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. 2023 Nov 19;12(22):3901. doi: 10.3390/plants12223901

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

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, Ya Liu 1,2,*
Editor: Peng Zhou
PMCID: PMC10675793  PMID: 38005798

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.

Keywords: Pogostemon cablin, CASPL family, bioinformatics, Casparian strip, expression analysis

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.

Table 1.

Physicochemical properties of CASPL gene family proteins in Pogostemon cablin.

Gene ID Gene Name Amino Acids Molecular Weight (DA) Theoretical pI Instability Index Aliphatic Index Gravy
Pat_A01G155900 PatCASPL5C2 174 18,737.06 6.08 40.99 119.37 0.87
Pat_A02G232800 PatCASPL5C3 155 16,722.93 8.43 38.68 127.10 1.12
Pat_A03G065000 PatCASPL1C8 163 17,595.99 8.88 35.43 113.80 0.84
Pat_A03G097400 PatCASPL2B2 202 21,785.90 9.68 23.44 111.44 0.66
Pat_A03G197700 PatCASPL4D10 173 19,008.18 9.12 31.33 110.98 0.44
Pat_A03G202900 PatCASPL4D13 122 13,830.31 9.10 26.09 104.84 0.62
Pat_A03G283300 PatCASPL4A15 184 20,313.68 9.44 45.11 108.64 0.49
Pat_A04G068200 PatCASPL1C6 163 17,533.92 8.88 32.79 115.58 0.84
Pat_A04G099600 PatCASPL2B1 202 21,785.90 9.68 23.44 111.44 0.66
Pat_A04G201600 PatCASPL4D11 345 39,281.21 8.73 33.56 84.43 −0.14
Pat_A04G257700 PatCASPL4A17 255 28,561.81 9.51 56.87 92.55 −0.11
Pat_A05G029500 PatCASPL3A3 211 22,711.54 9.47 35.96 109.05 0.46
Pat_A05G058400 PatCASPL4A7 358 38,903.50 8.55 57.00 65.39 −0.42
Pat_A05G090400 PatCASPL4D7 148 16,269.20 8.79 35.37 115.41 0.66
Pat_A05G091800 PatCASPL1F6 183 20,103.52 9.32 29.58 100.87 0.65
Pat_A05G144200 PatCASPL1B1 201 21,547.42 9.47 39.12 113.98 0.56
Pat_A05G199200 PatCASPL2D1 180 20,062.37 8.09 30.02 92.17 0.53
Pat_A06G029300 PatCASPL3A4 213 23,033.91 9.62 41.45 108.03 0.41
Pat_A06G056900 PatCASPL4A6 358 39,077.65 7.73 55.41 65.11 −0.42
Pat_A06G090000 PatCASPL1F7 179 19,708.02 9.32 30.94 99.27 0.65
Pat_A06G141700 PatCASPL1B3 201 21,663.45 9.12 39.24 112.54 0.51
Pat_A06G179600 PatCASPL2D3 180 20,071.38 8.10 27.79 92.17 0.53
Pat_A07G098800 PatCASPL5A12 188 20,282.53 8.45 63.79 108.94 0.34
Pat_A07G167500 PatCASPL1F12 172 18,802.58 9.63 28.60 114.07 0.88
Pat_A08G099100 PatCASPL5A9 178 18,825.80 6.05 45.93 103.71 0.60
Pat_A08G164800 PatCASPL1F9 172 18,754.51 9.72 27.48 119.19 0.94
Pat_A10G028900 PatCASPL5B5 124 13,552.02 6.50 23.84 114.92 1.05
Pat_A11G002900 PatCASPL1C9 123 13,753.60 9.47 33.02 123.66 0.90
Pat_A11G093600 PatCASPL2D8 183 20,488.08 6.53 30.97 104.97 0.63
Pat_A11G130300 PatCASPL2A2 190 20,283.41 5.34 33.29 97.68 0.48
Pat_A12G091200 PatCASPL2D6 183 20,446.97 5.27 31.60 106.56 0.65
