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Genome-wide analysis of the ABC gene family in almond and functional predictions during flower development, freezing stress, and salt stress

Abstract

ABC (ATP-binding cassette) transporter proteins are one of the most extensive protein families known to date and are ubiquitously found in animals, plants, and microorganisms. ABCs have a variety of functions, such as plant tissue development regulation, hormone transport, and biotic and abiotic stress resistance. However, the gene characterization and function of the ABC gene family in almond (Prunus dulcis) have not been thoroughly studied. In this study, we identified 117 PdABC genes using the whole genome of ‘Wanfeng’ almond obtained by sequencing and explored their protein characterization. The PdABC family members were classified into eight subfamilies. The members of the same subfamily had conserved motifs but poorly conserved numbers of exons and introns and were unevenly distributed among the eight subfamilies and on the eight chromosomes. Expression patterns showed that PdABC family members were significantly differentially expressed during almond development, dormant freezing stress, and salt stress. We found that PdABC59 and PdABC77 had extremely high expression levels in pollen. PdABC63 and PdABC64 had high expression levels during almond petal development and multiple stages of flower development. PdABC98 was highly expressed in annual dormant branches after six temperature-freezing stress treatments. PdABC29, PdABC69, and PdABC98 were highly expressed under different concentrations of salt stress. This study preliminarily investigated the expression characteristics of ABC genes in different tissues of almond during flower development, freezing stress and salt stress, and the results will provide a reference for further in-depth research and breeding of almond in the future.

Peer Review reports

Introduction

ABC (ATP-binding cassette) transporter proteins comprise one of the largest families of proteins discovered to date and are widely found in animals, plants, and microorganisms [1]. ABC transporter proteins can take up a wide range of substances, such as inorganic ions, nutrients, amino acids, and organic matter, to maintain the normal biological activities of the organism [2]. ABC transporter proteins have a highly conserved nucleotide-binding domain (NBD) and transmembrane domain (TMD) with five or six helices [3]. These transporter proteins are categorized into three types of structures: holomolecules, semimolecules, and soluble proteins. Holomolecular transporter proteins contain two NBDs and TMDs, semimolecular transporter proteins contain one NBD and TMD, and soluble proteins have only an NBD and no TMD [4]. Among them, the TMD functions as a recognition substrate to transport substances across the membrane, and the NBD is located on the inner side of the cell membrane, including the conserved Walker A and Walker B sequences and the less conserved LSGGQ motif [5].

To date, ABC transporter proteins have been extensively studied in various species, including humans, insects, microorganisms, and plants [6,7,8,9]. According to related research, plant ABC members are typically divided into eight subfamilies: ABCA, ABCB, ABCC, ABCD, ABCE, ABCF, ABCG, and ABCI, with no ABCH subfamily identified in plants [10]. Currently, the most extensively studied subfamilies in different species are the ABCB, ABCC, and ABCG subfamilies [11]. Among these subfamilies, the ABCA (AOH, ABC1 homolog), ABCB (MDR, multidrug resistance protein), ABCC (MRP, multidrug resistance-associated protein), and ABCG (PDR, pleiotropic drug resistance protein) subfamilies are classified as full-transporter ABC proteins, while the ABCA (ATH, ABC2 homolog), ABCB (ATM, ABC transporter of the mitochondrion), ABCB (TAP, transporter associated with antigen processing), ABCD (PMP, peroxisomal membrane protein 3), and ABCG (WBC, white‒brown complex protein) subfamilies are categorized as half-transporter ABC proteins. The ABCE (RLI, RNase L inhibitor), ABCF (GCN, general control nonrepressible protein), ABCI (SMC, structural maintenance of chromosome protein), and ABCI (NAP, nonintrinsic ABC proteins) subfamilies are soluble ABC transport proteins [12]. The ABCA subfamily includes both full-transporter AOH and half-transporter ATH types. For example, A. thaliana contains one AOH and 16 ATH type transporter proteins [13]. Notably, AOH-type genes have only been found in dicotyledonous plants such as Arabidopsis and grapes and are absent in monocotyledonous plants such as maize [14, 15]. The ABCB subfamily includes three classes of transporter proteins: MDR, ATM, and TAP. In Arabidopsis, 29 members of this subfamily have been identified [13]. Research has revealed that plant ABCB subfamily members are primarily involved in the regulation and transport of auxins (such as AtPGP1 and OsABCB14) and participate in ion transport and resistance to heavy metal stress (including OsABCB25 and OsABCB23) [16,17,18,19]. The ABCC subfamily encodes MRP-type transporter proteins, which are associated with transport and metabolic functions in plants. For instance, AtABCC4 is involved in folate transport, while VvABCC1 and AtABCC2 participate in anthocyanin transport [20,21,22]. Additionally, members of this subfamily in plants have detoxification functions. AtMRP1 and AtMRP2, among others, are involved in resistance to heavy metals [23, 24]. The ABCD subfamily encodes PMP-type transporter proteins, with AtPMP2 shown to inhibit seed germination [25]. The ABCG subfamily includes two classes of transporter proteins: PDR and WBC. This is the largest subfamily with members that have diverse functions, including regulating plant terpenoids, alkaloids, lipids, and volatile aromatic compounds [26,27,28]. The ABCE, ABCF, and ABCI subfamilies lack transmembrane domains and do not exhibit specific transport characteristics.

