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Article

Identification and Functional Analysis of CAD Gene Family in Pomegranate (Punica granatum)

by
Lei Hu
,
Xuan Zhang
,
Huihui Ni
,
Fangyu Yuan
and
Shuiming Zhang
*
Department of Ornamental Horticulture, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
*
Author to whom correspondence should be addressed.
Genes 2023, 14(1), 26; https://doi.org/10.3390/genes14010026
Submission received: 2 November 2022 / Revised: 8 December 2022 / Accepted: 19 December 2022 / Published: 22 December 2022
(This article belongs to the Section Plant Genetics and Genomics)
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Abstract

:
[Objective] Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis. The aim of this study was to identify CAD gene family members in pomegranate and its expression correlation with seed hardness. [Methods] Based on the reported CAD sequence of Arabidopsis, the CAD gene family of pomegranate was identified by homologous comparison, and then phylogenetic, molecular characterization, and expression profile analysis were performed. [Results] Pomegranate CAD gene family has 25 members, distributed on seven chromosomes of pomegranate. All pomegranate CAD proteins have similar physical and chemical properties. We divide the family into four groups based on evolutionary relationships. The member of group I, called bona fide CAD, was involved in lignin synthesis. Most of the members of group II were involved in stress resistance. The functions of groups III and IV need to be explored. We found four duplicated modes (whole genome duplication or segmental (WGD), tandem duplication (TD), dispersed duplication (DSD), proximal duplication (PD) in this family; TD (36%) had the largest number of them. We predicted that 20 cis-acting elements were involved in lignin synthesis, stress resistance, and response to various hormones. Gene expression profiles further demonstrated that the PgCAD gene family had multiple functions. [Conclusions] Pomegranate CAD gene family is involved in lignin synthesis of hard-seeded cultivar Hongyushizi and Baiyushizi, but its role in seed hardness of soft-seeded cultivar Tunisia needs to be further studied.