Pat_A12G123600 PatCASPL2A3 190 20,297.44 5.34 33.54 98.16 0.48
Pat_A13G026600 PatCASPL4B8 196 21,649.67 5.74 43.43 94.18 0.004
Pat_A13G039300 PatCASP7 204 21,541.21 6.81 22.06 115.78 0.74
Pat_A13G129500 PatCASPL2B6 199 21,402.50 9.56 26.51 112.71 0.64
Pat_A14G027100 PatCASPL4B5 199 21,921.03 5.74 43.12 94.72 −0.005
Pat_A14G039900 PatCASP6 204 21,622.37 7.69 21.23 117.7 0.74
Pat_A14G121300 PatCASPL2B8 199 21,423.56 9.66 25.27 114.67 0.63
Pat_A15G045000 PatCASPL1A9 182 19,520.78 8.88 19.13 112.64 0.61
Pat_A15G155900 PatCASPL5B6 154 16,555.60 8.34 26.73 112.21 1.02
Pat_A15G171700 PatCASPL4D3 173 18,398.69 9.64 25.70 123.53 0.89
Pat_A15G171900 PatCASPL4D1 170 17,879.91 9.47 38.89 118.24 0.80
Pat_A15G172200 PatCASPL4D6 166 17,610.64 7.66 18.61 115.72 0.87
Pat_A16G047300 PatCASPL1A11 121 13,427.72 9.06 24.30 106.45 0.46
Pat_A17G000600 PatCASP9 167 18,014.18 5.46 30.63 121.02 0.95
Pat_A17G012200 PatCASPL5B9 154 16,555.67 8.60 33.09 118.44 1.005
Pat_A17G030600 PatCASPL4B6 150 16,487.81 5.30 41.08 86.67 0.02
Pat_A17G063900 PatCASPL5A1 176 18,963.21 9.20 44.76 92.56 0.65
Pat_A17G094300 PatCASPL5A5 151 15,959.66 4.99 35.49 115.03 0.92
Pat_A17G121700 PatCASP3 208 22,068.68 9.15 26.79 108.94 0.69
Pat_A18G014400 PatCASPL5B10 154 16,555.67 8.60 33.09 118.44 1.005
Pat_A18G033100 PatCASPL4B2 197 21,716.96 5.85 35.23 95.18 0.15
Pat_A18G065500 PatCASPL5A2 176 18,963.21 9.20 44.76 92.56 0.65
Pat_A18G103000 PatCASPL5A6 181 19,094.24 5.51 37.05 107.29 0.68
Pat_A18G121000 PatCASP2 208 22,014.65 9.37 27.61 106.63 0.68
Pat_A19G009800 PatCASPL1D5 156 16,721.60 6.82 47.56 114.42 0.56
Pat_A20G008500 PatCASPL1D7 193 20,509.26 7.74 31.53 122.80 0.81
Pat_A21G011400 PatCASPL4A2 342 37,157.91 7.22 57.64 76.90 −0.38
Pat_A21G024900 PatCASPL1A7 187 20,028.60 9.95 27.68 117.91 0.78
Pat_A21G025000 PatCASPL1A2 188 20,162.56 6.90 32.00 110.16 0.63
Pat_A21G042100 PatCASPL5C6 152 16,340.38 4.93 35.02 125.07 1.11
Pat_A21G143800 PatCASPL1C2 162 17,433.89 9.16 31.88 122.84 0.89
Pat_A22G011800 PatCASPL4A1 335 36,352.02 7.19 55.74 78.51 −0.33
Pat_A22G025300 PatCASPL1A6 186 19,849.45 10.14 25.57 122.20 0.86
Pat_A22G025400 PatCASPL1A1 190 20,421.00 6.90 33.71 111.58 0.68
Pat_A22G042500 PatCASPL5C8 151 16,212.31 4.93 31.17 126.56 1.18
Pat_A22G142300 PatCASPL1C1 162 17,433.89 9.16 30.17 122.22 0.89
Pat_A23G122600 PatCASPL5B3 154 16,693.77 7.60 33.21 109.03 0.93
Pat_A23G137500 PatCASPL1F4 191 20,833.48 8.87 29.87 114.40 0.58
Pat_A24G110200 PatCASPL5B1 154 16,661.71 7.60 29.81 110.91 0.94
Pat_A24G124700 PatCASPL1F1 191 20,851.55 8.77 30.75 114.40 0.59
Pat_A25G140600 PatCASPL4A10 360 38,979.39 5.79 58.93 71.86 −0.29
Pat_A26G134800 PatCASPL4A12 360 38,827.08 5.42 56.84 70.50 −0.30