Almond, belonging to the genus Prunus in the family Rosaceae, is a medium-sized tree or shrub. Its kernel is highly nutritious and medicinally important, making it widely cultivated and utilized in various countries worldwide. Xinjiang is a major cultivation area of almonds in China, covering an area of approximately 66,000 hectares, and almonds are an important economic fruit tree in this region. However, a major challenge in almond production in Xinjiang is the low pollen activity and reduced fruit set due to self-incompatibility, which severely hinders the development of the almond industry. Therefore, it is of significance to explore the potential functions of ABC genes in different floral organs of almond. Additionally, there are other common issues that impact the almond industry, such as early flowering of native almond varieties in Xinjiang, making them vulnerable to late spring frosts, and freezing damage to floral organs in extremely low-temperature conditions during the winter dormancy period. This region also faces the challenge of severe soil salinity and alkalinity, which limits the development of the almond industry. To gain insight into the characteristics of ABC gene family members in almond, we conducted a comprehensive analysis based on ‘Wanfeng’ almond whole-genome data. We identified and characterized ABC gene family members and performed bioinformatics analyses to explore protein physicochemical properties, phylogenetic tree construction and classification, conserved motifs, gene structures, gene chromosomal localization, gene duplication types, cis-acting elements, and expression patterns. Furthermore, we conducted fluorescent quantitative expression analysis of 10 PdABC genes in various floral organs of almonds across six different stages of flower development under a gradient of six temperatures to simulate freezing stress conditions during the dormancy period and subjected them to three different salt stress treatments. The aim of this study was to explore the potential functions of ‘Wanfeng’ almond ABC gene family members in floral organ development and stress responses, thereby providing valuable insights for future research related to almonds.

Materials and methods

Identification of almond ABC family members

The whole genome data of Prunus dulcis ‘Wanfeng’ were used for the ABC gene family analysis [29]. The Pfam database (http://pfam.xfam.org/) was employed to download hidden Markov models (HMMs) for four ABC transporter domains: ABC transporter domain (PF00005), ABC transporter transmembrane region domain (PF00664), ABC 3 transport family (PF00950), and ABC 3 transport family (PF00950). The HMMER tool was used to search and compare the almond whole-genome protein sequences with the four ABC transporter HMMs, retaining proteins with e-value ≤ 1e−5 [30]. The BLASTP program was employed to compare almond whole-genome protein sequences with Arabidopsis ABC member protein sequences, retaining proteins with e-value ≤ 1e−5. Combining the HMMER and BLASTP results, duplicate sequences were removed, and ABC domains were validated using the NCBI-CDD tool (https://www.ncbi.nlm.nih.gov/cdd/). A total of 117 ABC genes were identified in the almond genome. Protein physicochemical properties were determined using ExPASy (http://web.ExPASy.org/protparam/), and subcellular localization was predicted using WoLF PSORT II (https://www.genscript.com/wolf-psort.html?src=leftbar) [31, 32].

Construction and classification of phylogenetic trees

A total of 129 protein sequences of A. thaliana ABC family members were downloaded from the UniProt database (https://www.uniprot.org/). MUSCLE multiple sequence alignment was performed using MEGA X. The maximum likelihood method was used to construct phylogenetic trees with 1,000 bootstrap replications, Poisson correction model, and pairwise deletion [33]. Further phylogenetic analysis included the examination of ABC members associated with flower organ development in A. thaliana, Petunia hybrida, Medicago truncatula, Vitis vinifera, and Malus domestica.

Motifs, domains, and gene structures

The MEME online tool (http://meme-suite.org/tools/meme) was used to identify motifs in PdABC family member protein sequences [34]. The NCBI CDD online tool (https://www.ncbi.nlm.nih.gov/cdd/) was used to retrieve information on the location and number of ABC domains in PdABC family member protein sequences [35]. Gene structure information, including exon and intron positions and numbers, was extracted from the almond genome GFF (General Feature Format) data. TBtools was employed for clustering and visualization of PdABC family members phylogenetic tree, motifs, domains, and gene structures [36].

Gene mapping, collinearity, and Ka/Ks analysis

The TBtools was used to map the positions of PdABC members on chromosomes. The MCScanX tool was used for segmental and tandem duplication gene analysis, and the Circos tool was used for drawing chromosome collinearity diagrams [37, 38]. ABC collinearity gene analysis was further conducted among P.dulcis, A.thaliana, Oryza sativa, M.domestica and Prunus persica. The Ka/Ks Calculator tool was used to calculate Ka (Nonsynonymous substitution rate), Ks (Synonymous substitution rate), and Ka/Ks values for duplicated genes [39].

Cis-acting element annotation

Upstream 2000 bp sequences of the 117 PdABC genes were extracted using TBtools. The PlantCARE online tool (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) was employed for cis-acting element annotation in the promoter regions [40]. Cis-acting elements associated with abiotic and biotic stresses, phytohormone responsiveness, and plant growth and development were selected and analyzed [41]. Cis-acting element distribution maps of PdABC members were generated using TBtools.

Expression patterns

FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values were obtained from transcriptome data for ‘Wanfeng’ almond, which included six flower developmental stages (GSA Number: CRA007615), a gradient of six freezing temperature stress conditions for dormancy (GSA Number: CRA007323), and salt stress treatments for ‘Amanisha’ almond (GSA Number: CRA013033). Transcriptome data are available through the CNCB database (https://www.cncb.ac.cn/).

Protein‒protein interaction network construction

Protein sequences of almond PdABC family members were compared in the STRING database (https://string-db.org/) to predict protein‒protein interactions among PdABC members. The Cytoscape tool was used to visualize the protein interaction network.

Fluorescence quantification

We selected three six-year-old ‘Wanfeng’ almond trees with good growth as material collection objects through the almond resource orchard of the state-owned second forest farm in Yarkand, Kashgar, Xinjiang, China. The three trees corresponded to three biological replicates. Various ‘Wanfeng’ almond tissues (leaves, sepals, petals, pollen, and pistils), flowers at six stages of development [29], dormant one-year-old branches under freezing stress (CK (—5 ℃), —10 ℃, —15 ℃, —20 ℃, —25 ℃, and —30 ℃) at different temperatures [42]. In August 2022, ‘Amanisha’ almond seeds were collected through the almond resource orchard, and dormancy was artificially broken in the laboratory in November 2022. The seeds were placed in seedling trays with soil and cultured in a solar greenhouse. By May 2023, 12 plants were selected to grow well. The seedlings (six months) were watered with NaCl solutions of four concentrations: CK (0), 50, 100, and 150 mM. Three columns of seedlings were treated with each solution concentration as three biological replicates, and the leaves were collected after 24 h.

