that EIF4A3 almost invariably contained six or seven introns (Figure 3A right). For Y14, algal species typically had a single intron, whereas nearly all other species had three introns (Figure 3B right). Nearly all MAGO genes contained two introns and BTZ harbored 9–11 introns (Figure 3C right). Notably, intron lengths of EJC core genes were generally longer in gymnosperms than other species, with BTZ exhibiting the most pronounced expansion (Figure 3D right). These results were consistent with the genome-wide trend toward longer introns in gymnosperms lineage [52,53].

3.4. Physicochemical Properties, and Protein Structure of the EJC Core Protein Families in Moso Bamboo

Moso bamboo is one of the world’s most important non-timber forest products, we next presented the gene information and physicochemical properties of PedEJCs in Table 1. As mentioned before, 14 candidate EJC core genes (2 EIF4A3s, 5 Y14s, 3 MAGOs, and 4 BTZs) were identified in P. edulis (Figure 1; Table 1). We next renamed PedEJCs based on their subgenome location (C or D) and their order of appearance from Chromosomes 1–12 (Table 1).
Predicted molecular weights for PedEIF4A3s, PedY14s, PedMAGOs, and PedBTZs proteins were 45.7–45.8, 22.0–22.6, 18.6–19.8, and 74.7–78.0 kDa, respectively, with BTZ being the largest and MAGO the smallest (Table 1). The theoretical isoelectric points (pI) of all PedEJC proteins ranged from 5.0 to 6.22, classifying them as acidic. Their GRAVY values ranged from −1.11 to −0.149, indicating overall hydrophilicity. In addition, the subcellular localization predictions found that all PedEIFA3s and PedBTZs were most likely localized to the nucleus. PedY14s and PedMAGOs displayed dual localization in both the nucleus and cytoplasm except for PedY14a-D and PedY14b-C only likely to be localized on the cytoplasm (Table 1).
We next analyzed the secondary and tertiary structures of the PedEJC proteins. Among the four EJC core gene families, PedEIF4A3s and PedMAGOs exhibited a higher proportion of α-helices, whereas PedY14s and PedBTZs showed a greater content of random coils (Figure S5), consistent with their tertiary structure models (Figure S6). We selected four representative members from each family (PedEIF4A3a-D, PedY14a-D, PedMAGO1-D, PedBTZ1-C) and used AlphaFold3 to predict EJC structures. The results indicated that the tertiary structure of EJC in Moso bamboo was consistent with that has been reported in mammals [5]: acting as a clamp, the PedMAGO–PedY14 heterodimer locked PedEIF4A3 into a closed two-domain conformation, while the conserved SELOR domain of PedBTZ encircled and stabilized both domains of PedEIF4A3 (Figure S7).

3.5. ChroMosomal Distribution and Synteny Analysis of PedEJCs

Two EIF4A3s (02D, 12D), five Y14s (01D, 03C, 03D, 05D, 09C), three MAGOs (02D, 05C, 08D), and four BTZs (01C, 01D, 05C, 05D) were distributed across different chromosomes, respectively (Figure 4A). Therefore, no tandem duplication events occurred in the EJC core genes in Moso bamboo. However, we identified seven PedEJC gene pairs generated through segmental duplication (Figure 4A, Table 2), suggesting that segmental duplication might be the primary driver of PedEJCs expansion. Among these, PedY14b-C/PedY14b-D, PedBTZ1-C/PedBTZ1-D, and PedBTZ2-C/PedBTZ2-D gene pairs originated from allopolyploidization in P. edulis [35].
To determine whether segmentally duplicated genes underwent selective pressure during evolution, the Ka/Ks ratio was calculated. The results revealed that all EJC core gene paralogs exhibited Ka/Ks ratios < 1 (Table 2), suggesting that these genes in P. edulis were subjected to strong purifying selection during evolution. The duplication time of the EJC core genes in P. edulis occurred in the span of 5.15 and 94.23 million years ago (mya) (Table 2). In the Y14 and BTZ families, gene pairs derived from allopolyploidization in P. edulis have more recent duplication times than those of other gene pairs except PedY14c-D/PedY14d-C.
Given the considerable evolutionary divergence between non-angiosperms and angiosperms [54], we generated four comparative syntenic maps between P. edulis and four representative angiosperms: Nymphaea colorata (basal angiosperm), Arabidopsis thaliana (eudicot), Oryza sativa (monocot), and D. latiflorus (Bambusoideae) (Figure 4B–E). Synteny analysis revealed that 12, 10 and 1 PedEJC genes exhibited syntenic relationships with D. latiflorus, Oryza sativa, and Nymphaea colorata, respectively, corresponding to 25, 11, and 1 orthologous gene pairs across these three species (Figure 4B–E, Table S4). No syntenic relationships were observed between any genes in Arabidopsis and PedEJC genes (Figure 4C). A greater number of EJC orthologous gene pairs were identified between P. edulis and D. latiflorus (Figure 4E), likely attributed to their taxonomic affiliation within the Bambusoideae subfamily of Poaceae, as well as the hexaploid nature of D. latiflorus.
Notably, EIF4A3 collinear gene pairs were identified exclusively between P. edulis and D. latiflorus (Figure 4E), suggesting that these orthologous pairs likely formed after the divergence of the Bambusoideae subfamily and other subfamilies of the Poaceae family. PedBTZ genes exhibited orthologous relationships with all species examined except Arabidopsis (Figure 4B–E), indicating that BTZ orthologous gene pairs existed prior to angiosperm diversification, and that genomic rearrangement event or extreme genome fractionation in dicotyledonous plants might have led to the loss of synteny between P. edulis and Arabidopsis BTZ genes.