Pat_A26G135400 PatCASPL4A13 362 38,985.23 5.42 57.11 70.39 −0.30
Pat_A29G083500 PatCASPL1E1 197 20,742.55 9.28 32.97 114.31 0.68
Pat_A29G084000 PatCASPL1D2 200 21,362.40 9.59 32.87 119.40 0.74
Pat_A30G087000 PatCASPL1E3 198 20,843.65 9.28 31.88 114.70 0.68
Pat_A30G087100 PatCASPL1D3 200 21,315.34 9.48 36.63 118.90 0.74
Pat_A31G096200 PatCASPL2C2 176 19,411.14 9.15 29.96 123.12 0.74
Pat_A32G099900 PatCASPL2C3 178 19,842.76 9.44 29.99 125.56 0.71
Pat_B01G208300 PatCASPL5C1 174 18,737.06 6.08 40.99 119.37 0.87
Pat_B02G201600 PatCASPL5C4 239 26,174.03 9.33 40.75 112.26 0.79
Pat_B03G060000 PatCASPL1C7 163 17,624.04 8.88 34.91 114.97 0.86
Pat_B03G092600 PatCASPL2B4 202 21,845.95 9.65 25.24 111.93 0.64
Pat_B03G186600 PatCASPL4D9 173 19,036.24 9.12 30.84 112.66 0.46
Pat_B03G261500 PatCASPL4A14 194 21,175.57 9.03 43.93 108.04 0.48
Pat_B04G064500 PatCASPL1C5 163 17,604.05 8.88 29.63 117.36 0.86
Pat_B04G095000 PatCASPL2B3 202 21,842.00 9.68 23.44 112.87 0.67
Pat_B04G197000 PatCASPL4D12 228 25,002.18 9.85 44.57 91.27 0.19
Pat_B04G241200 PatCASPL4A16 208 22,798.12 9.12 57.53 90.53 0.15
Pat_B05G029100 PatCASPL3A2 209 22,610.39 9.47 37.00 107.75 0.44
Pat_B05G054900 PatCASPL4A8 365 39,579.28 8.98 56.32 64.93 −0.41
Pat_B05G085300 PatCASPL4D8 148 16,255.17 8.79 37.18 115.41 0.66
Pat_B05G086500 PatCASPL1F8 213 23,110.08 9.57 28.73 93.52 0.55
Pat_B05G131000 PatCASPL1B2 201 21,571.40 9.47 40.29 112.04 0.53
Pat_B05G177300 PatCASPL2D2 180 20,062.37 8.09 30.02 92.17 0.53
Pat_B06G029300 PatCASPL3A1 212 22,919.85 9.84 39.47 108.54 0.44
Pat_B06G055200 PatCASPL4A5 358 38,998.60 8.25 56.75 65.67 −0.42
Pat_B06G087000 PatCASPL1F5 183 20,123.51 9.32 30.64 98.74 0.65
Pat_B06G133700 PatCASPL1B4 201 21,635.44 9.33 39.00 112.54 0.53
Pat_B06G179700 PatCASPL2D4 180 20,161.50 8.09 27.37 92.17 0.53
Pat_B07G090500 PatCASPL5A11 188 20,285.57 8.84 66.99 109.47 0.34
Pat_B07G153300 PatCASPL1F11 172 18,722.48 9.75 31.64 118.55 0.93
Pat_B08G094100 PatCASPL5A10 178 18,853.85 6.05 46.41 104.78 0.62
Pat_B08G157700 PatCASPL1F10 172 18,740.48 9.72 27.48 118.60 0.94
Pat_B10G009400 PatCASPL4D14 105 12,171.19 9.33 29.48 97.33 0.27
Pat_B11G071200 PatCASPL2D7 183 20,442.99 5.74 32.02 104.97 0.61
Pat_B11G102300 PatCASPL2A4 190 20,328.51 5.06 34.55 99.21 0.52
Pat_B12G066000 PatCASPL2D5 183 20,487.08 5.27 29.96 109.23 0.67
Pat_B12G095400 PatCASPL2A1 189 20,260.42 5.78 35.12 97.67 0.48
Pat_B13G025200 PatCASPL4B6 198 21,762.83 6.74 44.34 93.23 −0.002
Pat_B13G036500 PatCASP8 204 21,580.29 7.69 22.06 116.27 0.73
Pat_B13G115900 PatCASPL2B5 199 21,458.52 9.66 26.51 110.75 0.58
Pat_B14G025500 PatCASPL4B7 199 22,009.18 5.74 41.72 95.68 0.02
Pat_B14G037300 PatCASP5 204 21,606.37 7.69 21.23 118.19 0.76
Pat_B14G109400 PatCASPL2B7 199 21,368.48 9.56 26.51 114.67 0.65
