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Article

A Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Pogostemon cablin in Response to p-HBA-Induced Continuous Cropping Obstacles

by
Yating Su
1,2,
Muhammad Zeeshan Ul Haq
1,
Xiaofeng Liu
1,2,
Yang Li
1,2,
Jing Yu
1,2,
Dongmei Yang
1,2,
Yougen Wu
1,2 and
Ya Liu
1,2,*
1
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
2
School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
*
Author to whom correspondence should be addressed.
Plants 2023, 12(22), 3901; https://doi.org/10.3390/plants12223901
Submission received: 22 September 2023 / Revised: 13 November 2023 / Accepted: 17 November 2023 / Published: 19 November 2023
(This article belongs to the Special Issue Plant Stress Physiology and Molecular Biology)
Browse Figures
Versions Notes

Abstract

:
Casparian strip membrane domain protein-like (CASPL) genes are key genes for the formation and regulation of the Casparian strip and play an important role in plant abiotic stress. However, little research has focused on the members, characteristics, and biological functions of the patchouli PatCASPL gene family. In this study, 156 PatCASPL genes were identified at the whole-genome level. Subcellular localization predicted that 75.6% of PatCASPL proteins reside on the cell membrane. A phylogenetic analysis categorized PatCASPL genes into five subclusters alongside Arabidopsis CASPL genes. In a cis-acting element analysis, a total of 16 different cis-elements were identified, among which the photo-responsive element was the most common in the CASPL gene family. A transcriptome analysis showed that p-hydroxybenzoic acid, an allelopathic autotoxic substance, affected the expression pattern of PatCASPLs, including a total of 27 upregulated genes and 30 down-regulated genes, suggesting that these PatCASPLs may play an important role in the regulation of patchouli continuous cropping obstacles by affecting the formation and integrity of Casparian strip bands. These results provided a theoretical basis for exploring and verifying the function of the patchouli PatCASPL gene family and its role in continuous cropping obstacles.

1. Introduction

Pogostemon cablin (Blanco) Benth is a perennial herb or semi-shrub plant of Labiatae, mainly distributed in the tropical and subtropical regions of Asia [1], such as India, Sri Lanka, Malaysia, Indonesia, and the Philippines [2]. In China, P. cablin, also called ‘Guanghuoxiang’, is mainly distributed in Hainan and Guangdong provinces [3,4]. According to the cultivation and production areas, it can be divided into four cultivation types, ‘Hainan Guanghuoxiang’ (Nanxiang), ‘Zhanjiang Guanghuoxiang’ (Zhanxiang), ‘Shipai Guanghuoxiang’ (Paixiang), and ‘Zhaoqing Guanghuoxiang’ (Zhaoxiang) [5,6]. As one of the ‘Ten Southern Medicines’ and a traditional Chinese medicine, it has been used for aromatic dampness, clearing heat, and as an antiemetic [7,8], and shows important medicinal and economic value [9]. However, continuous cropping obstacles are a key problem in the cultivation and production of P. cablin, which seriously affects its yield and quality [10,11]. Previous studies have found that the deterioration of soil physiochemical properties, the accumulation of allelochemicals, and the imbalance of microbial communities are the main causes of continuous cropping obstacles [12,13,14]. Among them, p-hydroxybenzoic acid (p-HBA) has been proved as a key allelochemical inducing the occurrence of P. cablin continuous cropping obstacles [15,16]. However, how does p-HBA induce the occurrence of P. cablin continuous cropping obstacles? Which signaling pathways are involved in the regulation process? These issues need to be further studied.
The Casparian strip is a bolted and lignified band-thickening wall structure surrounded by the radial wall and transverse wall of the endothelial cells, which plays an important role in screening, blocking, and cutting off unwanted ions or macromolecules into the vascular column [17,18]. It has been found that the formation and regulation of the Casparian strip involve multiple genes and signaling pathways [19,20]. It mainly contains the following key genes: Casparian strip membrane domain proteins (CASPs) [21], leucine receptor kinase (GSO1/SGN3) [22], enhanced suberin 1 (ESB1) [23], MYB domain protein 36 (MYB36) [24], and endodermis Casparian strip integrity factors 1/2 (CIF1/2) [25]. Among them, CASPLs are pivotal membrane proteins specifically expressed in the Casparian strip formation region. These proteins contain a four-transmembrane domain with cytoplasmic amino and carboxyl ends and conserved extracellular loops, which play a key role in the formation of the Casparian strip [26,27]. At present, the number of CASPL family members varies among different plant species, with 39 identified in the Arabidopsis genome, 19 in rice [28], 48 in cotton [29], 61 in banana [30], and 33 in litchi [31] genomes, implying the diversity of CASPL family composition across species. Moreover, it has been found that CASPL family genes play an important role in abiotic stress, including salt tolerance [32,33,34] and cold tolerance [35,36]. However, the research on the function of plant CASPL genes is mainly focused on model plants such as Arabidopsis thaliana and rice, and there is no research reported on PatCASPL genes in P. cablin. Previous transcriptome data showed that PatCASPLs can respond to the allelochemical p-HBA, suggesting that the Casparian strip may play an important role in continuous cropping obstacles [16]. How many PatCASPL family genes are there in P. cablin? Which CASPL genes are involved in the continuous cropping obstacles of P. cablin? These questions need to be further answered.
In this study, based on the whole-genome data of P. cablin, a total of 156 PatCASPL family members were screened and identified through a bioinformatics analysis, and their protein physicochemical properties, chromosome distribution, promoter cis-acting elements, and evolutionary expression characteristics were analyzed in detail. Furthermore, 57 key CASPL candidate genes involved in the continuous cropping obstacles of P. cablin were screened and identified, via an analysis of the transcriptome data of P. cablin treated with p-HBA. The results of this study provide a theoretical basis for exploring the functions of the PatCASPL gene family and its role in continuous cropping obstacles.

2. Results

2.1. Identification of PatCASPL Gene Family Members and Analysis of Protein Physicochemical Properties in P. cablin

According to the 39 CASPL protein sequences of A. thaliana, 176 and 168 CASPL candidate genes were screened preliminarily in the P. cablin genome database by using the BLASTP [37] and HMM [38] alignment search methods, respectively. After further comparison and analysis using the SMART online program on the NCBI website (https://blast.ncbi.gov/ accessed on 10 May 2023), a total of 156 members of the PatCASPL gene family were finally identified. The physicochemical properties of the 156 CASPL protein sequences were analyzed, and the isoelectric point and molecular weight of the PatCASPL protein were predicted using the ExPASy [39] online analysis tool (Table 1). The results showed that the number of amino acids of PatCASPL protein varied from 102 (PatCASPL5C8) to 365 (PatCASPL1A6). The molecular weight of PatCASPL protein was between 11,043.99 and 39,579.28 Da, including 43 acidic proteins (pI ≤ 7) and 113 basic proteins (pI ≥ 7). The aliphatic index ranged from 64.93 to 127.1. The theoretical pI of the 156 CASPL proteins ranged from 4.93 to 10.14. In the CASPL gene family, the instability index of 40 CASPL genes is greater than 40, which highlights an unstable protein; the instability index of 116 CASPL genes was less than 40, which highlights stable proteins. The grand average of hydropathicity (GRAVY) of the PatCASPL2B4, PatCASPL2B2, PatCASPL1F10, PatCASPL2B5, PatCASPL4D12, PatCASPL1A8, PatCASPL1F11, PatCASPL2B8, PatCASPL4D3, PatCASPL2B1, PatCASPL1F9, PatCASPL1A7, PatCASPL4D4, PatCASPL1A9, PatCASPL2B3, PatCASPL1B1, and PatCASPL3A3 proteins was less than zero, implying that they are hydrophilic proteins; the average hydrophilicity of the remaining 139 CASPL genes was greater than zero, indicating that they were hydrophobic proteins.
A secondary structure analysis of the PatCASPL protein in P. cablin using the SOPMA online tool [40] showed that the PatCASPL protein contained four types of structures: Alpha helix (α-helix, 22.09~71.31%), Beta turn (β-turn, 3.88~53.44%), random coil (1.06~10.4%), and extended strand (11.48~53.91%) (Table 2).
A subcellular localization prediction analysis showed that the PatCASPL protein was mainly distributed on the cell membrane, accounting for 75%, and the possibility of prediction analysis on the cell membrane was between 50.31% and 100%. Among them, PatCASPL1C9, PatCASPL4D3, PatCASPL4D6, PatCASPL1C2, PatCASPL1C1, PatCASPL1C7, PatCASPL1C5, and PatCASPL4D4 gene distribution predicted the possibility of distribution on the cell membrane as high as 100%. In addition, 18 PatCASPL proteins were only distributed in the nucleus, with a probability of 51.39% to 98.88%. Eight gene proteins (PatCASPL4D11, PatCASPL4D7, PatCASPL1A6, PatCASPL5B3, PatCASPL4D8, PatCASPL1B2, PatCASPL1A8, PatCASPL5B4) were distributed on the chloroplast, and the probability ranged from 49.45% to 86.61%. PatCASPL2B5, PatCASPL2B7, and PatCASPL2B8 were distributed on peroxisomes, with a probability of 49.45% to 95%. The different subcellular localization of PatCASPL family proteins indicates that the gene family may play different biological functions and mainly act on the cell membrane, which is consistent with the characteristics of membrane proteins. These prediction results provide a reference for subsequent experiments.