1. Introduction

Pomegranate (Punica granatum L.) originated in Iran, Afghanistan, and other Middle East regions. It grows well in tropical and subtropical regions [1,2]. This fruit has health benefits and medicinal properties. Studies have shown that pomegranate juice has high antioxidant activity [3,4], which is loved by consumers all over the world. Most of the pomegranate cultivars in the market have hard seeds and are increasingly unpopular with consumers [5,6], which encourages investigators and breeders to progress and breed soft-seed cultivars [7]. It takes a long time to breed a fruit crop, so identifying relevant genes to help speed up the breeding process is an important task [8].
The seed coat of pomegranate contains high levels of lignin [9]. Some studies have pointed out that there was a positive correlation between pomegranate seed hardness and seed-coat lignin content [10,11], and that the soft-seeded pomegranate had lower lignin content, while having a relatively higher amount of cellulose compared with the hard-seeded one [12]. Development of hardness in pomegranate seeds is regulated by multiple gene families. For example, according to the study of Luo et al., the expression of caffeic acid O-methyltransferase (COMT), caffeoyl Co A3-O-methyltransferase (CCOMT), phenylalanine ammonia-lyase (PAL), 4-coumarate: CoA ligase (4CL), cinnamoyl-CoA reductase (CCR), and cinnamyl alcohol dehydrogenase (CAD) genes in soft-seeded pomegranates and hard-seeded pomegranates were different [13]. Dai et al. found that the expressions of COMT, ferulate 5-hydroxylase (F5H), and hydroxycinnamoyl transferase (HCT) genes in soft-seeded hawthorn were significantly down-regulated compared with those in hard-seeded hawthorn [14]. In addition, many transcription factors are also involved in lignin synthesis. Xue et al. found that the expression patterns of transcription factors NAC, MYB, and WRKY were different in soft-seeded pomegranates and hard-seeded pomegranates [15]. Development of hardness in pomegranate seeds is a complex process. Some studies have pointed out that mdm-miR164e and mdm-miR172b targeted transcription factors NAC1, MYB, and WRKY. The miRNA-mRNA network regulated seed hardness by changing cell wall structure through a series of complex biological processes [16].
Lignin is a kind of phenolic polymer widely existing in plants, and its content is second only to cellulose, which is the second largest organic matter in plants. The synthesis of lignin can be divided into three pathways: shikimic acid pathway, phenylpropane metabolic pathway, and lignin synthesis specific pathway [17,18]. The synthesis of lignin monomers involves 11 enzyme families. Cinnamyl alcohol dehydrogenase (CAD) catalyzes the final step of monolignol biosynthesis. Its activity is dependent on zinc ions and NADPH, and it belongs to the middle-chain dehydrogenase/reductase (MDR) superfamily [19,20]. Thomas and Hans isolated CAD enzymes in spruce cambium and soybean cells and first determined CAD activity [21]. The CAD gene was first identified in the stem of tobacco [22]. Subsequently, CAD genes have been identified in various plants.
In plants, CAD genes have a high degree of homology and have developed into a large family. Phylogenetic analysis divides CAD genes into three major groups, the first of which was considered to be true CAD [23]. Nine CAD genes were found in Arabidopsis [24]. AtCAD4 and AtCAD5, classified as group I, were mainly involved in the synthesis of coniferol and sinapyl alcohol [24,25,26], and several CADs of group II and III were mainly expressed in lignin [24]. There were 15 CAD genes in poplar genome, which could be divided into three categories, and the expression level of class I genes was higher in lignified tissues [27]. Twenty-six CADs were identified in pear and it was confirmed that CAD2 plays a role in lignin synthesis in the stone cells of white pear [28] and sand pear [29,30]. A total of 14 and 24 CAD genes were identified in wild strawberry and cultivated strawberry, and CAD genes were related to strawberry firmness, and it may be involved in the formation of strawberry flavor traits [31]. There were eight CAD genes in Phryma leptostachya; its main members showed substrate preference [32]. A total of 31 and 25 CAD genes were identified in two mulberry cultivars (Morus notabilis and Fengchi) [33]; CADs exhibited various expression patterns in response to diverse stresses in mulberry [34]. CADs have many functions and are involved in lignin synthesis and plant defense response [20,25].
In recent years, analysis of CAD genes in pomegranate has been reported. Zarei et al. isolated a CAD gene from pomegranate and indicated that it was highly expressed in the hard-seed genotype [17]. Niu et al. studied the protein expression profiles of soft-seeded pomegranate and hard-seeded pomegranate, in which the expression of CAD genes showed strong correlations with their encoding proteins [12]. However, the study of CAD genes family in pomegranate has not been reported. The members of the CAD family of pomegranate were identified and analyzed for the first time in this paper. Specifically, we constructed a phylogenetic tree of the gene members of PgCAD family, and analyzed their protein properties, gene structure, motif, chromosome position, and gene duplication events. In addition, we also performed cis-acting element analysis on the promoter region of PgCAD genes. The transcriptome data of soft-seeded pomegranate ‘Tunisia’ and hard-seeded pomegranate ‘Hongyushizi’ and ‘Baiyushizi’ were used to draw the expression heat map of all identified PgCAD genes. This study provides important clues for the role of CAD genes in lignin synthesis.

2. Materials and Methods

2.1. Plant Material

The pomegranate cultivars selected in this study were Tunisia, Hongyushizi, and Baiyushizi, which were all 9-year-old pomegranate cultivars grown in Anhui Agricultural University experimental base. All pomegranate trees were of similar growth and grow robustly. Fruit samples were collected at 40, 80, and 120 days after flowering, with three biological replicates per cultivar, and a total of 27 samples were collected. Seeds and arils were immediately extracted, placed in liquid nitrogen, and finally frozen at −80 degrees Celsius in the laboratory.