3.6. Expression Profiles of PedEJCs in Different Tissues

To obtain functional insights, we first investigated the expression patterns of PedEJCs across different tissues. Based on RNA-seq data retrieved from the SRA, we obtained transcriptome data from 10 distinct tissues across two independent research projects (PRJEB2956 [33]: five vegetative tissues and two flowering tissues; PRJNA354950 [55]: three vegetative tissues) (Table S2). The results showed that PedEIF4A3s, PedMAGOs, and PedBTZs were expressed across all examined tissues, with certain genes exhibiting tissue-specific expression patterns. The two PedEIF4A3s displayed similar overall expression patterns, with higher expression levels observed in roots (Figure 5A, Table S5). PedEIF4A3a-D showed significantly higher expression than PedEIF4A3b-D across all tissues, suggesting that it may play a more important or ubiquitous functional role in various tissues (Figure 5A,B, Table S5). PedMAGO3-D exhibited elevated expression in shoot tips (Figure 5A,B, Table S5), while PedBTZ2-C and PedBTZ2-D displayed higher expression in flowering tissues (Figure 5A, Table S5). For PedY14s, all members were expressed across all tissues except PedY14b-C and PedY14b-D (Figure 5A,B, Table S5). PedY14b-C was exclusively expressed in Panicle2 (flowering stage), with minimal or no expression in other tissues (Figure 5A,B, Table S5), demonstrating strong tissue specificity. PedY14b-D showed low expression in Panicle1 (early stage) and roots, while exhibiting moderate expression in 20 cm shoot tip (Figure 5A,B, Table S5), rhizome tip, and lateral bud (Figure 5B, Table S5).

3.7. Expression Profiles of PedEJCs at Different Growth Stages of Bamboo Shoots

Rapid growth represents one of the most prominent biological traits of P. edulis shoots, with significant scientific and economic implications. To explore the potential role of EJC core genes in the rapid growth of P. edulis, we obtained public RNA-seq data from four independent research projects, including PRJNA342231 [56], PRJNA547876 [57], PRJNA414226 [58], and PRJNA820321 [59] (Table S2). Our analysis revealed that almost all PedEJCs exhibited preferential expression in juvenile tissues characterized by vigorous growth and active cell division (Figure 6A–D, Table S5).
Except for PedMAGO1-D and PedBTZ2-C, almost all PedEJCs exhibited the highest expression levels in the shoot apical meristem region (SAM) and the lowest in the mature node (MNO) (Figure 6A, Table S5). The expression levels of PedEJCs in young tissues, including SAM, young internode (YIN), and young node (YNO), were generally higher than those in mature tissues, including mature internode (MIN) and MNO (Figure 6A, Table S5). Notably, the expression levels of PedY14b-D, PedY14c-D, and PedY14d-C in MNO decreased to 0.09, 0.32, and 0.31 times those in SAM, respectively (Figure 6A, Table S5).
With the exception of PedBTZ2-C and PedBTZ2-D, which exhibited stable expression across the rapid elongation (RE), rapid division (RD), and start division (SD) stages, the remaining PedEJCs showed a progressive increase in expression from RE to RD further to SD (Figure 6B, Table S5). PedY14b-D, PedY14c-D, and PedY14d-C were upregulated in SD, with expression levels increasing to 6.27, 3.45, and 5.00 times those observed in RE, respectively (Figure 6B, Table S5). Additionally, two MAGO genes, PedMAGO1-D and PedMAGO3-D, exhibited 2.00- and 2.12-fold upregulation in SD compared to RE, respectively (Figure 6B, Table S5).
The overall expression levels of PedEJCs were negatively correlated with the growth height of P. edulis shoots (Figure 6C, Table S5). Expression levels of most PedEJCs initially decreased and then increased with shoot height, although the peak expression in taller shoots (7 m) were still lower than the initial levels observed at 0.2 m (Figure 6C, Table S5). PedY14c-D and PedY14d-C showed the greatest downregulation, reaching their lowest levels at 3 m, where expression dropped to 0.07 and 0.09 times that in 0.2 m shoots, respectively (Figure 6C, Table S5). Furthermore, PedEIF4A3b-D, PedY14a-D, PedMAGO1-D, PedMAGO2-C, PedMAGO3-D, PedBTZ1-C, PedBTZ1-D, PedBTZ2-C, and PedBTZ2-D reached their lowest expression at 5 m, 3 m, 3 m, 6 m, 6 m, 1 m, 2 m, 2 m, and 2 m, respectively, with expression levels reduced to 0.42, 0.31, 0.41, 0.32, 0.39, 0.22, 0.43, 0.24, and 0.39 times those observed at 0.2 m shoots, respectively (Figure 6C, Table S5).
Except for PedBTZs, the expression levels of PedEJCs in 2 m bamboo shoots were higher than in 4 m shoots and the expression levels in basal internode shoot were greater than those in middle internode shoots (Figure 6D, Table S5). A marked decrease in PedEJCs expression was observed in 4M samples (Figure 6D, Table S5). In the 4M vs. 2B comparison, the expression levels of PedY14b-D, PedY14c-D, and PedY14d-C in 4M were reduced to 0.21, 0.32, and 0.39 times those in 2B, respectively (Figure 6D, Table S5).