2.2. Genetic Characterization and Phylogenetic Analysis of PatCASPL Gene Family Members in P. cablin

Based on the sequences of the PatCASPL gene family of P. cablin, the introns/exons and conserved motifs [41] were analyzed (Figure 1). A gene structure analysis showed that PatCASPL gene family members contained two to seven exons and two to eight introns. The members of the same subcluster have the same exons/introns, and this highly conserved gene structure affects the phylogenetic evolution relationship. Pfam (http://pfam.xfam.org/ accessed on 31 March 2023) and Batch CD-Search (https://www.ncbi.nlm.nih.gov/ accessed on 17 May 2023) were used to test whether the PatCASPL genes contained a complete domain, and the results showed that 156 PatCASPL gene family members contained DUF588 or MARVEL conserved domains. The two domains are selectively distributed in specific phylogenetic tree branches, showing the structural similarity between proteins in the same group. PatCASP10, PatCASPL1A3, PatCASPL1C9, PatCASPL1F2, and the other 34 genes containing the conserved domain of MARVEL were distributed in the E-subcluster (Group E) of the phylogenetic tree, and the remaining 122 genes containing the conserved domain of DUF588 were distributed in other subclusters of the phylogenetic tree (Figure 2). A subcellular localization prediction analysis showed that 25 genes, including PatCASPL1C1, PatCASPL1E3, PatCASPL1F2, and PatCASPL1D6, in 34 genes containing the MARVEL conserved domain were distributed on the cell membrane, and eight genes, including PatCASPL1A5, PatCASPL1A8, PatCASPL1B4, and PatCASPL1B2, were distributed on the chloroplast.
In addition to the DUF588 structure, PatCASPL4A4 and PatCASPL4D11 also contain the KLF6_7_N-like superfamily and HAD_like superfamily, respectively, suggesting that these two genes may have multiple functions. The analysis found that the function of the conserved domain of DUF588 has not been identified, containing a conserved arginine and aspartic acid, which constitutes a site that may have catalytic activity [42]. It has been reported that some scholars have extended phylogenetic analysis beyond the plant kingdom and found that there is conservation between the CASPL and MARVEL protein families, and conserved residues are located in transmembrane domains, indicating that these domains are involved in the localization of CASPL [21].
In order to explore the phylogenetic relationship of the PatCASPL gene family in P. cablin, the phylogenetic tree of 195 CASPL protein sequences in P. cablin and A. thaliana was constructed using the MEGA11 software [43]. The results showed that 195 PatCASPL and AtCASPL members could be divided into five subclusters, among which the A-subcluster (Group A) had the largest number of members, containing 15 AtCASPL members and 59 PatCASPL members. The B-Subcluster (Group B) contains six AtCASPL members and 23 PatCASPL members. The C-subcluster (Group C) contains seven AtCASPL members and 39 PatCASPL members. The number of members in the D-subcluster (Group D) is the lowest, containing only four AtCASPL members and three PatCASPL members. The E-subcluster (Group E) contains eight AtCASPL members and 31 PatCASPL members (Figure 2). The proportion of AtCASPL members to PatCASPL members in each cluster was 1:1~1:3.9, indicating that the CASPL genes in the same subcluster of P. cablin and A. thaliana may be derived from the same ancestor, and the chromosome doubling event of P. cablin led to the expansion of the number of PatCASPL family genes in P. cablin.
The E-subcluster (Group E) contains 11 genes with the highest homology with AtCASP. AtCASP1-5 was identified as a gene related to the formation of Arabidopsis Casparian strip in A. thaliana. The function of AtCASPL protein in other subclusters has not been reported in depth. The genes distributed in the B-subcluster (Group B) may be involved in the response to abiotic stress. At3g55390 (AtCASPL4C1) has been reported to be induced by low-temperature and negatively regulates plant growth [35]. Therefore, it is speculated that PatCASPLs with high homology may have similar functions. Up to now, the biological function of most PatCASPL genes in P. cablin is still unclear. However, more and more CASPL genes of Arabidopsis have been functionally characterized. Therefore, the clustering and comparison of PatCASPL proteins and AtCASP proteins can predict their functions through a homologous analysis.

2.3. Analysis of Cis-Acting Elements of PatCASPL Gene Family in P. cablin

In order to explore the PatCASPL-involved signal regulation pathways, the cis-acting elements of the PatCASPL gene were analyzed [44]. A variety of different cis-elements were identified in the 2000 bp sequence upstream of the initiation codon of 156 PatCASPL gene families in P. cablin. Among them, the light response element is the most frequent in the CASPL gene, and 138 of the 156 genes contain light response elements, which is the most in the PatCASPL gene family, suggesting that the PatCASPLs may be involved in regulating the photomorphogenesis of P. cablin (Figure 3). Among the 156 members of the PatCASPL family, 152 members contained hormone-responsive elements, including 135 for abscisic acid, 88 for methyl jasmonate, 80 for gibberellin, 61 for auxin, and 61 for salicylic acid. There are 70 and 56 PatCASPL genes containing drought and low-temperature response elements, respectively, indicating that the PatCASPLs may play an important role in hormone regulation and the mitigation of stress. The cis-elements of different genes in the same subcluster of the PatCASPL gene family are not the same, suggesting that different PatCASPLs may play different functions in different growth, development, and stress response processes of P. cablin.

2.4. Chromosome Localization of PatCASPL Gene Family in P. cablin

A phylogenetic analysis showed that the PatCASPL gene family members were distributed in five subclusters, and their distribution showed an apparent chromosome preference, essentially distributed at both ends of the chromosome. Gene density information was obtained and analyzed using a gene density profile tool. The results of the gene density analysis (Figure 4) showed that the gene density of the 21 chromosome front segments of the CASPL gene was low, and the gene density of the back end was high. The gene density of the front and back ends of the remaining chromosomes was high, and the gene density of the middle was low. Twelve genes such as PatCASPL4A15, PatCASPL4A1, PatCASPL2D1, and PatCASPL2D3 were distributed in the low-gene-density region, and 92% of the genes were located in the high-gene-density region.
A total of 156 CASPL genes identified in the whole genome of P. cablin were distributed on 57 of 63 chromosomes of P. cablin (Figure 4). The number of CASPL genes on each chromosome ranged from zero to six (Table 3). Among them, chromosomes 5, 37, 49, and 50 were the most distributed members, with six CASPL genes; five CASPL genes were distributed on chromosomes 6, 15, 17, 18, 21, 22, 38, 47, 53, and 54, respectively. Four CASPL genes were distributed on chromosomes 4, 35, and 36. There are one to three CASPL genes on another 40 chromosomes, while there is no PatCASPL gene on chromosomes 9, 27, 28, 41, 59, and 60. It is speculated that the number of CASPL members on each chromosome is not related to chromosome size. In addition, no tandem duplication was found in the PatCASPL gene family of P. cablin.