2.2. RNA Extraction, Library Construction, and Sequencing

Total RNA was extracted from samples using a Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, mRNA was enriched by Oligo(dT) beads, and prokaryotic mRNA was enriched by removing rRNA by a Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then, the enriched mRNA was fragmented into short fragments using a fragmentation buffer and reversely transcribed into cDNA by using a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, a base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP beads (1.0X). Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

2.3. Identification of CAD Gene Family Members and Physicochemical Properties Analysis in Pomegranate

To identify the gene members of the CAD family in the pomegranate genome, CAD protein sequences in Arabidopsis thaliana were downloaded from TAIR (https://www.arabidopsis.org/, accessed on 3 September 2022). The amino acid sequence of AtCAD family (AT2G21890.1, AT2G21730.1, AT3G19450.1, AT4G34230.1, AT4G37970.1, AT4G37980.1, AT4G37990.1, AT4G39330.1, AT1G72680.1) was used as the query sequence to align the pomegranate genome in NCBI BLASTp online (https://blast.ncbi.nlm.nih.gov/Blast.cgi, accessed on 3 September 2022) (Gap costs: Existence: 11, Extension: 1) and extracted the sequence with E-value < 1 × 10−20. We downloaded the zinc-binding dehydrogenase domain from the protein database Pfam (http://pfam.xfam.org/, accessed on 4 September 2022) and used hmmsearch of Hmmer (https://www.ebi.ac.uk/Tools/hmmer/search/hmmer, accessed on 4 September 2022) to validate our results. After verification, we finally obtained all the members of the PgCAD family.
In order to preliminarily understand these identified CAD genes, we used the ProtParam tool of Expasy (https://web.expasy.org/protparam/, accessed on 10 September 2022) to analyze the basic properties of proteins; WoLF PSORT (https://wolfpsort.hgc.jp/, accessed on 11 September 2022) was used to predict protein subcellular localization.

2.4. Phylogenetic Analysis

To understand the evolutionary relationship of PgCAD, we used ClustalW to perform multiple sequence alignment of 25 PgCAD and 9 AtCAD protein sequences together; this result was imported into MEGA11 [35]. The neighbor-joining (NJ) statistical method was used for phylogenetic analysis. The bootstrap value was set to 1000, other parameters were default, and the result was imported into ITOL (https://itol.embl.de/, accessed on 20 September 2022) for visualization [36].

2.5. Chromosomal Position, Duplication Mode, and Collinearity Analysis

We downloaded a gene annotation file from NCBI (https://www.ncbi.nlm.nih.gov accessed on 2 September 2022) and used TBtools (v1.098769) [37] software to display gene positions on chromosomes. MCScanX of TBtools was used to identify gene duplication patterns and collinearity analysis.

2.6. Gene Structure and Protein Motif Analysis

We extracted the structural information of genes in pomegranate genome annotation to draw the gene structure map. The online software MEME (https://meme-suite.org/meme/, accessed on 23 September 2022) was used to predict the motif of pomegranate protein sequence. The MEME parameter was set to ‘Select the number of motif = 15’, and the other parameters were default. The above information was used to draw images in TBtools.

2.7. Analysis of Promoter Cis-Acting Elements

We used the Gtf/GFF3 Sequences Extractor option in TBtools to obtain 2000 bp upstream sequences of CAD gene and submitted them to Plant CARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 25 September 2022) for promoter cis-acting element analysis. Finally, the common functional components were visualized by TBtools.

2.8. Expression of CAD Gene in Pomegranate

The expression information of pomegranate CAD genes was extracted from transcriptome data, and the log2(FPKM + 1) calculation was performed using TBtools and the expression heat map was drawn.

3. Results

3.1. Physicochemical Properties of Pomegranate CAD Proteins

We identified 25 CAD genes from the pomegranate genome, and they were named based on their position on the chromosome. The results of ExPASy analysis (Table 1) showed that the number of aminos of protein encoded by CAD proteins ranged from 202 to 431, and the molecular weight ranged from 21,601.50 to 45,082.65; there was no significant difference in the number and molecular weight of amino acids. The isoelectric points of these proteins were more acidic except for CAD10 and CAD24, which were basic. The instability coefficients of proteins were all less than 40, which were stable proteins, and their aliphatic index ranged from 77.60 to 98.64. Among the 25 proteins, only CAD4, 7, 16, 18, 19, 24, and 25 were hydrophobins, while other CADs were hydrophilic proteins. According to the prediction results of subcellular localization, we can see that all CAD proteins are localized in the cytoplasm.