In this study, we primarily focused on PdABC genes related to almond pollen development. Therefore, based on the phylogenetic clustering results shown in Fig. 1B, we selected 10 PdABC genes closely associated with pollen development for fluorescent quantitative analysis. Three independent biological replicates containing three independent plants were used for qRT‒PCR. The qRT‒PCR primers of the selected PdABC genes were designed by Primer Premier 5 (Table S1). The fluorescent quantitative analysis process followed the same methodology as previously described by our research team [43]. The obtained cycle threshold (CT) values were quantitatively analyzed by the 2^-Ct method (Table S2) [44].

Fig. 1
figure 1

Phylogenetic Tree of PdABC Family Members. A Phylogenetic tree of Wanfeng almond and Arabidopsis ABC family members. Each colored region represents a subfamily, with yellow font denoting AOH, orange font denoting ATH, light blue font denoting ATM, purple font denoting TAP, green font denoting MDR, red font denoting PDR, and dark blue font denoting WBC. B Phylogenetic tree of PdABC family members in relation to ABC genes associated with flower organ development in five species: A. thaliana, P. hybrida, M. truncatula, V. vinifera, and M. domestica. Each coloured region represents a group

Results

Characteristics of PdABC family members

We identified 117 ABC genes in the ‘Wanfeng’ almond genome, and NCBI-CDD database verification confirmed the presence of an ABC domain in each protein sequence of each gene. These 117 ABC genes were renamed PdABC1 to PdABC117 based on their chromosomal and positional distribution. The physicochemical properties of PdABC family members exhibited significant variation (Table S3). Notably, the number of amino acids in these members ranged from 108 aa (amino acids) (PdABC13) to 2837 aa (PdABC20). The molecular weight of PdABC family members ranged from 11,621.36 Da (Dalton) to 319,923.26 Da. Members were categorized into four groups by molecular weight: 10,000 Da to 49,999 Da, 50,000 Da to 99,999 Da, 100,000 Da to 149,999 Da, and over 150,000 Da, comprising 11, 50, 23, and 33 members, respectively. The isoelectric point of PdABC members ranged from 5.29 to 9.67, with 27 members having isoelectric point values less than 7 and 90 members having isoelectric point values greater than 7. Protein hydrophilicity analysis revealed that 37 members were hydrophilic proteins, while 80 members were hydrophobic proteins. Subcellular localization prediction placed members in five subcellular locations: nucleus, cytoplasm, plasma membrane, chloroplasts, and mitochondria, with 7, 19, 79, 10, and 2 members, respectively.

Phylogenetic analysis of PdABC family members

We constructed a maximum likelihood phylogenetic tree using protein sequences of PdABC (117) and ATABC (129) members. The clustering of PdABC members was further explored based on the subfamily classification of ATABC members (Fig. 1A). We categorized PdABC members into eight subfamilies: ABCA, ABCB, ABCC, ABCD, ABCE, ABCF, ABCG, and ABCI, with each subfamily having 6, 27, 13, 2, 4, 4, 52, and 9 members, respectively (Table S3). Based on the clustering results of ATABC members, we further classified PdABC members into seven subcategories: ABCA (AOH), ABCA (ATH), ABCB (ATM), ABCB (TAP), ABCB (MDR), ABCG (PDR), and ABCG (WBC), with each category containing 1, 5, 1, 18, 8, 21, and 31 members, respectively. A comparison of ABC member numbers in nine different species revealed a high level of conservation in the distribution of ABC members across the eight subfamilies (Table S4). Notably, the number of ABC members in Wanfeng almond was similar to that in Prunus avium. The trends in ABC member distribution across the eight subfamilies in P. avium, Prunus mume, P. persica, and P. dulcis were similar. Additionally, based on the clustering of PdABCs with ABC genes associated with flower organ development in five species, the phylogenetic tree was divided into seven groups, labeled I to VII. Each group consisted of 3 (PdABC59/77/105), 1 (PdABC75), 5 (PdABC88/107/108/109/110), 4 (PdABC63/64/92/94), 1 (PdABC69), 2 (PdABC32/68), and 7 (PdABC18/29/48/50/51/67/98) members. It is hypothesized that these genes may play specific roles in almond flower organ development (Fig. 1B, Table S5).

Analysis of conserved motifs, domains, and gene structures of PdABC family members

Based on the MEME tool, we annotated 10 motifs within the 117 PdABC family members and identified each motif sequence in the NCBI-CDD database. Notably, Motif 1, Motif 2, Motif 4, Motif 5, Motif 6, and Motif 10 correspond to the Walker A/Walker B motifs (ABC), while Motif 3, Motif 7, and Motif 9 are related to ABC transporter G family members, and Motif 8 represents the ABC-type lipoprotein export system (Fig. S1). The phylogenetic tree clustering of PdABC family members showed that members within the same subfamily exhibit a high degree of motif conservation (Fig. 2A, B). Specifically, ABCA subfamily members consist of a single type of Motif 2, Motif 4, and Motif 5. Members of the ABCB subfamily predominantly possess two regions, Motif 2, Motif 6, Motif 5, and Motif 10. ABCC subfamily members primarily contain two regions: Motif 2, Motif 5, Motif 10 or Motif 2, Motif 6, Motif 5, and Motif 10. Members of the ABCD, ABCE, ABCF, and ABCI subfamilies consist of Motif 2 and Motif 5. In contrast, ABCG subfamily members exhibit eight different motif types, namely, Motif 1, Motif 2, Motif 3, Motif 4, Motif 5, Motif 7, Motif 8, and Motif 9. Notably, the ABCG subfamily features three unique ABC transporter G motifs, Motif 9, Motif 3, and Motif 7, arranged sequentially. In addition, the distribution characteristics and quantity of PdABC protein domains are consistent with those of conserved motifs, further indicating the high accuracy of subfamily clustering corresponding to PdABC family members (Fig. 2C).