3.8. Expression Profiles of PedEJCs at Postharvest Storage Periods of Bamboo Shoots

During the initial rapid growth phase, a portion of bamboo shoots naturally undergo rapid senescence, resulting in shoot degradation before reaching full maturity. The rapid senescence characteristic of bamboo shoots results in poor storability of edible shoots, thereby limiting bamboo production and consumption. To investigate the involvement of PedEJCs in the postharvest senescence process of bamboo shoots, we analyzed the expression changes of PedEJCs at different time points after harvest using publicly available RNA-seq datasets (PRJNA554957) [60] (Table S2). The results demonstrated that the expression levels of PedEIF4A3s, PedY14s, and PedMAGOs gradually decreased with extended storage duration, whereas the expression levels of PedBTZs exhibited an ascending trend (Figure 7). For instance, PedY14c-D, PedY14d-C, and PedMAGO1-D decreased to 0.22-, 0.19-, and 0.41-fold of their initial levels at 0 h storage after 48 h of storage, respectively (Figure 7). In contrast, PedBTZ2-C and PedBTZ2-D increased to 2.82- and 3.75-fold of their initial levels at 0 h storage after 48 h of storage, respectively (Figure 7). Specifically, PedY14c-D, PedY14d-C, and PedMAGO1-D decreased to 0.22-, 0.19-, and 0.41-fold of their baseline expression after 48 h storage, respectively, whereas PedBTZ2-C and PedBTZ2-D increased to 2.82- and 3.75-fold, respectively (Figure 7).

3.9. PedEJCs Expression Patterns in Response to Various Abiotic Stresses and Hormone Treatment

To investigate whether PedEJCs are involved in abiotic stress and phytohormone responses, we analyzed publicly available RNA-seq datasets from Moso bamboo treated with various stimuli. These datasets included treatments of Moso bamboo seedlings with cold (PRJNA535488) [61], polyethylene glycol (PEG, simulating drought), sodium chloride (NaCl, simulating salt stress), salicylic acid (SA), abscisic acid (ABA) (PRJNA715101) [62], and gibberellin (GA3) (PRJNA413166) [34], as well as treatments of Moso bamboo roots with brassinosteroid (BR) following propiconazole (PPZ, a BR biosynthesis inhibitor) treatment (PRJNA509131) [63] and naphthaleneacetic acid (NAA) (PRJNA390902) [64] (Table S2). Our results revealed that few PedEJCs were responsive to abiotic stress or hormone treatments (Figure 8A–H, Table S5).
Under PEG treatment, PedY14c-D exhibited a gradual downregulation, decreasing to 0.56-fold of the CK level at 24 h post-treatment. PedBTZ1-C and PedBTZ1-D showed the most pronounced downregulation at 3 h after PEG treatment, declining to 0.42- and 0.45-fold of their CK levels, respectively (Figure 8B, Table S5). Following ABA treatment, PedY14c-D was progressively downregulated, reaching its lowest expression at 24 h (0.31-fold of the CK level), whereas PedY14b-D exhibited an opposite trend, peaking at 3 h with 2.83-fold upregulation (Figure 8E, Table S5). For other abiotic stresses or phytohormone treatments, no substantial changes in PedEJCs expression were observed. For instance, upon NaCl and SA treatments, PedEIF4A3a-D displayed the greatest expression change among PedEJCs, peaking at 1.42-fold of its CK level at 3 h and 24 h, respectively (Figure 8C,D, Table S5). Under cold stress, PedY14d-C exhibited the largest variation among PedEJCs, decreasing to 0.84-fold of the 0 h level after 24 h treatment (Figure 8A, Table S5). In response to NAA treatment, PedY14d-C showed the maximum upregulation among PedEJCs (1.32-fold) (Figure 8G, Table S5). Following GA3 treatment, PedBTZ1-C displayed the greatest reduction among PedEJCs (0.69-fold) (Figure 8H, Table S5). Collectively, these findings indicate that most PedEJCs do not respond significantly to the tested phytohormones and abiotic stresses. However, whether the PedEJCs responds to other hormones and abiotic stresses warrants further investigation.