2.5. Expression Analysis of PatCASPL Gene Family in P. cablin

In order to screen and identify the potential candidate genes of P. cablin in response to continuous cropping obstacles, the root transcriptome database (NCBI accession number PRJNA850618) of different periods (0 h, 6 h, 12 h, 24 h, 48 h, and 96 h) of p-HBA treatment was constructed in the previous study [16]. Cluster heat maps of 57 CASPL gene family transcripts were screened and constructed using the FPKM value of transcriptome data (Figure 5). The results showed that the CASPL genes in response to p-HBA could be divided into two types, namely p-HBA inhibited expression, and p-HBA promoted expression. In the first type, compared with the control (0 h), the expression levels of genes (PatCASPL1A2, PatCASPL1F2, PatCASPL2A2, PatCASPL4A10, PatCASPL4A11, PatCASPL4D9, PatCASPL5A5, PatCASPL5A7, PatCASPL5A10, and PatCASP6) were significantly down-regulated at 6 h, 12 h, and 24 h, while the expression levels of some genes (PatCASPL1A10, PatCASPL1D5, PatCASPL2D4, PatCASPL5C1, PatCASPL5A1, and PatCASPL5A3) were up-regulated at 48 h or 96 h, indicating that p-HBA inhibited the expression of these genes in the early stage, and the inhibitory effect gradually weakened over time or p-HBA consumption. In the second type, p-HBA treatment can promote the expression of CASPL genes such as PatCASPL1A3, PatCASPL1A4, PatCASPL1A5, PatCASPL1C3, PatCASPL1D3, PatCASPL4A5, PatCASPL4B5, PatCASPL4A8, and PatCASPL5A4, although the response time is different. Specifically, the gene expression levels of PatCASPL1D3 and PatCASPL4A8 peaked at 6 h and then decreased. The gene expression levels of PatCASPL5B7, PatCASPL4D3, and PatCASPL1C3 were the highest at the 12 h treatment period. The gene expression levels of PatCASPL4B5, PatCASPL1A4, PatCASPL1A3, PatCASPL1A7, and PatCASPL4A5 were the most significantly up-regulated at 24 h, while the gene expression levels of PatCASPL2D4, PatCASPL5A4, and PatCASPL1A5 were at the maximum at 48 h. The gene expression of PatCASPL4D9, PatCASPL1A2, PatCASPL1F1, PatCASP6, PatCASPL2A4, PatCASPL5A5, PatCASPL2B3, PatCASPL2A3, PatCASPL5A10, PatCASPL5A7, PatCASPL4A10, PatCASPL4A11, PatCASPL1F2, PatCASPL1F3, and PatCASPL1E3 showed a downward trend. The gene expression of PatCASPL4B3 was most significantly down-regulated at 6 h, while the gene expression levels of PatCASPL4D4 and PatCASPL5A12 were significantly down-regulated at 96 h. The above 57 genes were highly expressed in their corresponding periods.
In the first type, the promoter regions of the significantly down-regulated genes at 6 h, 12 h, and 24 h contained abscisic acid-responsive elements, suggesting that their response to p-HBA may involve ABA signaling. Except PatCASPL5A3, which is distributed on chloroplasts, other genes are distributed on cell membranes, PatCASPL1A2 and PatCASPL1A10 contain MARVEL conserved domains, and other genes contain DUF588 conserved domains. In the second type, the promoter regions of PatCASPL1A9, PatCASPL1E1, PatCASPL5A12, PatCASPL4D4, and PatCASPL4A8, which were down-regulated in expression, contained drought response elements; PatCASPL4A8 was distributed in the nucleus, and the other genes were distributed on the cell membrane. In addition to PatCASPL1E1 containing the MARVEL conserved structure, other genes contained the DUF588 conserved domain. In summary, 34 genes containing the MARVEL conserved domain were more likely to be distributed on the cell membrane and contained a large number of MYB binding sites. It is speculated that they may indirectly affect the structure of the Casparian strip. In addition, the PatCASPL gene family of Pogostemon cablin also contains many other types of cis-acting elements, among which the number of light-responsive elements is the largest. It can be judged that the CASPL family genes may have biological functions on the regulation of circadian rhythm and photomorphogenesis.
The expression of PatCASPLs changed after p-HBA treatment, suggesting that it may play an important role in the response of P. cablin to p-HBA treatment. It can be used as a candidate in gene screening for further resistance research and functional analysis. It is speculated that p-HBA may affect the expression of these genes, thereby affecting the formation and integrity of the Casparian strip, reducing the tolerance of P. cablin to stress, and ultimately leading to continuous cropping obstacles. The specific functions of these genes need to be further verified.

3. Discussion

In this study, 156 CASPL genes were identified via a bioinformatics analysis based on the genome data of P. cablin. The number of PatCASPLs is much larger than those of A. thaliana (39) [21], rice (19) [28], cotton (48) [29], banana (61) [30], and litchi (33) [31]. The number of gene family members among species is affected by the number of genome doublings, tandem repeats, and natural selection [45]. Long-terminal repeat retrotransposons (LTR-RTs) can proliferate rapidly in the host, thus affecting the expression of genes. It has been reported that the transposition and amplification of LTR-RTs is an important factor in the expansion of the plant genome [46,47]. Previous studies have found that the genome of P. cablin had a chromosome doubling event (3.3 million years ago) and an LTR-RT insertion event (1.1 million years ago) [48]. This also explains why the number of PatCASPL family members in P. cablin is far more than that of other species and is consistent with the results that the number of AtCASPL members and PatCASPL members in each cluster is 1:1~1:3.9. The conserved domains of the CASPL gene family are also various in different species. The MARVEL domain is present in the CASPL gene family of A. thaliana, banana, and litchi [21]; however, it has not been reported in rice, indicating that the number and domain of CASPL gene family members in different species are also diverse.
In this research, the cis-elements analysis showed that the PatCASPL gene family has more hormone response and stress response elements, and it is speculated that the gene family may play an important role in regulating growth and development and stress tolerance. Previous studies have found that the expression of TaCASPLs can be induced in response to salt stress, osmotic stress, and calcium ion stress, and their expression is inhibited under low-temperature stress [49]. Moreover, Liu et al. [32] found that the SbCASP-LP1C1 gene was involved in the formation of an extracellular barrier and improved the salt tolerance of sweet sorghum. Similarly, Rushil et al. [50] showed that the OsCASPL1 protein has a certain role in salt stress tolerance. Yang et al. [35] identified a cold-inducible protein ClCASPL gene in watermelon. In addition, AtCASPL4C1, the homologous gene in A. thaliana, plays an important role in cold tolerance [51]. The above results suggest that the PatCASPL gene may also play a key role in abiotic stress responses.
In agricultural practice, the continuous planting of P. cablin on the same land will lead to changes in the soil’s physical and chemical properties [52,53], the microbial community structure, the aggravation of soil diseases, and more serious allelopathic autotoxicity, resulting in serious continuous cropping obstacles [54,55,56,57]. Previous studies have found that p-HBA is the main allelochemical that induces continuous cropping obstacles of P. cablin [16,58]. In this study, 30 down-regulated candidate genes and 27 up-regulated candidate genes were identified by analyzing the transcriptome data of P. cablin roots treated with p-HBA. The down-regulated expression of candidate genes may contribute to the incomplete Casparian strip, and then to the diffusion of the allelochemicals through the incomplete Casparian strip and long-distance transportation in a vascular bundle. These allelochemicals cause plant metabolic disorder, affecting plant growth and development, finally leading to the occurrence of P. cablin continuous cropping obstacles. The up-regulated expression of some genes may partially compensate for the incomplete Casparian strip and slow down the entry of allelochemicals into plant vascular bundles. The functions of these candidate genes need to be further verified.