3.2. Phylogenetic Analysis of the CAD Gene Family in Pomegranate

To reveal the evolutionary relationships for PgCAD, we downloaded the CAD protein sequences of five species and constructed the phylogenetic tree together with the CAD protein of pomegranate. The 88 CAD proteins were grouped into four subgroups (Figure 1). Group I was considered to be bona fide CAD, and its members were associated with lignin synthesis. Therefore, we suggested that PgCAD7 in this group might be involved in lignin synthesis. Group II was divided into two subgroups, group II-a and group II-b. In Arabidopsis, AtCAD7 and AtCAD8 were associated with plant resistance [24,27]. Therefore, we hypothesized that most PgCAD gene members of group II were involved in plant resistance. Group III contained PgCAD4 and PgCAD19. Among this group in Arabidopsis, AtCAD1 did not show high catalytic activity for lignin synthesis. Thus, whether PgCAD4 and PgCAD19 catalyze lignin synthesis remains to be determined. Group V contained CADs from five species except Arabidopsis. In this group, OsCAD6 and PtoCAD3 were not involved in lignin synthesis. Therefore, the functions of PgCAD24 and PgCAD25 need to be explored. Group IV only had CADs of rice, which was consistent with a previous study [38].

3.3. Chromosomal Position, Duplication Mode, and Collinearity Analysis

Twenty-five PgCAD genes were distributed on seven chromosomes of pomegranate (Figure 2), and the highest number of CAD was located in Chr3, followed by Chr1 and Chr6; few PgCAD genes were localized in the rest of the chromosome. We identified three pairs of paralogous gene in the pomegranate, all of which were located at high gene density positions on the chromosome. In addition, we also analyzed the Ka/Ks ratio of PgCAD gene pairs (Table 2). The Ka/Ks ratio of all gene pairs was less than one, indicating that they had undergone strong purification selection and played an important role in the evolution of CAD genes.
In the collinearity analysis between pomegranates and other species (Figure 3), we found five orthologous gene pairs between P. granatum and A. thaliana, and eight orthologous gene pairs between P. granatum and Eucalyptus grandis, and it was clear that there was a higher collinearity in CAD gene families between pomegranate and E. grandis.
There were five different kinds of duplication events in genes: whole genome duplication or segmental (WGD), tandem duplication (TD), dispersed duplication (DSD), proximal duplication (PD), and singleton duplication (SD). We found four of these in PgCADs and no SD events (Table 3). TD (36%) accounted for the majority of CAD genes, followed by WGD (20%) and DSD (20%); PD (12%) was the least. In Chr3, which had a large number of CAD genes, TD was absolutely dominant. On the whole, TD was also the most important replication mode; WGD and DSD also played an important role in the expansion of PgCADs.

3.4. The Gene Structures and Protein Domains Analysis of the CAD Gene Family in Pomegranate

In order to explore the gene structure characteristics of PgCAD, the exon–intron analysis of these genes was performed (Figure 4b). In some studies, the organization of exon–intron in CAD was divided into three modes; we found that the genetic structure of PgCAD was similar.
The CAD family members of exon–intron pattern I have five exons, with the third exon being the longest; the members of exon–intron pattern II have five exons, with the fourth exon being the longest; the members of exon–intron pattern III have six exons, with the fourth exon being the longest [6]. In our study, most PgCAD gene structures in group II were consistent with pattern I, the PgCAD gene structure of group I (PgCAD7, PgCAD18) was consistent with pattern II, the members of groups III and IV were consistent with pattern III, and PgCAD10 and PgCAD13 did not fall into any of these three modes. Similar findings were found for CAD genes in other species [28,39].
We predicted 15 conserved motifs of PgCAD (Figure 4c), and the results showed that motif1-6 appeared in all PgCADs, while motif7 and 9 only appeared in group II; motif15 only appeared in group IV. Clearly, PgCADs had highly similar structures and motifs, but there were still differences among different groups. In addition, motif 5 contained the Zn1 binding site and Zn2 binding site, and motif 4 contained the NADPH binding site.