Pat_B15G046400 PatCASPL1A10 182 19,477.75 8.50 18.54 114.78 0.66
Pat_B15G144800 PatCASPL5B7 154 16,569.62 8.34 26.73 112.86 1.01
Pat_B15G158100 PatCASPL4D4 173 18,382.65 9.64 28.24 121.27 0.86
Pat_B15G158200 PatCASPL4D2 170 17,868.88 9.26 41.73 117.65 0.81
Pat_B15G158500 PatCASPL4D5 166 17,651.73 8.47 18.61 116.33 0.85
Pat_B16G041300 PatCASPL1A12 174 19,290.61 9.28 34.81 99.25 0.41
Pat_B17G001300 PatCASP11 141 15,161.67 5.99 35.21 111.56 0.75
Pat_B17G012900 PatCASPL5B11 154 16,555.67 8.60 33.09 118.44 1.005
Pat_B17G030600 PatCASPL4B3 129 14,404.54 5.70 27.96 88.68 0.12
Pat_B17G058000 PatCASPL5A3 176 19,005.29 9.20 45.24 94.20 0.68
Pat_B17G090900 PatCASPL5A7 181 19,035.16 5.51 40.28 108.95 0.69
Pat_B17G110800 PatCASP1 208 22,040.67 9.37 27.80 108.03 0.68
Pat_B18G001200 PatCASP10 167 18,014.18 5.46 30.63 121.02 0.95
Pat_B18G012300 PatCASPL5B8 141 15,078.88 8.61 30.17 114.82 0.98
Pat_B18G028600 PatCASPL4B1 133 15,018.22 7.69 29.85 80.08 0.14
Pat_B18G055600 PatCASPL5A4 176 18,975.20 9.41 45.02 93.12 0.63
Pat_B18G089000 PatCASPL5A8 181 19,025.13 5.10 36.78 107.85 0.70
Pat_B18G103200 PatCASP4 208 22,111.72 9.15 27.61 105.67 0.65
Pat_B19G008300 PatCASPL1D8 193 20,528.17 6.26 33.63 119.74 0.79
Pat_B20G008600 PatCASPL1D6 190 20,477.88 8.84 29.53 98.11 0.37
Pat_B21G010200 PatCASPL4A4 342 36,900.68 8.14 54.87 77.75 −0.33
Pat_B21G023100 PatCASPL1A5 187 20,041.69 9.95 23.85 120.00 0.82
Pat_B21G023200 PatCASPL1A4 188 20,159.55 6.41 31.90 111.70 0.62
Pat_B21G039100 PatCASPL5C5 102 11,043.99 7.68 41.53 112.75 0.86
Pat_B21G131300 PatCASPL1C3 162 17,432.91 9.33 31.12 122.84 0.89
Pat_B22G012300 PatCASPL4A3 345 37,637.43 6.84 57.25 76.06 −0.34
Pat_B22G025600 PatCASPL1A8 180 19,425.94 9.93 26.11 121.33 0.80
Pat_B22G025700 PatCASPL1A3 188 20,273.76 6.90 34.33 111.70 0.63
Pat_B22G041800 PatCASPL5C7 151 16,228.31 4.93 34.08 125.89 1.17
Pat_B22G135200 PatCASPL1C4 162 17,417.89 9.16 31.88 123.46 0.91
Pat_B23G102000 PatCASPL5B2 154 16,661.71 7.60 29.81 110.91 0.94
Pat_B23G117100 PatCASPL1F3 191 20,808.52 8.77 28.47 114.92 0.62
Pat_B24G101400 PatCASPL5B4 154 16,675.74 7.60 31.55 111.56 0.94
Pat_B24G116200 PatCASPL1F2 191 20,857.51 8.77 31.68 111.83 0.59
Pat_B25G125300 PatCASPL4A9 310 33,975.81 5.53 53.22 71.48 −0.23
Pat_B26G124600 PatCASPL4A11 360 39,014.24 5.59 58.05 68.89 −0.34
Pat_B29G065200 PatCASPL1E2 197 20,772.57 9.28 32.97 114.31 0.66
Pat_B29G065600 PatCASPL1D1 200 21,303.33 9.48 34.80 119.40 0.76
Pat_B30G065400 PatCASPL1D4 200 21,287.24 9.25 35.15 118.90 0.75
Pat_B31G082800 PatCASPL2C1 176 19,524.25 9.15 31.35 123.12 0.70
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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).