4. Materials and Methods

4.1. Genome-Wide Identification of CASPL from P. cablin

The Arabidopsis genome data were downloaded from the TAIR website (https://www.arabidopsis.org/ accessed on 24 March 2023.), and the patchouli genome sequence file, protein sequence file, and gene structure annotation file were downloaded from the GSA website (https://ngdc.cncb.ac.cn/gsa/ accessed on 24 April 2023). The amino acid sequences of 39 CASPL proteins in A. thaliana were extracted using the TBTools (v1.120) software [59]. To obtain homologous sequences, the Arabidopsis CASPL gene protein sequences were aligned with the patchouli protein data (e-value < 1× 10−5) using BLASTP [60], followed by dereplication. At the same time, the Pfam (number PF04535) of CASPL was obtained in the InterPro [61] database (www.ebi.ac.uk/interpro accessed on 24 March 2023), and its hidden Markov model (HMM) file was downloaded. The HMM [62] file of CASPL was used as input and compared in the TBtools software to obtain candidate gene IDs and extract candidate gene protein sequences. The amino acid sequences of the candidate proteins obtained via the two alignment methods were merged and the repeat sequences were deleted. The conserved domain of the CASPL gene was further analyzed, the candidate genes with an incomplete or missing CASPL domain were deleted, and the PatCASPL genes were finally obtained. The Expasy [63] website (https://www.expasy.org// accessed on 19 July 2023) was used to predict the number of amino acids and the protein molecular weight of CASPL family members. The subcellular localization of CASPL family proteins was predicted using the Plant-mPLoc [64,65] online software (http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc2/ accessed on 11 September 2023) and the YLoc [66] online software (https://abi-services.cs.uni-tuebingen.de/yloc/webloc.cgi accessed on 12 November 2023), and the secondary structure of the CASPL family proteins was predicted and analyzed using the SOPMA [40] online software (https://npsa-prabi.ibcp.fr// accessed on 11 September 2023).

4.2. Genetic Characteristics and Phylogenetic Analysis

The position information of the exons, introns, and UTR of CASPL family genes was obtained from the patchouli genome annotation information (gff) file, and the CASPL gene structure map was drawn using the TBtools software. We used MEME [67] online (http://meme-suite.org/ accessed on 17 May 2023) to analyze the conserved motifs of CASPL proteins. The maximum number and the length of motifs was set at eight and 6–50 amino acids, respectively. The TBtools software was used for a visual analysis. Using the original sequence, the PF04535.15 domain was found in the Pfam [68] database (http://pfam.xfam.org/ accessed on 31 March 2023). The domain information was extracted and the CASPL protein sequence from P. cablin and A. thaliana were compared using the muscle program [69]. The results were compared with the ProtTest to predict the optimal model [70]. The phylogenetic tree of the CASPL protein in P. cablin and A. thaliana was constructed with the MEGA11 software using the maximum likelihood method, and then visualized with the ITOL online tool (itol.embl.de/). The promoter sequences of the CASPL gene family members in P. cablin were extracted with TBtools, and the promoter cis-elements were predicted and analyzed with the PlantCARE [71] online program (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ accessed on 8 August 2023).

4.3. Chromosomal Localization Analysis

Based on the patchouli genome annotation file, the length information of 63 chromosomes and the location information of all PatCASPL genes on chromosomes were obtained, followed by visualization. The gene density profile tool of the Tbtools software was used to obtain the gene density information of the PatCASPL gene. And the location information and distance relationship of all patchouli PatCASPL gene family members were marked on chromosomes via the TBtools software.

4.4. Expression Analysis

According to the previous transcriptome study [6,72] of P. cablin roots, the transcriptome data of P. cablin roots at different time points (0 h, 6 h, 12 h, 24 h, 48 h, and 96 h) under p-hydroxybenzoic acid (p-HBA) treatment were obtained. The above raw data have been uploaded to the NCBI (https://www.ncbi.nlm.nih.gov/ accessed on 28 July 2023) sequence read file (SRA) (accession number PRJNA850618) [11]. The transcript expression of CASPL genes were extracted from the above transcriptome data, and were preliminarily screened using the Excel software of Microsoft office 2019. After that, the selected data were further processed with the TBtools (v1.120) software and the clustering heat map was drawn.

5. Conclusions

In summary, in order to explore the biological function of the PatCASPL gene family and its role in continuous cropping obstacles, the members of the PatCASPL family were identified and analyzed at the genome-wide level. The composition, physicochemical properties, evolutionary relationship, and potential biological function of PatCASPL family members were characterized and figured out. These results provide an important theoretical basis for further exploring the biological function of the PatCASPL gene family and its role in continuous cropping obstacles.

Author Contributions

Conceptualization, Y.S. and Y.L. (Ya Liu); methodology, Y.S. and M.Z.U.H.; software, Y.S. and X.L.; data curation, Y.S., Y.L. (Yang Li), and M.Z.U.H.; visualization, Y.S. and J.Y.; writing—original draft preparation, Y.S.; writing—review and editing, Y.S., X.L., Y.L. (Yang Li), M.Z.U.H., J.Y., D.Y. and Y.W.; supervision, Y.W. and Y.L. (Ya Liu); funding acquisition, Y.L. (Ya Liu) and Y.W. All authors have read and agreed to the published version of the manuscript.

Funding

This work was financially supported by the National Natural Science Foundation of China (Nos. 82304658 and 82260737), Startup Funding from Hainan University (No. KYQD(ZR)23018), and the Key Research and Development Program of Hainan Province (No. ZDYF2021SHFZ075).

Conflicts of Interest

The authors declare no conflict of interest.