3.10. Cis-Acting Elements Present in the Promoters of the PedEJCs

The 2000 bp sequences upstream of the ATG start codon of each PedEJCs were submitted to the PlantCARE [45] for cis-regulatory element analysis. Beyond core elements, such as TATA-box and CAAT-box, the promoters harbored various specific regulatory elements (Figure 9), which are recognized by diverse transcription factors that may confer expression specificity to these PedEJCs. These cis-acting elements were classified into four functional categories: tissue and development-related, light response-related, stress response-related, and hormone response-related (Figure 9A). In the tissue and development-related category, five types of elements were identified: As-1 (shoot expression), CAT-box (meristem expression), W-box (senescence expression), and AAGAA-motif and GCN4-motif (both for endosperm expression) (Figure 9A). The As-1 element was most abundant, accounting for 47.27% of this category, with 26 copies detected across 11 PedEJC promoters (Figure 9B). The light response-related category comprised eleven elements: G-Box, chs-CMA2a, I-box, GATA-motif, Sp1, Box 4, GT1-motif, TCT-motif, AE-box, TCCC-motif, and circadian (Figure 9A). Among these, the Sp1 element was most prevalent (16.35%), with 17 copies identified in 6 PedEJC promoters (Figure 9C). Nine elements associated with stress responses were identified, including those related to anaerobic induction (ARE, GC-motif), defense (STRE, TC-rich repeats), cold response (LTR), metal response (MRE), drought response (MBS), and wound induction (WRE3, WUN-motif) (Figure 9A). The STRE element was predominant in this category (42.94%), with 70 copies found across 12 PedEJCs promoters (Figure 9D). The hormone response-related category contained fifteen element types responsive to abscisic acid (ABRE, ABRE3a, ABRE4), auxin (TGA-element, AuxRR-core), gibberellin (P-box, TATC-box, GARE-motif), jasmonic acid (CGTCA-motif, TGACG-motif), salicylic acid (TCA-element), and ethylene (ERE) (Figure 9A). Additionally, MYB and MYC binding sites, which are involved in multiple hormone and stress responses including jasmonic acid signaling, were the most abundant elements in this category (both 21.46%), with 50 copies each identified across 13 and 12 PedEJC promoters, respectively (Figure 9E).
Next, we integrated the cis-element prediction results with the expression profiles of the PedEJCs. Although there is no strict one-to-one correspondence between the number of cis-acting elements and PedEJCs expression levels, we identified several supporting lines of evidence. In our study, PedY14c-D, PedY14d-C, and PedMAGO1-D were the three genes most significantly downregulated during postharvest senescence of bamboo shoots, with PedY14d-C exhibiting the most pronounced reduction (Figure 7). As shown in Figure 9A, we found that PedY14d-C contains three W-box elements, which were associated with senescence-related expression. PedY14b-D and PedY14c-D were among the few PedEJC genes responsive to ABA treatment, showing upregulation (2.83-fold) and downregulation (0.31-fold), respectively (Figure 8E). Correspondingly, we identified 9, 2, and 2 ABRE, ABRE3a, and ABRE4 elements (ABA-responsive elements) in the promoter region of PedY14b-D, and 5, 1, and 1 of these elements in PedY14c-D, respectively.