Fig. 2
figure 2

Conserved motifs and gene structures of PdABC family members. A Maximum likelihood phylogenetic tree of PdABC family members. B Conserved protein motifs. C ABC protein domains. D Gene structure

In terms of gene structure, the number of exons in PdABC family members ranged from 1 to 48, and the number of introns varied from 0 to 47, indicating a wide distribution (Fig. 2D, Table S3). The conservation of protein sequence lengths differs between different subfamilies. The sequence lengths of the three subfamilies ABCA, ABCB and ABCG are poorly conserved, with 3 (3), 16 (11) and 21 (31) members having sequence lengths greater than 1000 (less than 1000) amino acids, respectively. Notably, the sequence length of most members of the two categories ABCB (MDR) and ABCG (PDR) is more than 1000 amino acids, and they are highly conserved. The sequence lengths of the four subfamilies ABCC, ABCE, ABCF and ABCI are highly conserved, with average lengths of 1461, 597, 685 and 332 amino acids, respectively. There are only 2 members of the ABCD subfamily, which are 1340 and 764 amino acids. Similarly, the exon numbers of PdABC members among the eight subfamilies also varied greatly. The exon numbers of the six members of the ABCA subfamily are 8, 14, 16, 18, 34 and 40. The number of exons of the ABCB subfamily members is less than 20, with 1, 1, 2, 3, 1, 3, 6, 1, 5, 2, 1 and 1 members containing 2, 3, 6, and 7, respectively. Exons 8, 9, 10, 11, 12, 15, 17 and 18. The ABCC subfamily has 1, 1, 5, 2, 1, 1, 1 and 1 members with 7, 8, 10, 11, 12, 26, 28 and 36 exons, respectively. The exon numbers of the two members of the ABCD subfamily are 10 and 25, respectively. The number of exons among the four members of the ABCE subfamily is 11. The exon numbers of the four members of the ABCF subfamily are 1, 5, 9 and 18. The exon numbers of the ABCG subfamily members are relatively wide, with 4 members having 1 exon and 10, 12, 9 and 16 members having exon numbers ranging from 2 to 5, 7 to 9, 10 to 19, and 20 to 25, respectively, and one member has 48 exons. The ABCI subfamily has one exon, 6 exons with 3 to 8 exons, and 2 exons with 10 exons. Notably, in addition to the highly conserved exon number among members of the ABCE subfamily, the number of exons varies greatly among other subfamily members, which is one of the reasons for the functional diversity of members of the same subfamily. There is a strong correlation between the number of exons and the length of the protein of most PdABC members. The longer the protein sequence is, the greater the number of exons.

PdABC family member chromosome location, collinearity, and Ka/Ks analyses

The 117 PdABC family members are unevenly distributed across eight chromosomes, with chromosomes 1 to 8 carrying 21, 12, 20, 13, 8, 19, 9, and 15 genes, respectively. To calculate the gene density on each chromosome, we used a genetic distance of 200 kb and represented it in Fig. 3 as a color gradient from blue (low gene density) to red (high gene density). Blank regions indicate a lack of gene distribution information (Fig. 3; Table S6). Notably, 36.75% (43) of the PdABC family members on chromosomes 1 to 8 are located in low gene density regions. Similar to other plant ABC family studies, there is no significant correlation between chromosome length and the number of PdABC genes.

Fig. 3
figure 3

Chromosome locations of PdABC family members. The left scale represents chromosome lengths. Black squares represent PdABC genes located in low gene density regions, and green lines indicate tandem repeat gene pairs

We identified 12 pairs of segmental duplicate genes and 11 pairs of tandem duplicate genes in the PdABC family members (Table S7). Notably, the ABCG (PDR) subfamily has 8 pairs of segmental duplicate genes and 6 pairs of tandem duplicate genes. The 12 pairs of segmental duplicate genes were distributed on all seven chromosomes except chromosome 8, with chromosomes 1 to 7 carrying 2, 4, 3, 1, 1, 3, and 2 genes, respectively (Fig. 4). The 11 pairs of tandem duplicate genes are distributed on five chromosomes, with chromosomes 1, 3, 4, 5, and 8 carrying 3, 3, 1, 2, and 2 genes, respectively. Additionally, four pairs of tandem duplicate genes, PdABC5/PdABC6, PdABC43/PdABC44, PdABC107/PdABC108, and PdABC108/PdABC109, are located in regions with low gene density on chromosomes (Fig. 3). Furthermore, the Ka/Ks values for the duplicated PdABC gene pairs are all less than 1, indicating significant purifying selection pressure during the evolution of PdABC family members (Table S8).

Fig. 4
figure 4

Interchromosomal relationships of PdABC genes in the almond genome. The red lines connect duplicated PdABC gene pairs

To investigate the evolution of PdABC family members, we assessed the collinearity of ABC family member genes in P. dulcis with those of four other species: A. thaliana, O. sativa, M. domestica, and P. persica (Fig. 5). The results show that almond has 32, 0, 108, and 94 collinear gene pairs with A. thaliana, O. sativa, M. domestica, and P. persica ABC family members, respectively (Table S7). In A. thaliana and M. domestica, some PdABC genes have collinear relationships with two or more ABC members, suggesting their important roles during the evolution of the PdABC gene family. The collinear gene pairs between P. dulcis and P. persica are generally one-to-one, indicating a high degree of conservation. Notably, there were no collinear gene pairs between almond and rice, suggesting a strong separation between monocots and dicots in the evolution of ABC genes. Furthermore, the Ka/Ks values for collinear gene pairs between P. dulcis and A. thaliana, M. domestica, and P. persica are all less than 1, indicating the influence of purifying selection pressure on PdABC family members during evolution.