Table 2.

Subcellular localization and protein secondary structure analysis of CASPL gene family proteins in P. cablin.

Gene Name Subcellular Location Prediction Probability % Alpha Helix % Extended Strand % Beta Turn % Random Coil %
PatCASPL5C2 Cell membrane 84.60 53.45 16.09 3.45 27.01
PatCASPL5C3 Cell membrane 77.10 55.48 14.84 2.58 27.10
PatCASPL1C8 Cell membrane 93.50 57.67 16.56 4.29 21.47
PatCASPL2B2 Cell membrane/Chloroplast/Peroxisome 51.80/39.00/5.00 61.39 15.35 3.96 19.31
PatCASPL4D10 Cell membrane 86.00 53.18 16.18 10.40 20.23
PatCASPL4D13 Cell membrane 83.00 69.67 13.93 4.92 11.48
PatCASPL4A15 Cell membrane 53.30 54.89 15.22 1.09 28.80
PatCASPL1C6 Cell membrane 93.40 57.06 18.40 4.29 20.25
PatCASPL2B1 Cell membrane/Chloroplast/Peroxisome 51.81/30.10/17.00 61.39 15.35 3.96 19.31
PatCASPL4D11 Chloroplast 90.10 38.26 18.84 6.96 35.94
PatCASPL4A17 Nucleus 96.50 45.88 12.55 6.67 34.90
PatCASPL3A3 Nucleus 81.10 46.45 9.00 5.21 39.34
PatCASPL4A7 Nucleus 91.00 30.17 13.69 6.42 49.72
PatCASPL4D7 Chloroplast 86.10 54.05 20.27 6.08 19.59
PatCASPL1F6 Cell membrane 92.40 53.55 17.49 2.19 26.78
PatCASPL1B1 Chloroplast/Nucleus 99.10/33.03 46.77 16.92 8.96 27.36
PatCASPL2D1 Cell membrane 75.00 56.67 17.78 2.78 22.78
PatCASPL3A4 Nucleus 81.08 47.42 8.92 3.76 39.91
PatCASPL4A6 Nucleus 92.60 27.93 14.80 3.63 53.63
PatCASPL1F7 Cell membrane 95.70 51.40 16.76 3.91 27.93
PatCASPL1B3 Chloroplast/Nucleus 98.90/32.93 51.74 12.94 6.97 28.36
PatCASPL2D3 Cell membrane 88.30 57.78 15.56 1.67 25.00
PatCASPL5A12 Cell membrane 85.90 37.77 15.96 7.98 38.30
PatCASPL1F12 Cell membrane 78.60 56.98 16.28 4.65 22.09
PatCASPL5A9 Cell membrane/Golgi apparatus/Nucleus 62.30/95.00/17 51.12 10.67 3.93 34.27
PatCASPL1F9 Cell membrane 55.20 57.56 15.7 4.65 22.09
PatCASPL5B5 Cell membrane 99.97 62.90 10.48 5.65 20.97
PatCASPL1C9 Cell membrane 100.00 41.46 30.89 4.07 23.58
PatCASPL2D8 Cell membrane 98.50 56.28 20.22 2.73 20.77
PatCASPL2A2 Cell membrane/Nucleus 92.65/28.00 55.79 17.89 1.58 24.74
PatCASPL2D6 Cell membrane/Chloroplast 98.50/28.00 57.38 18.03 3.83 20.77
PatCASPL2A3 Cell membrane/Nucleus 92.65/36.00 56.32 17.89 2.63 23.16
PatCASPL4B8 Cell membrane/Chloroplast/Cytoplasm/Mitochondrion/Nucleus 78.42/49.00/7.00/95.00/7.00 60.20 4.59 2.04 33.16
PatCASP7 Cell membrane/Golgi apparatus/Nucleus 80.48/16.00/23.00 50.49 17.65 3.92 27.94
PatCASPL2B6 Mitochondrion 81.00 63.82 12.06 4.02 20.10
PatCASPL4B5 Chloroplast/Cytoplasm/Golgi apparatus/Nucleus/Vacuole 73.42/51.00/49.00/17.00/49.00 59.30 4.02 4.02 32.66
PatCASP6 Cell membrane/Golgi apparatus/Nucleus 54.70/14.00/17.00 49.51 20.59 4.41 25.49
PatCASPL2B8 Peroxisome 86.61 62.31 12.56 4.52 20.60
PatCASPL1A9 Cell membrane 53.00 46.70 21.43 1.65 30.22
PatCASPL5B6 Cell membrane 73.97 59.09 12.99 5.19 22.73
PatCASPL4D3 Cell membrane/Golgi apparatus 100.00/69.00 45.66 24.28 5.20 24.86
PatCASPL4D1 Cell membrane/Golgi apparatus 99.90/15.00 44.71 22.94 5.29 27.06
PatCASPL4D6 Cell membrane/Golgi apparatus 100.00/36.00 51.81 18.07 3.01 27.11
PatCASPL1A11 Cell membrane 83.78 32.23 26.45 7.44 33.88
PatCASP9 Cell membrane 99.87 46.71 22.75 5.39 25.15
PatCASPL5B9 Cell membrane 84.07 64.94 8.44 4.55 22.08
PatCASPL4B6 Cell membrane 72.47 56.67 10.00 5.33 28.00
PatCASPL5A1 Cell membrane 60.23 48.30 14.20 5.11 32.39
PatCASPL5A5 Cell membrane 81.40 60.26 11.92 4.64 23.18