References

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Figure 1. Conserved domain (a) and gene structure (b) of CASPL family members in Pogostemon cablin.
Figure 1. Conserved domain (a) and gene structure (b) of CASPL family members in Pogostemon cablin.
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Figure 2. Phylogenetic trees of CASPL genes in P. cablin (Pat) and Arabidopsis (At). The phylogenetic tree of CASPL protein in P. cablin and A. thaliana was constructed with MEGA11 software using maximum likelihood method, and then visualized with the ITOL online tool. Different subfamilies are represented by branches and frames of different colors.
Figure 2. Phylogenetic trees of CASPL genes in P. cablin (Pat) and Arabidopsis (At). The phylogenetic tree of CASPL protein in P. cablin and A. thaliana was constructed with MEGA11 software using maximum likelihood method, and then visualized with the ITOL online tool. Different subfamilies are represented by branches and frames of different colors.
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Figure 3. Cis-acting elements of CASPL family members in P. cablin. The 2000 bp promoter sequences of P. cablin CASPL genes contain a variety of cis-acting elements, including photo responsive elements, hormone responsive elements, drought, low-temperature, anaerobic, wound and other response elements, as well as specific elements of meristem, seed, and endosperm.
Figure 3. Cis-acting elements of CASPL family members in P. cablin. The 2000 bp promoter sequences of P. cablin CASPL genes contain a variety of cis-acting elements, including photo responsive elements, hormone responsive elements, drought, low-temperature, anaerobic, wound and other response elements, as well as specific elements of meristem, seed, and endosperm.
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Figure 4. Chromosomal mapping of CASPL family genes in P. cablin. The leftmost scales represent the chromosome length; A01–A63 represent the names of 57 chromosomes of mustard. There is no PatCASPL gene on chromosomes 9, 27, 28, 41, 59, and 60. Blue indicates low gene density and red indicates high gene density.
Figure 4. Chromosomal mapping of CASPL family genes in P. cablin. The leftmost scales represent the chromosome length; A01–A63 represent the names of 57 chromosomes of mustard. There is no PatCASPL gene on chromosomes 9, 27, 28, 41, 59, and 60. Blue indicates low gene density and red indicates high gene density.
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Figure 5. Expression of PatCASPL gene in P. cablin at different treatment stages of p-HBA.
Figure 5. Expression of PatCASPL gene in P. cablin at different treatment stages of p-HBA.
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Table 1. Physicochemical properties of CASPL gene family proteins in Pogostemon cablin.
Table 1. Physicochemical properties of CASPL gene family proteins in Pogostemon cablin.
Gene IDGene NameAmino AcidsMolecular Weight (DA)Theoretical pIInstability IndexAliphatic IndexGravy
Pat_A01G155900PatCASPL5C217418,737.066.0840.99119.370.87
Pat_A02G232800PatCASPL5C315516,722.938.4338.68127.101.12
Pat_A03G065000PatCASPL1C816317,595.998.8835.43113.800.84
Pat_A03G097400PatCASPL2B220221,785.909.6823.44111.440.66
Pat_A03G197700PatCASPL4D1017319,008.189.1231.33110.980.44
Pat_A03G202900PatCASPL4D1312213,830.319.1026.09104.840.62
Pat_A03G283300PatCASPL4A1518420,313.689.4445.11108.640.49
Pat_A04G068200PatCASPL1C616317,533.928.8832.79115.580.84
Pat_A04G099600PatCASPL2B120221,785.909.6823.44111.440.66
Pat_A04G201600PatCASPL4D1134539,281.218.7333.5684.43−0.14
Pat_A04G257700PatCASPL4A1725528,561.819.5156.8792.55−0.11
Pat_A05G029500PatCASPL3A321122,711.549.4735.96109.050.46
Pat_A05G058400PatCASPL4A735838,903.508.5557.0065.39−0.42
Pat_A05G090400PatCASPL4D714816,269.208.7935.37115.410.66
Pat_A05G091800PatCASPL1F618320,103.529.3229.58100.870.65
Pat_A05G144200PatCASPL1B120121,547.429.4739.12113.980.56
Pat_A05G199200PatCASPL2D118020,062.378.0930.0292.170.53
Pat_A06G029300PatCASPL3A421323,033.919.6241.45108.030.41
Pat_A06G056900PatCASPL4A635839,077.657.7355.4165.11−0.42
Pat_A06G090000PatCASPL1F717919,708.029.3230.9499.270.65
Pat_A06G141700PatCASPL1B320121,663.459.1239.24112.540.51
Pat_A06G179600PatCASPL2D318020,071.388.1027.7992.170.53
Pat_A07G098800PatCASPL5A1218820,282.538.4563.79108.940.34
Pat_A07G167500PatCASPL1F1217218,802.589.6328.60114.070.88
Pat_A08G099100PatCASPL5A917818,825.806.0545.93103.710.60
Pat_A08G164800PatCASPL1F917218,754.519.7227.48119.190.94
Pat_A10G028900PatCASPL5B512413,552.026.5023.84114.921.05
Pat_A11G002900PatCASPL1C912313,753.609.4733.02123.660.90
Pat_A11G093600PatCASPL2D818320,488.086.5330.97104.970.63
Pat_A11G130300PatCASPL2A219020,283.415.3433.2997.680.48
Pat_A12G091200PatCASPL2D618320,446.975.2731.60106.560.65
Pat_A12G123600PatCASPL2A319020,297.445.3433.5498.160.48
Pat_A13G026600PatCASPL4B819621,649.675.7443.4394.180.004
Pat_A13G039300PatCASP720421,541.216.8122.06115.780.74
Pat_A13G129500PatCASPL2B619921,402.509.5626.51112.710.64
Pat_A14G027100PatCASPL4B519921,921.035.7443.1294.72−0.005
Pat_A14G039900PatCASP620421,622.377.6921.23117.70.74
Pat_A14G121300PatCASPL2B819921,423.569.6625.27114.670.63
Pat_A15G045000PatCASPL1A918219,520.788.8819.13112.640.61
Pat_A15G155900PatCASPL5B615416,555.608.3426.73112.211.02
Pat_A15G171700PatCASPL4D317318,398.699.6425.70123.530.89
Pat_A15G171900PatCASPL4D117017,879.919.4738.89118.240.80
Pat_A15G172200PatCASPL4D616617,610.647.6618.61115.720.87
Pat_A16G047300PatCASPL1A1112113,427.729.0624.30106.450.46
Pat_A17G000600PatCASP916718,014.185.4630.63121.020.95
Pat_A17G012200PatCASPL5B915416,555.678.6033.09118.441.005
Pat_A17G030600PatCASPL4B615016,487.815.3041.0886.670.02
Pat_A17G063900PatCASPL5A117618,963.219.2044.7692.560.65
Pat_A17G094300PatCASPL5A515115,959.664.9935.49115.030.92
Pat_A17G121700PatCASP320822,068.689.1526.79108.940.69
Pat_A18G014400PatCASPL5B1015416,555.678.6033.09118.441.005
Pat_A18G033100PatCASPL4B219721,716.965.8535.2395.180.15
Pat_A18G065500PatCASPL5A217618,963.219.2044.7692.560.65
Pat_A18G103000PatCASPL5A618119,094.245.5137.05107.290.68
Pat_A18G121000PatCASP220822,014.659.3727.61106.630.68
Pat_A19G009800PatCASPL1D515616,721.606.8247.56114.420.56
Pat_A20G008500PatCASPL1D719320,509.267.7431.53122.800.81
Pat_A21G011400PatCASPL4A234237,157.917.2257.6476.90−0.38
Pat_A21G024900PatCASPL1A718720,028.609.9527.68117.910.78
Pat_A21G025000PatCASPL1A218820,162.566.9032.00110.160.63
Pat_A21G042100PatCASPL5C615216,340.384.9335.02125.071.11
Pat_A21G143800PatCASPL1C216217,433.899.1631.88122.840.89
Pat_A22G011800PatCASPL4A133536,352.027.1955.7478.51−0.33
Pat_A22G025300PatCASPL1A618619,849.4510.1425.57122.200.86
Pat_A22G025400PatCASPL1A119020,421.006.9033.71111.580.68
Pat_A22G042500PatCASPL5C815116,212.314.9331.17126.561.18
Pat_A22G142300PatCASPL1C116217,433.899.1630.17122.220.89
Pat_A23G122600PatCASPL5B315416,693.777.6033.21109.030.93
Pat_A23G137500PatCASPL1F419120,833.488.8729.87114.400.58
Pat_A24G110200PatCASPL5B115416,661.717.6029.81110.910.94
Pat_A24G124700PatCASPL1F119120,851.558.7730.75114.400.59
Pat_A25G140600PatCASPL4A1036038,979.395.7958.9371.86−0.29
Pat_A26G134800PatCASPL4A1236038,827.085.4256.8470.50−0.30
Pat_A26G135400PatCASPL4A1336238,985.235.4257.1170.39−0.30
Pat_A29G083500PatCASPL1E119720,742.559.2832.97114.310.68
Pat_A29G084000PatCASPL1D220021,362.409.5932.87119.400.74
Pat_A30G087000PatCASPL1E319820,843.659.2831.88114.700.68
Pat_A30G087100PatCASPL1D320021,315.349.4836.63118.900.74
Pat_A31G096200PatCASPL2C217619,411.149.1529.96123.120.74
Pat_A32G099900PatCASPL2C317819,842.769.4429.99125.560.71
Pat_B01G208300PatCASPL5C117418,737.066.0840.99119.370.87
Pat_B02G201600PatCASPL5C423926,174.039.3340.75112.260.79
Pat_B03G060000PatCASPL1C716317,624.048.8834.91114.970.86
Pat_B03G092600PatCASPL2B420221,845.959.6525.24111.930.64