Fig. 5
figure 5

Synteny analysis of almond with ABC family members from four species. Each horizontal line represents a chromosome, and the numbers represent chromosome numbers. The red lines indicate collinear gene pairs

Upstream Cis-acting element analysis of PdABC family members

We annotated 120 cis-acting elements in the 2,000 bp promoter regions of 117 PdABC genes, 45 of which have known functions (Table S9). In addition to basic elements such as CAAT-box and TATA-box, the promoter regions contain various light-related elements, including ACE, G-Box, and P-box. We chose to present the distribution of three functional cis-acting elements related to plant growth and development, abiotic and biotic stresses, and phytohormone responsiveness (Fig. 6). Plant growth and development-related elements include G-box, TCT-motif, circadian, GATA-motif, TCCC-motif, CAT-box, I-box, Box 4, AE-box, and GT1-motif elements. Abiotic and biotic stress-related elements include ARE, MBS, MYB, MYC, STRE, W box, WUN-motif, TC-rich repeats, LTR, and DRE core. Phytohormone responsiveness-related elements include ABRE, CARE, CGTCA-motif, P-box, TGACG-motif, as-1, ERE, TCA-element, TGA-element, and GARE-motif. We also counted the number of these elements in the promoter regions of each PdABC gene (Figure S2). The results show that PdABC44 has the fewest elements (18), while PdABC88 has the most elements (53). In plant growth and development, there are a total of 999 elements, with the circadian element being the least (21) and the Box 4 element being the most (254). In abiotic and biotic stresses, there are a total of 1919 elements, with the DRE core element being the least abundant (21) and the MYC element being the most abundant (505). In phytohormone responsiveness, there are a total of 1124 elements, with the CAREs being the least (10) and the ABREs being the most (272). In summary, based on the results of cis-acting elements, PdABC family members are widely involved in various biological processes.

Fig. 6
figure 6

Cis-acting elements in the promoter regions of PdABC family members. A Promoter regions of PdABC1 to PdABC58. B Promoter regions of PdABC59 to PdABC117. Each coloured square represents a type of cis-acting element. C Number of cis-acting elements for PdABC members. The redder the box is, the more elements it contains, and the whiter the box is, the fewer elements it contains. The numbers in the boxes represent the number of cis-acting elements

Expression pattern analysis of PdABC family members

We first removed PdABC family members with FPKM values consistently below 1 in all transcriptome samples (Table S10). For the six developmental stages of ‘Wanfeng’ almond flowers, we analyzed the expression patterns of 92 PdABC genes based on transcriptome data (Fig. 7A). The results showed that among the five stages (A1, A2, A3, A4, and A5), 30, 22, 11, 30, and 12 PdABC genes were significantly upregulated, respectively, whereas no significant upregulation was observed at A6 (full blooming stage). Notably, ABCG (PDR) subfamily members exhibited significant upregulation in stages A1 to A4, while ABCG (WBC) subfamily members were primarily upregulated in stage A1. Furthermore, several PdABC genes showed upregulation in multiple stages, such as PdABC4, PdABC7, PdABC87, PdABC100, and PdABC104.

Fig. 7
figure 7

Expression patterns of PdABC family members. A Expression patterns of PdABC family members during the six developmental stages of ‘Wanfeng’ almond flowers. A1 (Bud stage), A2 (Enlargement stage), A3 (Inflorescence elongation stage), A4 (Small bud stage), A5 (Large bud stage), and A6 (Full blooming stage). B Expression patterns of PdABC family members in dormant one-year-old branches of ‘Wanfeng’ almond under freezing stress. C Expression patterns of PdABC family members in leaves of ‘Amanisha’ almond under salt stress. ROW normalization was used, with red squares indicating upregulation and blue squares indicating downregulation. The different colored vertical lines on the left represent different subfamilies. Numbers in the squares represent positive or negative correlation values, with values greater than or equal to 0.8 considered significant upregulation

For the dormant one-year-old branches of ‘Wanfeng’ almond under freezing stress, we analyzed the expression patterns of 61 PdABC genes based on transcriptome data (Fig. 7B). The results showed that among the CK, —10 °C, —15 °C, —20 °C, —25 °C, and —30 °C treatments, 29, 21, 2, 9, 11, and 9 PdABC genes were significantly upregulated, respectively. Genes from the ABCG (PDR) and ABCG (WBC) subfamilies were mainly upregulated in CK. Notably, genes from the ABCB (MDR and TAP), ABCC, ABCD, and ABCI subfamilies included PdABC genes upregulated at —25 °C and —30 °C. For instance, PdABC2, PdABC3, and PdABC91.

For salt-stressed leaves of ‘Amanisha’ almond, we analyzed the expression patterns of 72 PdABC genes based on transcriptome data (Fig. 7C). The results showed that among the CK, 50 mM, 100 mM, and 150 mM salt stress treatments, 11, 23, 16, and 17 PdABC genes were significantly upregulated, respectively. Most genes from eight subfamilies were upregulated after salt stress.

Protein interaction and GO enrichment analysis of PdABC family members

We used STRING to predict potential protein‒protein interactions among PdABC family members based on the A. thaliana database (Table S11). The results revealed that 67 PdABC family members formed a protein interaction network with 80 nodes and 460 edges. Not all nodes interacted with each other (Fig. 8A). Some proteins directly interacted with each other, such as PdABC1/PdABC22, PdABC29/PdABC100, and PdABC41/PdABC116, while others showed more complex relationships, such as PdABC45, PdABC69, and PdABC87. Additionally, PdABC37 was predicted to be a hub gene, interacting with 41 genes. The GO enrichment analysis showed that the 67 PdABC genes have various protein functions (Table S12). In Biological Processes, functions such as Transmembrane Transport (GO:0055085), Transport (GO:0006810), and Cellular Processes (GO:0009987) were significant (Fig. 8B). In Cellular Components, functions including the Integral Component of Membrane (GO:0016021), Membrane (GO:0016020), and Cellular Anatomical Entity (GO:0110165) were significant (Fig. 8C). In Molecular Functions, functions such as ATPase-Coupled Transmembrane Transporter Activity (GO:0042626), ABC-Type Transporter Activity (GO:0140359), and Active Transmembrane Transporter Activity (GO:0022804) were significant (Fig. 8D).