4. Discussion

Accurate, exhaustive characterization is critical for investigating a gene family’s function and evolutionary history. In this study, we selected 17 species spanning major lineages of green plants, including chlorophytes, bryophytes, gymnosperms, basal angiosperms, monocots, and eudicots, to identify EIF4A3, Y14, MAGO, and BTZ genes (Table S1). EIF4A3, Y14, MAGO, and BTZ members were identified in unicellular algae (Figure 1), suggesting that the EJC-mediated post-transcriptional regulatory system emerged early in the common ancestor of green plants. These four gene families were widely distributed across all major evolutionary lineages of green plants, and phylogenetic analyses revealed that each gene family formed a monophyletic clade according to taxonomic relationships (Figure 2), indicating that the EJC-mediated regulatory mechanism is evolutionarily conserved.
We observed divergence in motif composition across different lineages. For example, the motif architecture of algal BTZ proteins differs markedly from that of BTZs in other plants (Figure 3), pointing to substantial motif remodeling and functional refinement of BTZ after the emergence of land plants. Despite these lineage-specific differences in motif composition, all EJC core genes retained their characteristic conserved domains (Figure 3) and continue to perform essential functions. Gene structure analysis further showed that while exon numbers were conserved across species, intron length varies substantially (Figure 3). In gymnosperms, introns in EJC core genes were generally longer than in other plant lineages, especially for BTZ. These results are consistent with the genome-wide trend toward longer introns in gymnosperms lineage [52,53]. Long introns in plants often harbor regulatory sequences and splicing-control elements. Accordingly, we hypothesize that the expanded introns of gymnosperm BTZ genes may increase the density of cis-regulatory motifs and splicing factor, thereby providing greater potential for transcriptional modulation and alternative splicing.
In this study, we focused on PedEJCs. We identified 14 EJC core genes in tetraploid Moso bamboo (Table 1), exceeding the numbers reported for diploid species, with five in Arabidopsis, eight in rice, and five in Physalis floridana [65]. In animals, the EJC has been reported to be a nucleocytoplasmic shuttling complex that localizes to both the nucleus and the cytoplasm [5]. Consistent with this, our subcellular localization predictions indicated that nearly all EJC components were localized to the nucleus, with the exception of PedY14a-D and PedY14b-C, and that MAGO and Y14 were also present in the cytoplasm (Table 1). The similar EJC tertiary structures in Moso bamboo and mammals (Figure S7) suggests that the mechanism of EJC function might be conserved across plants and animals.
Gene duplication is pervasive across organisms and generates novel functions that drive evolutionary innovation [66]. In this study, we identified seven PedEJC paralogous pairs arising from segmental duplication, with no evidence of tandem duplication (Figure 4A). Thus, expansion of the PedEJCs repertoire appears to have been shaped primarily by segmental duplication. Notably, three of these seven pairs (PedY14b-C/PedY14b-D, PedBTZ1-C/PedBTZ1-D, and PedBTZ2-C/PedBTZ2-D) originated during the allopolyploidization of Moso bamboo [35]. Paralogous pairs generated by segmental duplication often exhibit similar expression patterns. For example, the PedY14b-C/PedY14b-D pair showed the lowest expression among PedEJCs and is undetectable in some tissues (Figure 5, Figure 6, Figure 7 and Figure 8). The four BTZ family members were syntenic and, correspondingly display comparable baseline expression levels (Figure 5, Figure 6, Figure 7 and Figure 8) as well as similar transcriptional changes during rapid growth (Figure 6) and postharvest senescence (Figure 7). In particular, the allopolyploidization-derived pairs PedBTZ1-C/PedBTZ1-D and PedBTZ2-C/PedBTZ2-D showed especially similar absolute expression levels and amplitudes of change (Figure 5, Figure 6, Figure 7 and Figure 8). Not all genes follow this trend. In the PedMAGO2-C/PedMAGO3-D pair, PedMAGO3-D is consistently expressed at higher levels than PedMAGO2-C under all conditions examined (Figure 5, Figure 6, Figure 7 and Figure 8). PedY14a-D and PedY14c-D were syntenic with PedY14d-C, yet PedY14d-C is more highly expressed than the other two (Figure 5, Figure 6, Figure 7 and Figure 8). Even the seemingly similar pair PedY14b-C/PedY14b-D exhibits tissue-specific divergence: PedY14b-C was panicle-specific and nearly silent elsewhere, whereas PedY14b-D was expressed in rhizome, shoot, and lateral bud (Figure 5). Together, these results indicate that, following duplication, PedEJCs paralogs are progressively diverging in expression, which may underlie functional diversification. Moreover, the three pairs that arose during Moso bamboo allopolyploidization showed less expression divergence than the other four pairs, suggesting correspondingly lower degrees of functional divergence.
Moso bamboo is among the fastest-growing plants, a trait that directly underpins its ecological, economic, and cultural value [33]. Mining transcriptomes from four independent studies, we found that within shoots of the same height, regions with more vigorous growth and cell division—the shoot apical meristem (Figure 6A), the rapid division region (Figure 6B), and the basal portion of the shoot (Figure 6D)—show higher expression of nearly all PedEJCs (Figure 6A,B). Across shoots of different heights, expression of almost all PedEJCs declines as shoot height increases (Figure 6C,D). These patterns indicate that PedEJCs play important roles in shoot growth and likely contribute to rapid elongation. The near-uniform expression pattern of PedEJCs (Figure 6) implies that they are co-regulated and function as a complex to support rapid growth. Furthermore, PedY14b-D, PedY14c-D, and PedY14d-C exhibited the most pronounced changes in expression (Figure 6), implying prominent roles in this process. Because PedY14b-D was tissue-specific and was low or undetectable in some tissues (Figure 5, Figure 6, Figure 7 and Figure 8), PedY14c-D and PedY14d-C may be preferable initial targets for knockout or overexpression to dissect their functions in rapidly growing shoots.
Bamboo shoots are a nutritious food rich in protein, minerals, and fiber, and low in fat. However, during the early phase of rapid growth, a subset of shoots undergo accelerated senescence and deteriorate before reaching full maturity. This propensity for rapid postharvest senescence compromises storability and constrains production and consumption [60]. We observed that with increasing postharvest storage time, PedEIF4A3s, PedY14s, and PedMAGOs showed progressive downregulation, whereas PedBTZs were upregulated (Figure 7). This pattern suggesting distinct module-level responses among EJC subunits during postharvest senescence. PedY14c-D, PedY14d-C, and PedMAGO1-D were the most strongly downregulated genes, with PedY14d-C showing the greatest decrease (Figure 7). W-box elements have been linked to senescence-associated expression [67]. Notably, PedY14d-C harbored three W-box elements (Figure 9), the highest number among PedEJCs, which may partly account for its downregulation.
In plants, functional studies of the EJC have largely focused on growth and reproduction [15,16,17,20,21,28,29,30,31], with relatively few reports addressing abiotic stress or hormone treatments [22,32]. In our datasets, only a small subset of PedEJCs responded to certain abiotic or hormonal cues (Figure 8). PedY14b-D and PedY14c-D were among the few that responded to ABA (Figure 8E), and the PedY14b-D promoter region contains multiple ABA-responsive elements (ABRE, ABRE3a, and ABRE4) (Figure 9A). MAGO and Y14 have been reported to be regulated by ethylene and jasmonates in H.brasiliensis [22]. In this study, promoters of several PedEJCs were enriched for jasmonic acid–responsive elements (CGTCA motif, TGACG motif) as well as MYB and MYC sites, suggesting potential responsiveness to jasmonic acid treatment. Loss of BTZ function in rice has been reported to diminish salt tolerance. In this study, we observed little to no change in the transcription of pedEJCs under salt stress (Figure 8C). We therefore hypothesize that PedBTZs respond to salt stress primarily through non-transcriptional mechanisms, such as post-transcriptional or translational regulation.