Pat_B03G186600PatCASPL4D917319,036.249.1230.84112.660.46
Pat_B03G261500PatCASPL4A1419421,175.579.0343.93108.040.48
Pat_B04G064500PatCASPL1C516317,604.058.8829.63117.360.86
Pat_B04G095000PatCASPL2B320221,842.009.6823.44112.870.67
Pat_B04G197000PatCASPL4D1222825,002.189.8544.5791.270.19
Pat_B04G241200PatCASPL4A1620822,798.129.1257.5390.530.15
Pat_B05G029100PatCASPL3A220922,610.399.4737.00107.750.44
Pat_B05G054900PatCASPL4A836539,579.288.9856.3264.93−0.41
Pat_B05G085300PatCASPL4D814816,255.178.7937.18115.410.66
Pat_B05G086500PatCASPL1F821323,110.089.5728.7393.520.55
Pat_B05G131000PatCASPL1B220121,571.409.4740.29112.040.53
Pat_B05G177300PatCASPL2D218020,062.378.0930.0292.170.53
Pat_B06G029300PatCASPL3A121222,919.859.8439.47108.540.44
Pat_B06G055200PatCASPL4A535838,998.608.2556.7565.67−0.42
Pat_B06G087000PatCASPL1F518320,123.519.3230.6498.740.65
Pat_B06G133700PatCASPL1B420121,635.449.3339.00112.540.53
Pat_B06G179700PatCASPL2D418020,161.508.0927.3792.170.53
Pat_B07G090500PatCASPL5A1118820,285.578.8466.99109.470.34
Pat_B07G153300PatCASPL1F1117218,722.489.7531.64118.550.93
Pat_B08G094100PatCASPL5A1017818,853.856.0546.41104.780.62
Pat_B08G157700PatCASPL1F1017218,740.489.7227.48118.600.94
Pat_B10G009400PatCASPL4D1410512,171.199.3329.4897.330.27
Pat_B11G071200PatCASPL2D718320,442.995.7432.02104.970.61
Pat_B11G102300PatCASPL2A419020,328.515.0634.5599.210.52
Pat_B12G066000PatCASPL2D518320,487.085.2729.96109.230.67
Pat_B12G095400PatCASPL2A118920,260.425.7835.1297.670.48
Pat_B13G025200PatCASPL4B619821,762.836.7444.3493.23−0.002
Pat_B13G036500PatCASP820421,580.297.6922.06116.270.73
Pat_B13G115900PatCASPL2B519921,458.529.6626.51110.750.58
Pat_B14G025500PatCASPL4B719922,009.185.7441.7295.680.02
Pat_B14G037300PatCASP520421,606.377.6921.23118.190.76
Pat_B14G109400PatCASPL2B719921,368.489.5626.51114.670.65
Pat_B15G046400PatCASPL1A1018219,477.758.5018.54114.780.66
Pat_B15G144800PatCASPL5B715416,569.628.3426.73112.861.01
Pat_B15G158100PatCASPL4D417318,382.659.6428.24121.270.86
Pat_B15G158200PatCASPL4D217017,868.889.2641.73117.650.81
Pat_B15G158500PatCASPL4D516617,651.738.4718.61116.330.85
Pat_B16G041300PatCASPL1A1217419,290.619.2834.8199.250.41
Pat_B17G001300PatCASP1114115,161.675.9935.21111.560.75
Pat_B17G012900PatCASPL5B1115416,555.678.6033.09118.441.005
Pat_B17G030600PatCASPL4B312914,404.545.7027.9688.680.12
Pat_B17G058000PatCASPL5A317619,005.299.2045.2494.200.68
Pat_B17G090900PatCASPL5A718119,035.165.5140.28108.950.69
Pat_B17G110800PatCASP120822,040.679.3727.80108.030.68
Pat_B18G001200PatCASP1016718,014.185.4630.63121.020.95
Pat_B18G012300PatCASPL5B814115,078.888.6130.17114.820.98
Pat_B18G028600PatCASPL4B113315,018.227.6929.8580.080.14
Pat_B18G055600PatCASPL5A417618,975.209.4145.0293.120.63
Pat_B18G089000PatCASPL5A818119,025.135.1036.78107.850.70
Pat_B18G103200PatCASP420822,111.729.1527.61105.670.65
Pat_B19G008300PatCASPL1D819320,528.176.2633.63119.740.79
Pat_B20G008600PatCASPL1D619020,477.888.8429.5398.110.37
Pat_B21G010200PatCASPL4A434236,900.688.1454.8777.75−0.33
Pat_B21G023100PatCASPL1A518720,041.699.9523.85120.000.82
Pat_B21G023200PatCASPL1A418820,159.556.4131.90111.700.62
Pat_B21G039100PatCASPL5C510211,043.997.6841.53112.750.86
Pat_B21G131300PatCASPL1C316217,432.919.3331.12122.840.89
Pat_B22G012300PatCASPL4A334537,637.436.8457.2576.06−0.34
Pat_B22G025600PatCASPL1A818019,425.949.9326.11121.330.80
Pat_B22G025700PatCASPL1A318820,273.766.9034.33111.700.63
Pat_B22G041800PatCASPL5C715116,228.314.9334.08125.891.17
Pat_B22G135200PatCASPL1C416217,417.899.1631.88123.460.91
Pat_B23G102000PatCASPL5B215416,661.717.6029.81110.910.94
Pat_B23G117100PatCASPL1F319120,808.528.7728.47114.920.62
Pat_B24G101400PatCASPL5B415416,675.747.6031.55111.560.94
Pat_B24G116200PatCASPL1F219120,857.518.7731.68111.830.59
Pat_B25G125300PatCASPL4A931033,975.815.5353.2271.48−0.23
Pat_B26G124600PatCASPL4A1136039,014.245.5958.0568.89−0.34
Pat_B29G065200PatCASPL1E219720,772.579.2832.97114.310.66
Pat_B29G065600PatCASPL1D120021,303.339.4834.80119.400.76
Pat_B30G065400PatCASPL1D420021,287.249.2535.15118.900.75
Pat_B31G082800PatCASPL2C117619,524.259.1531.35123.120.70
Table 2. Subcellular localization and protein secondary structure analysis of CASPL gene family proteins in P. cablin.
Table 2. Subcellular localization and protein secondary structure analysis of CASPL gene family proteins in P. cablin.
Gene NameSubcellular LocationPrediction Probability %Alpha Helix %Extended Strand %Beta Turn %Random Coil %
PatCASPL5C2Cell membrane84.6053.4516.093.4527.01
PatCASPL5C3Cell membrane77.1055.4814.842.5827.10
PatCASPL1C8Cell membrane93.5057.6716.564.2921.47
PatCASPL2B2Cell membrane/Chloroplast/Peroxisome51.80/39.00/5.0061.3915.353.9619.31
PatCASPL4D10Cell membrane86.0053.1816.1810.4020.23
PatCASPL4D13Cell membrane83.0069.6713.934.9211.48
PatCASPL4A15Cell membrane53.3054.8915.221.0928.80
PatCASPL1C6Cell membrane93.4057.0618.404.2920.25
PatCASPL2B1Cell membrane/Chloroplast/Peroxisome51.81/30.10/17.0061.3915.353.9619.31
PatCASPL4D11Chloroplast90.1038.2618.846.9635.94
PatCASPL4A17Nucleus96.5045.8812.556.6734.90
PatCASPL3A3Nucleus81.1046.459.005.2139.34
PatCASPL4A7Nucleus91.0030.1713.696.4249.72
PatCASPL4D7Chloroplast86.1054.0520.276.0819.59
PatCASPL1F6Cell membrane92.4053.5517.492.1926.78
PatCASPL1B1Chloroplast/Nucleus99.10/33.0346.7716.928.9627.36
PatCASPL2D1Cell membrane75.0056.6717.782.7822.78
PatCASPL3A4Nucleus81.0847.428.923.7639.91
PatCASPL4A6Nucleus92.6027.9314.803.6353.63
PatCASPL1F7Cell membrane95.7051.4016.763.9127.93
PatCASPL1B3Chloroplast/Nucleus98.90/32.9351.7412.946.9728.36
PatCASPL2D3Cell membrane88.3057.7815.561.6725.00
PatCASPL5A12Cell membrane85.9037.7715.967.9838.30
PatCASPL1F12Cell membrane78.6056.9816.284.6522.09
PatCASPL5A9Cell membrane/Golgi apparatus/Nucleus62.30/95.00/1751.1210.673.9334.27
PatCASPL1F9Cell membrane55.2057.5615.74.6522.09
PatCASPL5B5Cell membrane99.9762.9010.485.6520.97
PatCASPL1C9Cell membrane100.0041.4630.894.0723.58
PatCASPL2D8Cell membrane98.5056.2820.222.7320.77
PatCASPL2A2Cell membrane/Nucleus92.65/28.0055.7917.891.5824.74
PatCASPL2D6Cell membrane/Chloroplast98.50/28.0057.3818.033.8320.77
PatCASPL2A3Cell membrane/Nucleus92.65/36.0056.3217.892.6323.16
PatCASPL4B8Cell membrane/Chloroplast/Cytoplasm/Mitochondrion/Nucleus78.42/49.00/7.00/95.00/7.0060.204.592.0433.16
PatCASP7Cell membrane/Golgi apparatus/Nucleus80.48/16.00/23.0050.4917.653.9227.94
PatCASPL2B6Mitochondrion81.0063.8212.064.0220.10
PatCASPL4B5Chloroplast/Cytoplasm/Golgi apparatus/Nucleus/Vacuole73.42/51.00/49.00/17.00/49.0059.304.024.0232.66
PatCASP6Cell membrane/Golgi apparatus/Nucleus54.70/14.00/17.0049.5120.594.4125.49
PatCASPL2B8Peroxisome86.6162.3112.564.5220.60
PatCASPL1A9Cell membrane53.0046.7021.431.6530.22
PatCASPL5B6Cell membrane73.9759.0912.995.1922.73
PatCASPL4D3Cell membrane/Golgi apparatus100.00/69.0045.6624.285.2024.86
PatCASPL4D1Cell membrane/Golgi apparatus99.90/15.0044.7122.945.2927.06
PatCASPL4D6Cell membrane/Golgi apparatus100.00/36.0051.8118.073.0127.11
PatCASPL1A11Cell membrane83.7832.2326.457.4433.88
PatCASP9Cell membrane99.8746.7122.755.3925.15
PatCASPL5B9Cell membrane84.0764.948.444.5522.08
PatCASPL4B6Cell membrane72.4756.6710.005.3328.00
PatCASPL5A1Cell membrane60.2348.3014.205.1132.39
PatCASPL5A5Cell membrane81.4060.2611.924.6423.18
PatCASP3Cell membrane/Nucleus75.84/49.0052.4016.832.4028.37
PatCASPL5B10Cell membrane84.0764.948.444.5522.08
PatCASPL4B2Cell membrane73.4257.365.082.0335.53
PatCASPL5A2Cell membrane60.2348.3014.25.1132.39
PatCASPL5A6Cell membrane/Golgi apparatus/Nucleus81.40/28.00/26.0049.1710.503.3137.02
PatCASP2Cell membrane69.9150.0016.353.8529.81
PatCASPL1D5Cell membrane89.5639.1024.363.2133.33
PatCASPL1D7Cell membrane/Nucleus81.02/36.0058.5510.884.6625.91
PatCASPL4A2Chloroplast/Nucleus62.04/99.0024.5616.376.4352.63
PatCASPL1A7Cell membrane/Chloroplast84.37/36.0055.6115.513.2125.67