Fig. 8
figure 8

Protein interaction network and GO functional analysis of PdABC family members. A Protein interaction network of PdABC family members. The red font indicates hub genes. B Biological Process. C Cellular Component. D Molecular function

Fluorescence quantitative analysis of PdABC genes

We conducted qRT‒PCR to examine the expression levels of 10 PdABC genes in various tissues of ‘Wanfeng’ almond, including leaves, sepals, petals, pollen, and pistils (Fig. 9A). The results revealed that PdABC29, PdABC51, PdABC63, PdABC64, PdABC69, PdABC75, PdABC98, and PdABC105 had expression levels greater than 1 in all five tissues. Among them, PdABC63 had the highest expression level in leaves (72.08), followed by sepals (42.39) and pistils (42.24). PdABC64 had a relatively high expression level in leaves (33.69). PdABC98 had the highest expression level in petals (73.23). PdABC29, PdABC51, PdABC69, PdABC75, and PdABC105 had relatively consistent expression levels across all tissues. Notably, PdABC59 and PdABC77 showed exceptionally high expression levels in pollen, reaching 2063.61 and 1152.09, respectively. In summary, PdABC family members exhibited significant tissue-specific expression, with PdABC59 and PdABC77 potentially playing important roles in regulating almond pollen development and function.

Fig. 9
figure 9

Fluorescence quantitative expression levels of 10 PdABC genes. A Expression levels in five tissues of ‘Wanfeng’ almond: leaves, sepals, petals, pollen, and pistils. B Expression levels at six developmental stages of ‘Wanfeng’ almond flowers: A1 (Bud stage), A2 (Enlargement stage), A3 (Inflorescence elongation stage), A4 (Small bud stage), A5 (Large bud stage), and A6 (Full blooming stage). C Expression levels under freezing stress at six temperature conditions in dormant one-year-old branches of ‘Wanfeng’ almond. CK: —5 °C. D Expression levels under four salt stress conditions in leaves of ‘Amanisha’ almond. CK: 0 mM

For the six developmental stages of ‘Wanfeng’ almond flowers, we conducted qRT‒PCR to examine the expression levels of 10 PdABC genes (Fig. 9B). The results revealed that PdABC29, PdABC63, PdABC64, PdABC69, and PdABC98 had expression levels greater than 1 across all stages. PdABC29 had the highest expression level in stage A1 (45.00), PdABC51 in stage A2 (24.13), and PdABC63 had relatively high expression levels in stages A2 (60.45) and A3 (65.83). PdABC64 and PdABC69 had relatively high expression levels in stages A4 (53.11 and 46.04) and A5 (27.10 and 51.58). PdABC98 had the highest expression level in stage A5 (221.84), followed by stages A4 (55.19) and A6 (34.01). Moreover, PdABC59, PdABC75, PdABC77, and PdABC105 had relatively consistent expression levels across all stages, with most of their expression levels below 1. In summary, PdABC family members were involved in the development of ‘Wanfeng’ almond flowers and exhibited significant differential expression across different stages.

For the dormant one-year-old branches of ‘Wanfeng’ almond under freezing stress, we conducted qRT‒PCR to examine the expression levels of 10 PdABC genes (Fig. 9C). The results showed that PdABC29, PdABC69, and PdABC98 had expression levels greater than 1 under all six temperature conditions. PdABC29, PdABC51, PdABC64, and PdABC98 had relatively higher expression levels at specific temperature conditions. PdABC51, PdABC64, and PdABC98 had higher expression levels at —20 °C, —25 °C, and —35 °C. In contrast, PdABC59, PdABC63, PdABC69, and PdABC75 had relatively consistent expression levels across all temperatures, with most of their expression levels below 1. In summary, PdABC family members may be involved in the resistance of almond dormancy to freezing stress.

For salt-stressed leaves of ‘Amanisha’ almond, we conducted qRT‒PCR to examine the expression levels of 10 PdABC genes (Fig. 9D). The results showed that PdABC29, PdABC69, PdABC75, PdABC77, and PdABC98 had expression levels greater than 1 in all four treatment conditions. Among them, PdABC29, PdABC69, and PdABC77 had the highest expression levels in the CK and 50 mM treatments. PdABC69 and PdABC98 had higher expression levels in the 100 mM and 150 mM treatments. The remaining six genes had relatively consistent expression levels across all treatments. This result indicates that PdABC may improve the salt resistance of almonds, but whether it can truly improve the salt resistance of almonds needs to be verified by combining other experiments and research methods.

Discussion

ABC transport proteins are mainly distributed in plant cell membranes, mitochondria, and vacuolar membranes, among other organelles. They play a role in the transmembrane transport of various secondary metabolites in plants, helping them adapt to external environmental stresses [45]. To date, ABC transport proteins have been identified and studied in several plant species. For example, A. thaliana (129), O. sativa (123) [46], Zea mays (133) [47], Glycine max (261) [48], and Camellia sinensis (170) [49], among others. In the family Rosaceae, ABC transport protein members have been identified in various species, such as M. domestica (191), Rubus occidentalis (98), and Fragaria vesca (115) [30, 50].