5. Conclusions

We systematically identified 147 EJC core genes across 17 plant genomes and found that they formed a monophyletic clade consistent with established phylogenetic relationships. The expansion of the PedEJCs relied primarily on segmental duplication. Three duplicated gene pairs that arose during allopolyploidization in P. edulis exhibited less expression divergence than the other four pairs, suggesting a lower degree of functional differentiation. Expression profiling further indicated that most PedEJCs were likely involved in rapid shoot growth and postharvest senescence, whereas only a small subset responded to phytohormones and abiotic stresses. Notably, PedY14c-D and PedY14d-C were highly expressed across the surveyed tissues and displayed pronounced dynamics during rapid growth and postharvest senescence, making them prime candidates for subsequent functional studies of EJC-mediated regulation in these processes. Collectively, this work provides foundational insights into the evolution, expression, and function of EJC core genes in P. edulis and represents a first step toward their in-depth functional characterization.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/f16121822/s1, Figure S1: Multiple sequence alignment of the PedEIF4A3 proteins; Figure S2: Multiple sequence alignment of the PedY14 proteins; Figure S3: Multiple sequence alignment of the PedMAGO proteins; Figure S4: Multiple sequence alignment of the PedBTZ proteins; Figure S5: Secondary structure properties of the PedEJC proteins; Figure S6: Tertiary structure of single PedEJC proteins; Figure S7: Tertiary structure of EJC in Moso bamboo; Table S1: Sources of sequence and genome version information used in this study; Table S2: The sample information of RNA-seq data; Table S3: Protein sequence of 147 EJCs in 17 plants; Table S4: One-to-one orthologous relationships of EJCs between Moso bamboo and other; Table S5: The original TPM value and other information of PedEJCs.

Author Contributions

Conceptualization, Y.Z., and L.G.; Formal analysis, Y.W., J.Z., M.Z., X.L., M.W., W.Z., J.Y., T.H., S.X. and L.Z.; Data curation, Y.W., J.Z., M.Z., X.L., M.W., W.Z., J.Y., T.H., S.X. and L.Z.; Writing—original draft, Y.W. and J.Z.; Writing—review & editing, Y.Z. and L.G.; Visualization, Y.W., J.Z., M.Z., X.L., M.W., W.Z., J.Y., T.H., S.X. and L.Z.; Supervision, project administration, funding acquisition, L.G.; All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China (32371980), the Natural Science Foundation of Fujian Province (2025J02014), the S&T Innovation (KFB23180 and KFB24096A) and the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University (725025010 and 72202200205).

Data Availability Statement

This work is a re-analysis of previously published transcriptome data, and no new high-throughput sequencing data were generated. All data utilized in this study are from publicly available sources. The relevant RNA-seq datasets are accessible through the NCBI Sequence Read Archive (SRA) under the following BioProject accession numbers: PRJEB2956, PRJNA354950, PRJNA342231, PRJNA547876, PRJNA414226, PRJNA820321, PRJNA554957, PRJNA535488, PRJNA715101, PRJNA413166, PRJNA509131, and PRJNA390902 (detailed in Table S2 of our manuscript).