PatCASPL1A2Cell membrane88.8751.0618.091.6029.26
PatCASPL5C6Cell membrane96.1760.5311.181.3226.97
PatCASPL1C2Cell membrane100.0061.1116.053.0919.75
PatCASPL4A1Chloroplast/Nucleus62.04/28.0022.0920.607.1650.15
PatCASPL1A6Chloroplast90.1754.8417.744.3023.12
PatCASPL1A1Cell membrane88.8755.3217.551.6025.53
PatCASPL5C8Cell membrane96.1763.5810.603.3122.52
PatCASPL1C1Cell membrane100.0057.4119.143.0920.37
PatCASPL5B3Chloroplast86.4763.648.444.5523.38
PatCASPL1F4Cell membrane/Nucleus44.19/49.0046.6019.372.6231.41
PatCASPL5B1Cell membrane/Chloroplast86.47/26.0066.239.744.5519.48
PatCASPL1F1Cell membrane58.947.6420.943.1428.27
PatCASPL4A10Chloroplast/Nucleus75.73/51.0030.0013.066.9450.00
PatCASPL4A12Nucleus75.5631.7712.156.3549.72
PatCASPL4A13Nucleus75.5631.7712.156.3549.72
PatCASPL1E1Cell membrane51.3951.2716.246.0926.40
PatCASPL1D2Cell membrane/Nucleus79.86/41.0051.5012.001.5035.00
PatCASPL1E3Cell membrane51.3953.0316.675.5624.75
PatCASPL1D3Cell membrane/Nucleus79.86/36.0047.5014.003.5035.00
PatCASPL2C2Cell membrane99.9867.6111.363.4117.61
PatCASPL2C3Cell membrane/Chloroplast99.98/15.0069.6612.365.6212.36
PatCASPL5C1Cell membrane74.9552.3017.243.4527.01
PatCASPL5C4Cell membrane82.5344.7718.415.4431.38
PatCASPL1C7Cell membrane100.0056.4416.564.2922.70
PatCASPL2B4Chloroplast/Peroxisome49.45/81.0062.3815.843.9617.82
PatCASPL4D9Cell membrane50.3152.0216.7610.4020.81
PatCASPL4A14Cell membrane/Nucleus79.84/68.0052.0216.7610.4020.81
PatCASPL1C5Cell membrane100.0060.7415.343.6820.25
PatCASPL2B3Chloroplast/Peroxisome49.45/81.0061.3915.353.9619.31
PatCASPL4D12Nucleus98.8853.9518.863.9523.25
PatCASPL4A16Nucleus82.8049.5212.023.3735.10
PatCASPL3A2Nucleus69.5251.208.614.7835.41
PatCASPL4A8Nucleus63.3532.6013.705.7547.95
PatCASPL4D8Chloroplast99.9749.3222.305.4122.97
PatCASPL1F8Cell membrane47.85/95.0047.4224.415.1623.00
PatCASPL1B2Chloroplast59.6647.2616.926.9728.86
PatCASPL2D2Cell membrane98.1956.6717.782.7822.78
PatCASPL3A1Nucleus71.6950.478.494.7236.32
PatCASPL4A5Nucleus54.6829.8913.136.1550.84
PatCASPL1F5Cell membrane94.1655.1918.032.1924.59
PatCASPL1B4Chloroplast/Nucleus59.66/41.0049.7517.416.9725.87
PatCASPL2D4Cell membrane98.9760.0016.111.6722.22
PatCASPL5A11Nucleus70.6130.8516.492.6650.00
PatCASPL1F11Cell membrane75.8461.0512.213.4923.26
PatCASPL5A10Cell membrane/Golgi apparatus/Nucleus62.28/95.00/17.0051.1210.673.9334.27
PatCASPL1F10Cell membrane55.1759.3013.373.4923.84
PatCASPL4D14Cell membrane94.0836.1920.954.7638.10
PatCASPL2D7Cell membrane98.5057.3819.132.7320.77
PatCASPL2A4Cell membrane/Nucleus98.1557.3717.373.1622.11
PatCASPL2D5Cell membrane/Chloroplast/Nucleus98.5/28.00/26.0058.4719.673.8318.03
PatCASPL2A1Cell membrane/Nucleus98.15/26.0053.4453.441.0627.51
PatCASPL4B6Cell membrane/Chloroplast/Cytoplasm/Mitochondrion/Nucleus/Peroxisome78.42/39.00/49.00/7.00/95.00/17.0061.115.053.5430.30
PatCASP8Cell membrane/Golgi apparatus/Nucleus54.66/49.00/17.0051.4719.123.9225.49
PatCASPL2B5Peroxisome64.5563.3214.075.0317.59
PatCASPL4B7Nucleus73.4260.804.023.0232.16
PatCASP5Cell membrane/Golgi apparatus/Nucleus54.66/17.00/95.0045.5922.065.8826.47
PatCASPL2B7Peroxisome49.4561.3115.085.0318.59
PatCASPL1A10Cell membrane66.2048.9018.133.8529.12
PatCASPL5B7Cell membrane73.9761.0412.994.5521.43
PatCASPL4D4Cell membrane/Golgi apparatus100.00/69.0044.5124.285.2026.01
PatCASPL4D2Cell membrane/Golgi apparatus99.99/15.0040.0025.884.7129.41
PatCASPL4D5Cell membrane/Golgi apparatus99.98/36.0053.6119.883.6122.89
PatCASPL1A12Cell membrane98.2938.5120.696.9033.91
PatCASP11Cell membrane99.5347.5217.737.0927.66
PatCASPL5B11Cell membrane84.0764.948.444.5522.08
PatCASPL4B3Cell membrane/Cell wall/Chloroplast/Nucleus/Peroxisome/Vacuole68.02/16.00/17.00/2.00/95.00/19.0071.323.884.6520.16
PatCASPL5A3Cell membrane87.0250.5713.645.1130.68
PatCASPL5A7Cell membrane/Golgi apparatus/Nucleus49.05/26.00/28.0053.3716.832.8826.92
PatCASP1Cell membrane66.5750.8311.604.4233.15
PatCASP10Cell membrane99.8763.129.225.6721.99
PatCASPL5B8Cell membrane84.0746.7122.755.3925.15
PatCASPL4B1Cell membrane97.6152.2711.367.3928.98
PatCASPL5A4Cell membrane67.2760.906.779.0223.31
PatCASPL5A8Cell membrane/Golgi apparatus/Nucleus49.05/26.00/28.0050.839.944.4234.81
PatCASP4Cell membrane69.9148.5616.833.3731.25
PatCASPL1D8Cell membrane50.3156.998.813.6330.57
PatCASPL1D6Cell membrane67.1741.5815.7910.0032.63
PatCASPL4A4Chloroplast/Nucleus62.0422.2220.476.1451.17
PatCASPL1A5Cell membrane/Chloroplast/Golgi apparatus90.17/36.00/26.0057.7511.762.6727.81
PatCASPL1A4Cell membrane88.8752.6615.964.2627.13
PatCASPL5C5Cell membrane96.6842.1625.499.8022.55
PatCASPL1C3Cell membrane99.9858.6416.673.0921.60
PatCASPL4A3Nucleus71.2829.2813.043.7753.91
PatCASPL1A8Chloroplast84.3753.8917.783.8924.44
PatCASPL1A3Cell membrane88.8760.6413.833.1922.34
PatCASPL5C7Cell membrane96.1762.2510.601.3225.83
PatCASPL1C4Cell membrane99.5160.4915.432.4721.60
PatCASPL5B2Cell membrane/Chloroplast86.47/28.0066.239.744.5519.48
PatCASPL1F3Cell membrane/Chloroplast/Nucleus63.75/22.00/27.0049.7419.905.2425.13
PatCASPL5B4Chloroplast52.6267.539.095.1918.18
PatCASPL1F2Cell membrane/Chloroplast75.73/51.0051.8317.283.1427.75
PatCASPL4A9Nucleus75.5635.489.352.5852.58
PatCASPL4A11Nucleus51.3933.338.614.7253.33
PatCASPL1E2Cell membrane79.8647.2119.295.0828.43
PatCASPL1D1Cell membrane/Nucleus79.86/41.0048.0013.504.0034.50
PatCASPL1D4Cell membrane/Nucleus79.86/15.0050.0012.005.0033.00
PatCASPL2C1Cell membrane/Chloroplast99.96/53.0070.4511.363.4114.77
Table 3. Gene number per chromosome of CASPL gene family proteins in P. cablin.
Table 3. Gene number per chromosome of CASPL gene family proteins in P. cablin.
ChromosomeGene NumberGene Name
A011PatCASPL5C2
A021PatCASPL5C3
A035PatCASPL1C8/PatCASPL2B2/PatCASPL4D10/PatCASPL4D13/PatCASPL4A15
A044PatCASPL1C6/PatCASPL2B1/PatCASPL4D11/PatCASPL4A17
A056PatCASPL3A3/PatCASPL4A7/PatCASPL4D7/PatCASPL1F6/PatCASPL1B1/PatCASPL2D1
A065PatCASPL3A4/PatCASPL4A6/PatCASPL1F7/PatCASPL1B3/PatCASPL2D3
A072PatCASPL5A12/PatCASPL1F12
A082PatCASPL5A9/PatCASPL1F9
A090
A101PatCASPL5B5
A113PatCASPL1C9/PatCASPL2D8/PatCASPL2A2
A122PatCASPL2D6/PatCASPL2A3
A133PatCASPL4B8/PatCASP7/PatCASPL2B6
A143PatCASPL4B5/PatCASP7/PatCASPL2B6
A155PatCASPL1A9/PatCASPL5B6/PatCASPL4D3/PatCASPL4D1/PatCASPL4D6
A161PatCASPL1A11
A175PatCASP9/PatCASPL5B9/PatCASPL5A1/PatCASPL5A5/PatCASP3
A185PatCASPL5B10/PatCASPL4B2/PatCASPL5A2/PatCASPL5A6/PatCASP2
A191PatCASPL1D5
A201PatCASPL1D7
A215PatCASPL4A2/PatCASPL1A7/PatCASPL1A2/PatCASPL5C6/PatCASPL1C2
A225PatCASPL4A1/PatCASPL1A6/PatCASPL1A1/PatCASPL5C8/PatCASPL1C1
A232PatCASPL5B3/PatCASPL1F4
A242PatCASPL5B1/PatCASPL1F1
A251PatCASPL4A10
A262PatCASPL4A12/PatCASPL4A13
A270
A280
A292PatCASPL1E1/PatCASPL1D2
A302PatCASPL1E3/PatCASPL1D3
A311PatCASPL2C2
A321PatCASPL2C3
A331PatCASPL5C1
A341PatCASPL5C4
A354PatCASPL1C7/PatCASPL2B4/PatCASPL4D9/PatCASPL4A14
A364PatCASPL1C5/PatCASPL2B3/PatCASPL4D12/PatCASPL4A16
A376PatCASPL3A2/PatCASPL4A8/PatCASPL4D8/PatCASPL1F8/PatCASPL1B2/PatCASPL2D2
A385PatCASPL3A1/PatCASPL4A5/PatCASPL1F5/PatCASPL1B4/PatCASPL2D4
A392PatCASPL5A11/PatCASPL1F11
A402PatCASPL5A10/PatCASPL1F10
A410
A421PatCASPL4D14
A432PatCASPL2D7/PatCASPL2A4
A442PatCASPL2D5/PatCASPL2A1
A453PatCASPL4B6/PatCASP8/PatCASPL2B5
A463PatCASPL4B7/PatCASP5/PatCASPL2B7
A475PatCASPL1A10/PatCASPL5B7/PatCASPL4D4/PatCASPL4D2/PatCASPL4D5
A481PatCASPL1A12
A496PatCASP11/PatCASPL5B11/PatCASPL4B3/PatCASPL5A3/PatCASPL5A7/PatCASP1
A506PatCASP10/PatCASPL5B8/PatCASPL4B1/PatCASPL5A4/PatCASPL5A8/PatCASP4
A511PatCASPL1D8
A521PatCASPL1D6
A535PatCASPL4A4/PatCASPL1A5/PatCASPL1A4/PatCASPL5C5/PatCASPL1C3
A545PatCASPL4A3/PatCASPL1A8/PatCASPL1A3/PatCASPL5C7/PatCASPL1C4
A552PatCASPL5B2/PatCASPL1F3
A562PatCASPL5B4/PatCASPL1F2
A571PatCASPL4A9
A581PatCASPL4A11
A590
A600
A612PatCASPL1E2/PatCASPL1D1
A621PatCASPL1D4
A631PatCASPL2C1
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MDPI and ACS Style