The number of ABC transport proteins in plants is not strictly related to the size of their genomes. In ‘Wanfeng’ almond, we identified 117 PdABC genes, which is similar to the number in P. avium (118) but significantly different from that in P. persica (138) and P. mume (162) [50, 51]. PdABC members exhibit considerable variation in their physicochemical properties, such as amino acid number, molecular weight, and isoelectric point. Subcellular localization prediction suggests that over half (79) of the members are localized to the plasma membrane, consistent with the characteristics of ABC members in species such as M. domestica and C. sinensis. Based on the subfamily classification of A. thaliana ABC members, we divided PdABC members into eight subfamilies: ABCA (AOH and ATH), ABCB (ATM, TAP, and MDR), ABCC, ABCD, ABCE, ABCF, ABCG (PDR and WBC), and ABCI. The distribution of ABC numbers in these subfamilies among different species exhibits a high degree of conservation (see Table S4). Notably, the proportion of PdABC members in the ABCG subfamily is significantly higher than that in P. avium, P. mume, and P. persica. This difference may be due to segmental duplication and tandem repeat amplification, increasing the number of PdABC members in the ABCG subfamily. Additionally, based on clustering results with ABC genes associated with floral organ functions in five species, we predicted that PdABC members may regulate floral organ functions. This provides valuable insights for further research on almond floral organ development and self-incompatibility (see Fig. 1B).

Gene function is closely related to the presence of conserved motifs in protein sequences [52]. All ten motifs identified in the protein sequences of PdABC members are characteristic motifs of ABC transport proteins. Members within the same subfamily exhibit more conserved motif types, suggesting a higher level of conservation among PdABC members within the same subfamily. This result aligns with the findings of conserved motif analysis in ABC family members in other plant species [50]. Gene structure information can provide clues about the evolution of gene family members [52]. In the PdABC family, six members have no introns, and the number of exons and introns varies significantly, regardless of whether the members belong to the same subfamily. Only members clustered in the same branch exhibited a similar number of exons and introns. This result is consistent with the gene structure features of ABC family members in C. sinensis. In summary, the conserved motifs within members of the same subfamily and the differences in exon and intron numbers may be due to functional differentiation during gene evolution.

Almond and four other Prunus fruit trees, including P. persica, P. avium, and P. mume, exhibit an uneven distribution of ABC members across their eight chromosomes. This nonuniform distribution is likely a result of different gene duplication events on the chromosomes [50, 51]. Notably, 43 PdABC genes are located in regions of low gene density on the chromosomes, suggesting that these genes may serve crucial functions in the low gene density regions. Gene duplication is a major factor contributing to the expansion and evolution of gene family members, aiding species in adapting to environmental changes and maintaining vital life processes [53]. In this study, we identified 12 pairs of segmental duplications and 11 pairs of tandem duplicated genes within the PdABC family. The total number of duplicated PdABC genes is similar to that of P. persica (26) and C. sinensis (23) but lower than that of P. avium (47), P. mume (39), Linum usitatissimum (88) and other species [54]. Furthermore, there were 32, 0, 108, and 94 pairs of collinear genes between almond and A. thaliana, O. sativa, M. domestica, and P. persica, respectively. Specifically, the one-to-one relationship between almond and P. persica in terms of ABC collinear genes may result from the limited degree of evolutionary divergence between these two species, suggesting that their ABC genes may share similar functions. Ka/Ks values serve as an effective measure for studying the evolution and selection of duplicated genes [55]. The Ka/Ks values for duplicated PdABC genes are all less than 1, indicating that these duplicated genes have mainly undergone purifying selection, emphasizing their highly conserved functions. Similarly, the Ka/Ks values for collinear gene pairs between different species were all less than 1, indicating that the evolution of ABC genes in different species is under strong purifying selection pressure, suggesting that they may have similar or related gene functions.

Cis-regulatory elements in promoter regions can regulate gene expression [56]. The results of upstream cis-regulatory elements suggest that PdABC genes are involved in various functions, such as growth and development, stress responses, and hormone regulation in ‘Wanfeng’ almond. Investigating gene expression during tissue development and under adverse environmental conditions is essential for understanding the molecular mechanisms of biological development [57]. Based on transcriptome data, we explored changes in FPKM values for PdABC family members in leaf tissues of ‘Wanfeng’ almond at six stages of flower development, under six freezing stress treatments of one-year-old dormant branches, and under four different salt concentration stress treatments in ‘Amanisha’ almond leaves. In all different treatment samples, several PdABC family members showed upregulated gene expression. Many PdABC family members exhibited significant upregulation during three stages of flower development: sprouting, enlargement, and small flower bud formation. They also displayed significant expression under both control and 10 °C temperatures, with a decrease in gene expression as the temperature decreased further, and their expression was also altered under salt stress conditions. Overall, these results indicate that PdABC family members likely play a role in regulating the growth and development of various almond tissues and enhancing almond tolerance to abiotic stress. However, further in-depth research is needed to confirm their specific functions and regulatory mechanisms. Protein‒protein interactions are important in the study of species traits [58]. We predicted potential protein‒protein interactions among PdABC members. A protein‒protein interaction network composed of 67 PdABC members, with 80 nodes in total, was predicted. PdABC37 was predicted as a hub gene in this network, which can provide insights into the relationships among PdABC members for future research.

Research on the relationship between ABC genes and plant floral organ function has yielded important results [9]. For instance, OsMRP15 and VvABCC1 are involved in anthocyanin transport in O. sativa and M. truncatula, respectively [22, 59]. PhABCG1 is involved in the release of floral fragrance compounds in Clarkia breweri [28]. In our study, we used fluorescence quantification to examine the expression levels of 10 PdABC genes in five different tissues (leaves, sepals, petals, pollen, and pistils) and during six stages of flower development in ‘Wanfeng’ almond. The expression of these genes exhibited significant differences among the tissues and developmental stages. For example, ATABCB9 and ATABCB31 are known to promote the transport of sterol glycosides on the surface of Arabidopsis pollen, affecting pollen wall maturation and growth [60]. Similarly, PdABC59 and PdABC77 displayed high expression levels in pollen, clustering with ATABCB9 and ATABCB31, indicating their potential importance in regulating almond pollen development. Moreover, MdABCF is involved in the transfer of apple S-RNase to the pollen tube, leading to self-incompatibility [61]. PdABC69, which exhibits high conservation in clustering with MdABCF, was significantly expressed in both pollen and pistils, making it a candidate reference gene for studying self-incompatibility in almond. ATABCB13 and ATABCB15 are known to regulate the lipid substances necessary for petal epidermal cell cuticle formation in Arabidopsis, influencing petal development [62, 63]. In our study, PdABC63 and PdABC64 had high expression levels in petals and clustered with ATABCB13 and ATABCB15, particularly during the swelling, flower bud elongation, small flower bud, and large flower bud stages. We speculate that these two genes might play roles in almond petal development and flower morphology formation. Additionally, PdABC98 may also be involved in regulating almond petal growth and development. PdABC69 and PdABC98 exhibited higher expression levels during the small and large flower bud stages, suggesting their involvement in late-stage flower organ development and petal opening. In summary, PdABC family members likely play crucial roles in various stages of almond flower development and flower organ development, providing insights for future research in almond-related studies.