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Heatmap showed the number of EIF4A3, Y14, MAGO and BTZ members in 17 species. The species taxonomy relationship was depicted in the left.
Figure 1. Heatmap showed the number of EIF4A3, Y14, MAGO and BTZ members in 17 species. The species taxonomy relationship was depicted in the left.
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Figure 2. The phylogenetic trees of EIF4A3s (A), Y14 (B), MAGO (C), BTZ (D) in green plants. Trees were constructed from 30 EIF4A3, 41 Y14, 34 MAGO, and 42 BTZ protein sequences representing 17 species including 1 chlorophyte (red), 2 bryophytes (dark blue), 1 gymnosperm (light blue), 1 basal angiosperm (yellow), 4 monocots (green), and 8 eudicots (pinkish purple). The PedEJCs were marked with red five-pointed star.
Figure 2. The phylogenetic trees of EIF4A3s (A), Y14 (B), MAGO (C), BTZ (D) in green plants. Trees were constructed from 30 EIF4A3, 41 Y14, 34 MAGO, and 42 BTZ protein sequences representing 17 species including 1 chlorophyte (red), 2 bryophytes (dark blue), 1 gymnosperm (light blue), 1 basal angiosperm (yellow), 4 monocots (green), and 8 eudicots (pinkish purple). The PedEJCs were marked with red five-pointed star.
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Figure 3. (A) Distribution of conserved polypeptide motifs, function domains, and gene structures of the EIF4A3 genes in 17 species; (B) Distribution of conserved polypeptide motifs, function domains, and gene structures of the Y14 genes in 17 species; (C) Distribution of conserved polypeptide motifs, function domains, and gene structures of the MAGO genes in 17 species; (D) Distribution of conserved polypeptide motifs, function domains, and gene structures of the BTZ genes in 17 species. Different colors represent different taxonomy relationship, including chlorophytes (depicted in red), bryophytes (highlighted in dark blue), gymnosperms (illustrated in light blue), basal angiosperms (indicated in yellow), monocots (shown in green), eudicots (displayed in pinkish purple).
Figure 3. (A) Distribution of conserved polypeptide motifs, function domains, and gene structures of the EIF4A3 genes in 17 species; (B) Distribution of conserved polypeptide motifs, function domains, and gene structures of the Y14 genes in 17 species; (C) Distribution of conserved polypeptide motifs, function domains, and gene structures of the MAGO genes in 17 species; (D) Distribution of conserved polypeptide motifs, function domains, and gene structures of the BTZ genes in 17 species. Different colors represent different taxonomy relationship, including chlorophytes (depicted in red), bryophytes (highlighted in dark blue), gymnosperms (illustrated in light blue), basal angiosperms (indicated in yellow), monocots (shown in green), eudicots (displayed in pinkish purple).
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Figure 4. Chromosomal distribution and synteny analysis of EJC genes in Moso bamboo. (A) Schematic representations for the chromosomal distribution and synteny analysis of Moso bamboo EJC genes; (B) Synteny analysis of EJC genes between Moso bamboo and N. colorata; (C) Synteny analysis of EJC genes between Moso bamboo and A. thaliana; (D) Synteny analysis of EJC genes between Moso bamboo and O. sativa; (E) Synteny analysis of EJC genes between Moso bamboo and D. latiflorus. Gray lines in the background indicate all synteny blocks within Moso bamboo genome and other plants, and the blue, purple, yellow and green lines indicate duplicated EIF4A3, Y14, MAGO and BTZ gene pairs.
Figure 4. Chromosomal distribution and synteny analysis of EJC genes in Moso bamboo. (A) Schematic representations for the chromosomal distribution and synteny analysis of Moso bamboo EJC genes; (B) Synteny analysis of EJC genes between Moso bamboo and N. colorata; (C) Synteny analysis of EJC genes between Moso bamboo and A. thaliana; (D) Synteny analysis of EJC genes between Moso bamboo and O. sativa; (E) Synteny analysis of EJC genes between Moso bamboo and D. latiflorus. Gray lines in the background indicate all synteny blocks within Moso bamboo genome and other plants, and the blue, purple, yellow and green lines indicate duplicated EIF4A3, Y14, MAGO and BTZ gene pairs.
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Figure 5. Heatmap showing the gene expression profiles of PedEJCs from (A) five vegetative tissues and two flowering tissues, 1–2, biological repetition. (B) 3 growth tissues, 1–3, biological repetition. Z-score standardization were used of the original TPM for each gene.
Figure 5. Heatmap showing the gene expression profiles of PedEJCs from (A) five vegetative tissues and two flowering tissues, 1–2, biological repetition. (B) 3 growth tissues, 1–3, biological repetition. Z-score standardization were used of the original TPM for each gene.
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Figure 6. Heatmap showing the gene expression profiles of PedEJCs from (A) different parts of 0.25 m shoot, 1–4, biological repetition, SAM: shoot apical meristem region, YIN: young internode, YNO: young node, MIN: mature internode and MNO: mature node; (B) different parts of 3 m shoot, 1–3, biological repetition, RE: Rapid elongation, RD: Rapid division and SD: Start division; RE was sampled from the 15th internode of 3 m bamboo shoots, RD from the 25th and 26th internodes, and SD from the 40th, 41st, and 42nd internodes. (C) internodes in the middle parts of shoots of different heights, 1–3, biological repetition; (D) different internodes of bamboo shoots at different heights, 1–3, biological repetition; 2B: 2 m height basal internode; 2M: 2 m height middle internode; 4B: 4 m height basal internode; 4M: 4 m height middle internode. 2B, 2M, 4B and 4M were taken from the 18th internode of bamboo shoots. Z-score standardization were used of the original TPM for each gene.