3.5. Promoter Analysis of Pomegranate CAD Genes

To investigate the potential function of the gene members of the PgCAD family, we analyzed the 2000 bp sequence upstream of the CDS and predicted 20 cis-acting elements (Figure 5). Seven cis-acting elements were associated with phytohormones, including methyl jasmonate (MeJA), auxin, abscisic acid, salicylic acid, and gibberellin. This suggested that PgCAD might be involved in the response to these hormones. We also found elements involved in stress response, such as drought and low temperatures. We identified seven light responsive elements that were present in most CAD genes. It indicated that the expression of these PgCADs might be regulated by light. In addition, we found a large number of MYB binding sites upstream of the PgACDs promoter, and we hypothesized that MYB regulated PgCADs. We found no significant regularity in the cis-acting elements of these 25 genes.

3.6. Expression of PgCAD genes

To investigate expression patterns of CAD genes in soft-seed and hard-seed cultivars, we obtained transcriptomic date from both cultivars of fruit (Figure 6a). We found that two PgCAD genes (PgCAD2, PgCAD16) were not expressed at all stages of pomegranate fruit development, suggesting that these CAD genes might play roles in other organs. Overall, PgCAD genes expression showed spatiotemporal specificity. The expression of fourteen PgCAD genes was higher at T1 (40 days after anthesis). The expression of these genes was maintained at low levels in T2 (80 days after flowering) and T3 (120 days after flowering). PgCAD1, PgCAD4, PgCAD9, and PgCAD15 were highly expressed in T2 and T3. PgCAD3 and PgCAD25 showed high expression levels in all stages of seed development of Hongyushizi, and PgCAD10 and PgCAD24 showed higher expression levels in T2 and T3 stages of Tunisia.
In order to better reflect the differences in CAD gene expression among different pomegranate cultivars, we selected the data at T1 stage to draw a heat map (Figure 6b). For PgCAD7 and PgCAD18, which might be related to lignin synthesis, their expression patterns were different. The expression level of PgCAD7 was the highest in Tunisia and the lowest in Baiyushizi. The expression level of PgCAD18 was the highest in Hongyushizi and the lowest in Baiyushizi. Hongyushizi had the highest lignin content, followed by Baiyushizi, and Tunisia has the lowest lignin content [40]. The expression pattern of CAD genes in Hongyushizi and Baiyushizi was basically consistent with the content of lignin in the two cultivars. However, the expression of PgCAD7 and PgCAD18 in soft-seed cultivar ‘Tunisia’ was higher than that in a hard-seed cultivar.