PatCASP3 Cell membrane/Nucleus 75.84/49.00 52.40 16.83 2.40 28.37
PatCASPL5B10 Cell membrane 84.07 64.94 8.44 4.55 22.08
PatCASPL4B2 Cell membrane 73.42 57.36 5.08 2.03 35.53
PatCASPL5A2 Cell membrane 60.23 48.30 14.2 5.11 32.39
PatCASPL5A6 Cell membrane/Golgi apparatus/Nucleus 81.40/28.00/26.00 49.17 10.50 3.31 37.02
PatCASP2 Cell membrane 69.91 50.00 16.35 3.85 29.81
PatCASPL1D5 Cell membrane 89.56 39.10 24.36 3.21 33.33
PatCASPL1D7 Cell membrane/Nucleus 81.02/36.00 58.55 10.88 4.66 25.91
PatCASPL4A2 Chloroplast/Nucleus 62.04/99.00 24.56 16.37 6.43 52.63
PatCASPL1A7 Cell membrane/Chloroplast 84.37/36.00 55.61 15.51 3.21 25.67
PatCASPL1A2 Cell membrane 88.87 51.06 18.09 1.60 29.26
PatCASPL5C6 Cell membrane 96.17 60.53 11.18 1.32 26.97
PatCASPL1C2 Cell membrane 100.00 61.11 16.05 3.09 19.75
PatCASPL4A1 Chloroplast/Nucleus 62.04/28.00 22.09 20.60 7.16 50.15
PatCASPL1A6 Chloroplast 90.17 54.84 17.74 4.30 23.12
PatCASPL1A1 Cell membrane 88.87 55.32 17.55 1.60 25.53
PatCASPL5C8 Cell membrane 96.17 63.58 10.60 3.31 22.52
PatCASPL1C1 Cell membrane 100.00 57.41 19.14 3.09 20.37
PatCASPL5B3 Chloroplast 86.47 63.64 8.44 4.55 23.38
PatCASPL1F4 Cell membrane/Nucleus 44.19/49.00 46.60 19.37 2.62 31.41
PatCASPL5B1 Cell membrane/Chloroplast 86.47/26.00 66.23 9.74 4.55 19.48
PatCASPL1F1 Cell membrane 58.9 47.64 20.94 3.14 28.27
PatCASPL4A10 Chloroplast/Nucleus 75.73/51.00 30.00 13.06 6.94 50.00
PatCASPL4A12 Nucleus 75.56 31.77 12.15 6.35 49.72
PatCASPL4A13 Nucleus 75.56 31.77 12.15 6.35 49.72
PatCASPL1E1 Cell membrane 51.39 51.27 16.24 6.09 26.40
PatCASPL1D2 Cell membrane/Nucleus 79.86/41.00 51.50 12.00 1.50 35.00
PatCASPL1E3 Cell membrane 51.39 53.03 16.67 5.56 24.75
PatCASPL1D3 Cell membrane/Nucleus 79.86/36.00 47.50 14.00 3.50 35.00
PatCASPL2C2 Cell membrane 99.98 67.61 11.36 3.41 17.61
PatCASPL2C3 Cell membrane/Chloroplast 99.98/15.00 69.66 12.36 5.62 12.36
PatCASPL5C1 Cell membrane 74.95 52.30 17.24 3.45 27.01
PatCASPL5C4 Cell membrane 82.53 44.77 18.41 5.44 31.38
PatCASPL1C7 Cell membrane 100.00 56.44 16.56 4.29 22.70
PatCASPL2B4 Chloroplast/Peroxisome 49.45/81.00 62.38 15.84 3.96 17.82
PatCASPL4D9 Cell membrane 50.31 52.02 16.76 10.40 20.81
PatCASPL4A14 Cell membrane/Nucleus 79.84/68.00 52.02 16.76 10.40 20.81
PatCASPL1C5 Cell membrane 100.00 60.74 15.34 3.68 20.25
PatCASPL2B3 Chloroplast/Peroxisome 49.45/81.00 61.39 15.35 3.96 19.31
PatCASPL4D12 Nucleus 98.88 53.95 18.86 3.95 23.25
PatCASPL4A16 Nucleus 82.80 49.52 12.02 3.37 35.10
PatCASPL3A2 Nucleus 69.52 51.20 8.61 4.78 35.41
PatCASPL4A8 Nucleus 63.35 32.60 13.70 5.75 47.95
PatCASPL4D8 Chloroplast 99.97 49.32 22.30 5.41 22.97
PatCASPL1F8 Cell membrane 47.85/95.00 47.42 24.41 5.16 23.00
PatCASPL1B2 Chloroplast 59.66 47.26 16.92 6.97 28.86
PatCASPL2D2 Cell membrane 98.19 56.67 17.78 2.78 22.78
PatCASPL3A1 Nucleus 71.69 50.47 8.49 4.72 36.32
PatCASPL4A5 Nucleus 54.68 29.89 13.13 6.15 50.84
PatCASPL1F5 Cell membrane 94.16 55.19 18.03 2.19 24.59
PatCASPL1B4 Chloroplast/Nucleus 59.66/41.00 49.75 17.41 6.97 25.87
PatCASPL2D4 Cell membrane 98.97 60.00 16.11 1.67 22.22
PatCASPL5A11 Nucleus 70.61 30.85 16.49 2.66 50.00
PatCASPL1F11 Cell membrane 75.84 61.05 12.21 3.49 23.26
PatCASPL5A10 Cell membrane/Golgi apparatus/Nucleus 62.28/95.00/17.00 51.12 10.67 3.93 34.27
PatCASPL1F10 Cell membrane 55.17 59.30 13.37 3.49 23.84
PatCASPL4D14 Cell membrane 94.08 36.19 20.95 4.76 38.10