Su, Y.; Zeeshan Ul Haq, M.; Liu, X.; Li, Y.; Yu, J.; Yang, D.; Wu, Y.; Liu, Y. A Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Pogostemon cablin in Response to p-HBA-Induced Continuous Cropping Obstacles. Plants 2023, 12, 3901. https://doi.org/10.3390/plants12223901

AMA Style

Su Y, Zeeshan Ul Haq M, Liu X, Li Y, Yu J, Yang D, Wu Y, Liu Y. A Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Pogostemon cablin in Response to p-HBA-Induced Continuous Cropping Obstacles. Plants. 2023; 12(22):3901. https://doi.org/10.3390/plants12223901

Chicago/Turabian Style

Su, Yating, Muhammad Zeeshan Ul Haq, Xiaofeng Liu, Yang Li, Jing Yu, Dongmei Yang, Yougen Wu, and Ya Liu. 2023. "A Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Pogostemon cablin in Response to p-HBA-Induced Continuous Cropping Obstacles" Plants 12, no. 22: 3901. https://doi.org/10.3390/plants12223901

APA Style

Su, Y., Zeeshan Ul Haq, M., Liu, X., Li, Y., Yu, J., Yang, D., Wu, Y., & Liu, Y. (2023). A Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Pogostemon cablin in Response to p-HBA-Induced Continuous Cropping Obstacles. Plants, 12(22), 3901. https://doi.org/10.3390/plants12223901

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