4. Discussion

In recent years, there is no lack of reports about the medical effect of pomegranate, which makes this healthy fruit even more popular with consumers [6]. At present, the pomegranate on the market is divided into soft-seed pomegranate and hard-seed pomegranate; hard-seed pomegranate grain is harder, which creates troubles with edibility, and in the market is not welcomed by consumers. Therefore, more and more attention has been paid to the research on the formation mechanism of the pomegranate inner seed-coat hardness.
The seed hardness of pomegranate is positively correlated with the lignin content. Reducing the lignin content can significantly reduce the seed hardness [39]. CAD catalyzes the last step of lignin synthesis and is an important indicator of lignin content. In Arabidopsis phylogeny, AtCAD4 and AtCAD5 were grouped as group 1, which were considered to be true CAD, and they were confirmed to catalyze lignin biosynthesis. The AtCAD members of group 2 were involved in biotic and abiotic stress responses, while the AtCAD members of group 3 were not involved in lignin biosynthesis [25,26,41]. Because the gene members of CAD family of Arabidopsis were studied earlier and more thoroughly, we used it as a reference for the study of the CAD gene family of pomegranate.
In this study, CAD genes in the whole genome of pomegranate were studied for the first time, and 25 CAD genes were identified. We divided the gene members of the PgCAD family into four groups by phylogenetic analysis. Group I had only two members, PgCAD7 and PgCAD18, which were presumed to be involved in lignin synthesis. Group II had 19 members, which might respond to biotic and abiotic stress. PgCAD4 and PgCAD19 were members of group III, and group V had two members (PgCAD24, PgCAD25) whose functions need to be further defined. Interestingly, the number of CAD protein families varied greatly between species. There were nine CADs in Arabidopsis [26], thirteen in sweet potato [42], seven in oil palm [43,44], fifty-seven in pear [28], forty-two in apple [38], and twenty-four in strawberry [31]. No matter how large the CAD protein family was in a given species, there was only one or two true CADs. This suggested that CADs of group I were relatively stable during evolution, and their functions might not have changed much.
The differences in gene duplication patterns help us to study gene amplification and gene function diversity. Qi et al. analyzed the mode of the gene members of CAD family duplication in several different species and pointed out that WGD and SD were key to its expansion [38]. However, this conclusion was limited to the rose family. There were four duplication modes of the gene members of the PgCAD family, among which tandem duplication accounts for the majority, but does not have the absolute dominant position. WGD, DSD, and PD also play important roles in the expansion of pomegranate CAD genes. Historically, many ancient polyploid events had occurred in angiosperms, which promoted the amplification of many stress-related genes [41]. Many CAD gene families of group II in different kinds of plants were significantly affected by WGD, which may explain why most of them were involved in stress resistance.
Cis-acting elements are specific DNA sequences connected in series with structural genes. It binds transcription factors to regulate gene transcription [45]. We analyzed cis-acting elements in the promoter region of the gene members of the PgCAD family. We found several cis-acting elements in response to plant hormones, including: MeJA, auxin, abscisic acid, salicylic acid, and gibberellin. Plant hormones are closely related to the stress resistance of plants. This finding suggests that the gene members of the CAD family may be involved in plant stress response. In addition, we also found cis-acting elements in response to low temperature and drought. Much evidence points to the PgCAD gene being involved in plant stress response. More importantly, we found a MYB binding site in the promoter region of the CAD gene. MYB is a large family of transcription factors that regulate a variety of physiological processes, including lignin synthesis, plant stress tolerance, anthocyanin synthesis, etc. [46] This finding suggests that PgCAD may have multiple functions.
By analyzing the expression of the gene member of the PgCAD family, we found that the expression pattern of PgCAD showed obvious spatiotemporal specificity. Most PgCAD genes were highly expressed at T1 (including true group 1), and then decreased rapidly. Some genes were highly expressed at T2 and T3. This reflects the rich functions of the gene members of the PgCAD family. By analyzing the expression patterns of different pomegranate cultivars, we found that the expression levels of PgCAD7 and PgCAD18 were higher in soft-seed cultivar Tunisia, which was different from the variation trend of lignin content, Niu et al. also found a similar phenomenon [12]. The expression patterns of PgCAD7 and PgCAD18 in Hongyushizi and Baiyushizi were basically consistent with the lignin content between them; they may catalyze their lignin synthesis. However, functions of PgCAD7 and PgCAD18 in soft-seed cultivar ‘Tunisia’ are still unclear and need to be further explored.

5. Conclusions

We identified 25 CAD genes from the pomegranate genome and analyzed their phylogenetic relationships, duplication patterns, gene structures, conserved motifs, and cis-acting elements. The results showed that the PgCAD gene family may be involved in a variety of biological responses, group I may be involved in lignin synthesis, and group II may be involved in stress response. The gene expression profiles indicated that PgCAD genes expression showed spatiotemporal specificity. PgCAD7 and PgCAD18 showed a correlation with lignin synthesis in Hongyushizi and Baiyushizi, but not in Tunisia. Further study of their mechanisms of action in Tunisia may be helpful for breed improvement.