Figure 6. Heatmap showing the gene expression profiles of PedEJCs from (A) different parts of 0.25 m shoot, 1–4, biological repetition, SAM: shoot apical meristem region, YIN: young internode, YNO: young node, MIN: mature internode and MNO: mature node; (B) different parts of 3 m shoot, 1–3, biological repetition, RE: Rapid elongation, RD: Rapid division and SD: Start division; RE was sampled from the 15th internode of 3 m bamboo shoots, RD from the 25th and 26th internodes, and SD from the 40th, 41st, and 42nd internodes. (C) internodes in the middle parts of shoots of different heights, 1–3, biological repetition; (D) different internodes of bamboo shoots at different heights, 1–3, biological repetition; 2B: 2 m height basal internode; 2M: 2 m height middle internode; 4B: 4 m height basal internode; 4M: 4 m height middle internode. 2B, 2M, 4B and 4M were taken from the 18th internode of bamboo shoots. Z-score standardization were used of the original TPM for each gene.
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Figure 7. Heatmap showing the gene expression profiles of PedEJCs from different storage periods of bamboo shoots. 1–3, biological repetition; Z-score standardization were used of the original TPM for each gene.
Figure 7. Heatmap showing the gene expression profiles of PedEJCs from different storage periods of bamboo shoots. 1–3, biological repetition; Z-score standardization were used of the original TPM for each gene.
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Figure 8. Barplot showing the expression patterns of PedEJCs under low temperature (A), PEG (B), NaCl (C), SA (D), ABA (E), PPZ (F), NAA (G) and GA3 (H) treatment. The TPM value was used to characterize gene expression level and the value for each sample is the mean ± standard error (SE).
Figure 8. Barplot showing the expression patterns of PedEJCs under low temperature (A), PEG (B), NaCl (C), SA (D), ABA (E), PPZ (F), NAA (G) and GA3 (H) treatment. The TPM value was used to characterize gene expression level and the value for each sample is the mean ± standard error (SE).
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Figure 9. Distribution of cis-acting elements in the promoters of the PedEJCs. (A) Heatmap showing the distribution and counts of cis-acting elements in the promoters of the PedEJCs. (B–E). Pie chart showing the proportion of cis-acting elements distributed in four divided categories: the tissue and development-related category (B), the light response-related category (C), the stress response-related category (D), and the hormone response-related category (E).
Figure 9. Distribution of cis-acting elements in the promoters of the PedEJCs. (A) Heatmap showing the distribution and counts of cis-acting elements in the promoters of the PedEJCs. (B–E). Pie chart showing the proportion of cis-acting elements distributed in four divided categories: the tissue and development-related category (B), the light response-related category (C), the stress response-related category (D), and the hormone response-related category (E).
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Table 1. Information about identified EJC genes in Moso bamboo.
Table 1. Information about identified EJC genes in Moso bamboo.
NameIDLength (aa)MW (kDa)PIGRAVYSubcellular Localization
PedEIF4A3a-DPed02Dg30880.140545.86.15−0.157Nucleus
PedEIF4A3b-DPed12Dg11830.140445.76.22−0.149Nucleus
PedY14a-DPed01Dg25930.220122.04.69−0.544Cytoplasm
PedY14b-CPed03Cg03200.120222.15.75−0.356Cytoplasm
PedY14b-DPed03Dg03160.120822.85.18−0.479Cytoplasm/Nucleus
PedY14c-DPed05Dg18550.120522.65.43−0.757Cytoplasm/Nucleus
PedY14d-CPed09Cg23730.120722.65−0.787Cytoplasm/Nucleus
PedMAGO1-DPed02Dg09160.117119.85.86−0.64Cytoplasm/Nucleus
PedMAGO2-CPed05Cg20270.116318.75.84−0.521Cytoplasm/Nucleus
PedMAGO3-DPed08Dg00860.116318.65.61−0.547Cytoplasm/Nucleus
PedBTZ1-CPed01Cg29980.169274.75.67−1.052Nucleus
PedBTZ1-DPed01Dg22680.170175.85.19−1.11Nucleus
PedBTZ2-CPed05Cg09280.171078.06.04−1.012Nucleus
PedBTZ2-DPed05Dg03920.270877.36.17−0.968Nucleus
Table 2. Duplication pairs Ka/Ks.
Table 2. Duplication pairs Ka/Ks.
Gene NameGene NameKaKsKa/KsSelection PressureTime (Mya)
PedY14b-CPedY14b-D0.0270.1230.220Purifying selection9.46
PedY14a-DPedY14d-C0.1270.6550.193Purifying selection50.38
PedY14c-DPedY14d-C0.0240.1160.209Purifying selection8.92
PedMAGO2-CPedMAGO3-D0.0240.0670.362Purifying selection5.15
PedBTZ1-CPedBTZ1-D0.0380.1160.328Purifying selection8.92
PedBTZ2-CPedBTZ2-D0.0420.1090.387Purifying selection8.39
PedBTZ1-CPedBTZ2-D0.4061.2250.332Purifying selection94.23
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Wang, Y.; Zhang, J.; Zhao, M.; Liu, X.; Wang, M.; Zhong, W.; Yang, J.; Hua, T.; Xiang, S.; Zhao, L.; et al. Identification and Evolution of Exon Junction Complex Core Genes and Expression Profiles in Moso Bamboo. Forests 2025, 16, 1822. https://doi.org/10.3390/f16121822

AMA Style

Wang Y, Zhang J, Zhao M, Liu X, Wang M, Zhong W, Yang J, Hua T, Xiang S, Zhao L, et al. Identification and Evolution of Exon Junction Complex Core Genes and Expression Profiles in Moso Bamboo. Forests. 2025; 16(12):1822. https://doi.org/10.3390/f16121822

Chicago/Turabian Style

Wang, Yuhua, Jun Zhang, Mengna Zhao, Xiaoyu Liu, Mingzhe Wang, Wenwen Zhong, Jiajie Yang, Tian Hua, Shengcai Xiang, Liangzhen Zhao, and et al. 2025. "Identification and Evolution of Exon Junction Complex Core Genes and Expression Profiles in Moso Bamboo" Forests 16, no. 12: 1822. https://doi.org/10.3390/f16121822

APA Style

Wang, Y., Zhang, J., Zhao, M., Liu, X., Wang, M., Zhong, W., Yang, J., Hua, T., Xiang, S., Zhao, L., Zhang, Y., & Gu, L. (2025). Identification and Evolution of Exon Junction Complex Core Genes and Expression Profiles in Moso Bamboo. Forests, 16(12), 1822. https://doi.org/10.3390/f16121822

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