While extensive research has been conducted on the relationship between ABC genes and plant responses to abiotic stressors such as water, heavy metals, and ions [64], studies on temperature stress are more prevalent, with cold stress research mainly focused on C. sinensis, and studies on freezing stress are lacking. In our study, fluorescence quantification revealed that 10 PdABC genes showed significantly higher expression levels at one or more temperatures following freezing stress treatments on one-year-old dormant branches of ‘Wanfeng’ almond. These results can provide a reference for researching the response mechanisms of ABC genes to freezing stress in other plants. Notably, PdABC98 showed expression levels exceeding 10 at all six temperatures, with a particularly high expression level at —20 °C, suggesting a potential role for this gene in protecting almond during the dormancy period from freezing stress. Research has elucidated the role of ABC genes in plant responses to salt stress [65, 66]. In our study, fluorescence quantification revealed differential expression levels of 10 PdABC genes in ‘Amanisha’ almond under four different salt concentration stress treatments. PdABC29, PdABC69, and PdABC98 displayed relatively high expression levels under all four salt stress conditions, suggesting a possible role in almond’s response to salt stress. Conversely, PdABC59, PdABC63, and PdABC105 exhibited lower expression levels. This result shows that the expression levels of PdABC members change under different concentrations of salt stress. However, whether PdABC genes can improve the salt resistance of almonds requires further in-depth functional verification.

Conclusion

In this study, we identified 117 PdABC genes in the whole genome of ‘Wanfeng’ almond and conducted analyses on the protein characteristics, gene structure, gene duplication, and evolutionary aspects of the PdABC gene family. We classified the PdABC family members into 8 subfamilies, with the highest number of gene duplications occurring in the ABCG subfamily. Members of the same subfamily have high protein conservation motif types but have large differences in protein length and exon number. Gene mapping showed that PdABC members were unevenly distributed on the 8 chromosomes. The interspecies collinearity results indicate that ABC members of almond and peach have higher conservation. The promoter results indicate that PdABC members are widely involved in various functions, such as ‘Wanfeng’ almond growth and development, stress response, and hormone regulation. Expression patterns indicate that PdABC members are involved in almond flower development in response to freezing and salt stress. Using fluorescence quantification, we explored the expression levels of 10 PdABC genes in various almond tissues, including flowers during developmental stages, one-year-old dormant branches under freezing stress, and leaves under salt stress. These findings provide valuable resources for understanding the functions and molecular mechanisms of PdABC family members in almond.

Availability of data and materials

The transcriptome data are owned by our team and can be accessed through the CNCB database (https://www.cncb.ac.cn/). ‘Wanfeng’ almond six flower developmental stages (GSA Number: CRA007615), a gradient of six freezing temperature stress conditions for dormancy (GSA Number: CRA007323), and salt stress treatments for ‘Amanisha’ almond (GSA Number: CRA013033).

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Acknowledgements

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Funding

Sponsored by Natural Science Foundation of Xinjiang Uygur Autonomous Region, 2023D01A27.

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Contributions

D.Z. and Z.Y. wrote the main manuscript, completed the experimental part of this paper and made drawings. B.Z. assisted in writing manuscripts, completing experiments and drawing. X.L. assisted in drafting and revising the manuscript. The author(s) read and approved the final manuscript.

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Correspondence to Bin Zeng.

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This plant materials don’t include any species at risk of extinction. We declare that all the experimental plants were collected with permission from local authorities of agricultural department and the plant materials in the experiment. We comply with relevant institutional, national, and international guidelines and legislation for plant study.

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Supplementary Information

Additional file 1: Table S1.

Sequences of primers for qRT-PCR. Table S2. Fluorescence quantitative expression level statistics of 10 PdABC genes. Table S3. Characteristics of PdABC gene family members in almond genome. Table S4. Statistics of ABC gene family members in 9 species. Table S5. Prediction of functional genes for floral organ development of PdABC family members. Table S6. Gene density of each chromosome of the almond genome. Table S7. PdABC genes replication and homologous gene. Table S8. PdABC genes replication and homologous gene Ka/Ks values. Table S9. Cis-element analyses of the PdABC genes. Table S10. PdABC family member FPKM value. Table S11. String interactions. Table S12. Results of GO enrichment annotation for PdABC protein interaction members.

Additional file 2: Figure S1.

LOGO map corresponding to 10 Motif sequences. Figure S2. Statistics on the number of cis-acting elements in the PdABC family, including Plant growth and development, Abiotic and biological stresses, and Phytohormone response. (A) Statistics on the number of three functional cis-acting elements in PdABC1 ~ PdABC58 members. (B) Statistics on the number of three functional cis-acting elements in PdABC59 ~ PdABC117 members. (C) Total number of cis-acting elements for each type.

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Zhang, D., Yu, Z., Zeng, B. et al. Genome-wide analysis of the ABC gene family in almond and functional predictions during flower development, freezing stress, and salt stress. BMC Plant Biol 24, 12 (2024). https://doi.org/10.1186/s12870-023-04698-7

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