Author Contributions

L.H., X.Z., S.Z. and H.N. conceived and designed the experiments; X.Z. and L.H. performed the experiments; H.N., S.Z. and F.Y. contributed reagents/materials/analysis tools; L.H. wrote the paper. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Anhui Provincial Natural Science Foundation (2008085MC100) and the Anhui Provincial Natural Science Research Project Fund (KJ2019ZD19).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The original transcriptome data used in this study has been submitted to the NCBI, and the data is stored in the SRA database, the acession number is “PRJNA914887”.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Phylogenetic relationships of cinnamyl alcohol dehydrogenase (CAD) proteins in pomegranate. The color blocks on the right indicate the different groups, and the PgCADs are highlighted in red.
Figure 1. Phylogenetic relationships of cinnamyl alcohol dehydrogenase (CAD) proteins in pomegranate. The color blocks on the right indicate the different groups, and the PgCADs are highlighted in red.
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Figure 2. Chromosomal distribution of PgCAD genes. Chromosome numbers are shown next to each chromosome, and tandem duplicated genes are highlighted in red. The color bands on the chromosomes indicate gene density, with red indicating high gene density and blue indicating low gene density. The red line indicates three pairs of paralogous genes: PgCAD5 and PgCAD8, PgCAD6 and PgCAD9, PgCAD7 and PgCAD18.
Figure 2. Chromosomal distribution of PgCAD genes. Chromosome numbers are shown next to each chromosome, and tandem duplicated genes are highlighted in red. The color bands on the chromosomes indicate gene density, with red indicating high gene density and blue indicating low gene density. The red line indicates three pairs of paralogous genes: PgCAD5 and PgCAD8, PgCAD6 and PgCAD9, PgCAD7 and PgCAD18.
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Figure 3. Genome-wide synteny analysis for CAD genes among P. granatum, E. grandis, and A. thaliana. The blue lines indicate ortholgs gene pairs. Eg, E. grandis; Pg, P. granatum; At, A. thaliana.
Figure 3. Genome-wide synteny analysis for CAD genes among P. granatum, E. grandis, and A. thaliana. The blue lines indicate ortholgs gene pairs. Eg, E. grandis; Pg, P. granatum; At, A. thaliana.
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Figure 4. The gene structures and protein domains of PgCAD members. (a) Maximum likelihood phylogenetic tree of PgCADs; (b) Gene structures of PgCADs. Green boxes indicated UTR, yellow boxes indicated CDS, and gray lines indicated introns. UTR: untranslated region, CDS: coding sequence; (c) Protein motif of PgCADs. They were named according to the E-value of the motif. The scale at the bottom indicates the sequence length.
Figure 4. The gene structures and protein domains of PgCAD members. (a) Maximum likelihood phylogenetic tree of PgCADs; (b) Gene structures of PgCADs. Green boxes indicated UTR, yellow boxes indicated CDS, and gray lines indicated introns. UTR: untranslated region, CDS: coding sequence; (c) Protein motif of PgCADs. They were named according to the E-value of the motif. The scale at the bottom indicates the sequence length.
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Figure 5. Cis-acting elements in promoter regions of PgCAD. The color blocks on the right indicate the different cis-acting elements. The scale at the bottom indicates the sequence length.
Figure 5. Cis-acting elements in promoter regions of PgCAD. The color blocks on the right indicate the different cis-acting elements. The scale at the bottom indicates the sequence length.
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Figure 6. (a) Expression patterns of PgCAD. T1-T3 correspond to 40 days after anthesis, 80 days after anthesis, and 120 days after anthesis. (b) Expression patterns of different cultivars at T1. The scale on the left of the picture represents expression levels, with red indicating high expression and green indicating low expression.