PatCASPL2D7 Cell membrane 98.50 57.38 19.13 2.73 20.77
PatCASPL2A4 Cell membrane/Nucleus 98.15 57.37 17.37 3.16 22.11
PatCASPL2D5 Cell membrane/Chloroplast/Nucleus 98.5/28.00/26.00 58.47 19.67 3.83 18.03
PatCASPL2A1 Cell membrane/Nucleus 98.15/26.00 53.44 53.44 1.06 27.51
PatCASPL4B6 Cell membrane/Chloroplast/Cytoplasm/Mitochondrion/Nucleus/Peroxisome 78.42/39.00/49.00/7.00/95.00/17.00 61.11 5.05 3.54 30.30
PatCASP8 Cell membrane/Golgi apparatus/Nucleus 54.66/49.00/17.00 51.47 19.12 3.92 25.49
PatCASPL2B5 Peroxisome 64.55 63.32 14.07 5.03 17.59
PatCASPL4B7 Nucleus 73.42 60.80 4.02 3.02 32.16
PatCASP5 Cell membrane/Golgi apparatus/Nucleus 54.66/17.00/95.00 45.59 22.06 5.88 26.47
PatCASPL2B7 Peroxisome 49.45 61.31 15.08 5.03 18.59
PatCASPL1A10 Cell membrane 66.20 48.90 18.13 3.85 29.12
PatCASPL5B7 Cell membrane 73.97 61.04 12.99 4.55 21.43
PatCASPL4D4 Cell membrane/Golgi apparatus 100.00/69.00 44.51 24.28 5.20 26.01
PatCASPL4D2 Cell membrane/Golgi apparatus 99.99/15.00 40.00 25.88 4.71 29.41
PatCASPL4D5 Cell membrane/Golgi apparatus 99.98/36.00 53.61 19.88 3.61 22.89
PatCASPL1A12 Cell membrane 98.29 38.51 20.69 6.90 33.91
PatCASP11 Cell membrane 99.53 47.52 17.73 7.09 27.66
PatCASPL5B11 Cell membrane 84.07 64.94 8.44 4.55 22.08
PatCASPL4B3 Cell membrane/Cell wall/Chloroplast/Nucleus/Peroxisome/Vacuole 68.02/16.00/17.00/2.00/95.00/19.00 71.32 3.88 4.65 20.16
PatCASPL5A3 Cell membrane 87.02 50.57 13.64 5.11 30.68
PatCASPL5A7 Cell membrane/Golgi apparatus/Nucleus 49.05/26.00/28.00 53.37 16.83 2.88 26.92
PatCASP1 Cell membrane 66.57 50.83 11.60 4.42 33.15
PatCASP10 Cell membrane 99.87 63.12 9.22 5.67 21.99
PatCASPL5B8 Cell membrane 84.07 46.71 22.75 5.39 25.15
PatCASPL4B1 Cell membrane 97.61 52.27 11.36 7.39 28.98
PatCASPL5A4 Cell membrane 67.27 60.90 6.77 9.02 23.31
PatCASPL5A8 Cell membrane/Golgi apparatus/Nucleus 49.05/26.00/28.00 50.83 9.94 4.42 34.81
PatCASP4 Cell membrane 69.91 48.56 16.83 3.37 31.25
PatCASPL1D8 Cell membrane 50.31 56.99 8.81 3.63 30.57
PatCASPL1D6 Cell membrane 67.17 41.58 15.79 10.00 32.63
PatCASPL4A4 Chloroplast/Nucleus 62.04 22.22 20.47 6.14 51.17
PatCASPL1A5 Cell membrane/Chloroplast/Golgi apparatus 90.17/36.00/26.00 57.75 11.76 2.67 27.81
PatCASPL1A4 Cell membrane 88.87 52.66 15.96 4.26 27.13
PatCASPL5C5 Cell membrane 96.68 42.16 25.49 9.80 22.55
PatCASPL1C3 Cell membrane 99.98 58.64 16.67 3.09 21.60
PatCASPL4A3 Nucleus 71.28 29.28 13.04 3.77 53.91
PatCASPL1A8 Chloroplast 84.37 53.89 17.78 3.89 24.44
PatCASPL1A3 Cell membrane 88.87 60.64 13.83 3.19 22.34
PatCASPL5C7 Cell membrane 96.17 62.25 10.60 1.32 25.83
PatCASPL1C4 Cell membrane 99.51 60.49 15.43 2.47 21.60
PatCASPL5B2 Cell membrane/Chloroplast 86.47/28.00 66.23 9.74 4.55 19.48
PatCASPL1F3 Cell membrane/Chloroplast/Nucleus 63.75/22.00/27.00 49.74 19.90 5.24 25.13
PatCASPL5B4 Chloroplast 52.62 67.53 9.09 5.19 18.18
PatCASPL1F2 Cell membrane/Chloroplast 75.73/51.00 51.83 17.28 3.14 27.75
PatCASPL4A9 Nucleus 75.56 35.48 9.35 2.58 52.58
PatCASPL4A11 Nucleus 51.39 33.33 8.61 4.72 53.33
PatCASPL1E2 Cell membrane 79.86 47.21 19.29 5.08 28.43
PatCASPL1D1 Cell membrane/Nucleus 79.86/41.00 48.00 13.50 4.00 34.50
PatCASPL1D4 Cell membrane/Nucleus 79.86/15.00 50.00 12.00 5.00 33.00
PatCASPL2C1 Cell membrane/Chloroplast 99.96/53.00 70.45 11.36 3.41 14.77
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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.