Figure 6. (a) Expression patterns of PgCAD. T1-T3 correspond to 40 days after anthesis, 80 days after anthesis, and 120 days after anthesis. (b) Expression patterns of different cultivars at T1. The scale on the left of the picture represents expression levels, with red indicating high expression and green indicating low expression.
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Table
Table 1. The predicated protein information of PgCAD.
Table 1. The predicated protein information of PgCAD.
NameGene IDNo. of Amino AcideMol. Wt
(kDa)		Isoelectric Point (pI)Instability IndexAliphatic IndexGrand Average of HydropathicitySubcellular Localization
PgCAD1XM_031521130.136439,091.805.9431.8691.040.008Cytoplasm
PgCAD2XM_031521131.133035,401.705.7029.5794.210.050Cytoplasm
PgCAD3XM_031518621.136139,241.305.7332.2687.760.023Cytoplasm
PgCAD4XM_031521510.135439,203.867.5438.2077.60−0.244Cytoplasm
PgCAD5XM_031549529.135237,611.486.2127.4398.640.168Cytoplasm
PgCAD6XM_031549518.136138,767.916.6732.2996.620.096Cytoplasm
PgCAD7XM_031526044.135738,864.785.4622.5590.28−0.003Cytoplasm
PgCAD8XM_031530115.136138,658.475.9528.7492.020.066Cytoplasm
PgCAD9XM_031530113.136539,148.386.7029.7889.700.043Cytoplasm
PgCAD10XM_031530121.120221,601.507.7828.40114.410.279Cytoplasm
PgCAD11XM_031530114.136138,783.696.0627.4092.020.044Cytoplasm
PgCAD12XM_031532959.136138,792.615.7038.7992.880.015Cytoplasm
PgCAD13XM_031532961.129131,297.276.1424.0195.050.084Cytoplasm
PgCAD14XM_031532960.136138,892.136.3123.2293.910.099Cytoplasm
PgCAD15XM_031532956.137440,503.656.3128.2192.460.021Cytoplasm
PgCAD16XM_031532957.136139,055.976.4329.0492.27−0.025Cytoplasm
PgCAD17XM_031532280.136139,130.216.7929.4991.470.005Cytoplasm
PgCAD18XM_031536024.135638,861.855.7229.1291.91−0.055Cytoplasm
PgCAD19XM_031540038.135638,754.645.6526.9584.86−0.027Cytoplasm
PgCAD20XM_031545715.136139,273.566.4625.1597.450.023Cytoplasm
PgCAD21XM_031544474.136139,245.506.4625.3996.930.017Cytoplasm
PgCAD22XM_031544478.136139,238.275.7329.6790.690.021Cytoplasm
PgCAD23XM_031544479.136139,143.316.1328.5393.660.017Cytoplasm
PgCAD24XM_031548045.141345,082.658.6531.1983.80−0.138Cytoplasm
PgCAD25XM_031551278.135938,947.646.5928.0491.78−0.035Cytoplasm
Table
Table 2. Estimated divergence period of the PgCAD gene pairs. Ks, synonymous substitution rate; Ka, non-synonymous substitution rate.
Table 2. Estimated divergence period of the PgCAD gene pairs. Ks, synonymous substitution rate; Ka, non-synonymous substitution rate.
Gene PairKaKsKa/Ks
PgCAD5-PgCAD80.2806406393.2853170890.085422695
PgCAD6-PgCAD0.2079310282.2181532960.093740603
PgCAD7-PgCAD180.1135730121.1417852380.099469679
Table
Table 3. The four duplicated types of PgCADs.
Table 3. The four duplicated types of PgCADs.
Gene NameWhole Genome Duplication or SegmentalTandem DuplicationDispersed DuplicationProximal Duplication
PgCAD1 √
PgCAD2
PgCAD3 √
PgCAD4 √
PgCAD5√
PgCAD6√
PgCAD7√
PgCAD8√
PgCAD9 √
PgCAD10 √
PgCAD11 √
PgCAD12 √
PgCAD13
PgCAD14 √
PgCAD15 √
PgCAD16
PgCAD17 √
PgCAD18√
PgCAD19 √
PgCAD20
PgCAD21 √
PgCAD22 √
PgCAD23 √
PgCAD24 √
PgCAD25 √
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Hu, L.; Zhang, X.; Ni, H.; Yuan, F.; Zhang, S. Identification and Functional Analysis of CAD Gene Family in Pomegranate (Punica granatum). Genes 2023, 14, 26. https://doi.org/10.3390/genes14010026

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Hu L, Zhang X, Ni H, Yuan F, Zhang S. Identification and Functional Analysis of CAD Gene Family in Pomegranate (Punica granatum). Genes. 2023; 14(1):26. https://doi.org/10.3390/genes14010026

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Hu, Lei, Xuan Zhang, Huihui Ni, Fangyu Yuan, and Shuiming Zhang. 2023. "Identification and Functional Analysis of CAD Gene Family in Pomegranate (Punica granatum)" Genes 14, no. 1: 26. https://doi.org/10.3390/genes14010026

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