Figure 1.

Figure 1

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Conserved domain (a) and gene structure (b) of CASPL family members in Pogostemon cablin.

Figure 2.

Figure 2

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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.

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.

Figure 3.

Figure 3

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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.

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.

Figure 4.

Figure 4

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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.

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.

Table 3.

Gene number per chromosome of CASPL gene family proteins in P. cablin.

Chromosome Gene Number Gene Name
A01 1 PatCASPL5C2
A02 1 PatCASPL5C3
A03 5 PatCASPL1C8/PatCASPL2B2/PatCASPL4D10/PatCASPL4D13/PatCASPL4A15
A04 4 PatCASPL1C6/PatCASPL2B1/PatCASPL4D11/PatCASPL4A17
A05 6 PatCASPL3A3/PatCASPL4A7/PatCASPL4D7/PatCASPL1F6/PatCASPL1B1/PatCASPL2D1
A06 5 PatCASPL3A4/PatCASPL4A6/PatCASPL1F7/PatCASPL1B3/PatCASPL2D3
A07 2 PatCASPL5A12/PatCASPL1F12
A08 2 PatCASPL5A9/PatCASPL1F9
A09 0
A10 1 PatCASPL5B5
A11 3 PatCASPL1C9/PatCASPL2D8/PatCASPL2A2
A12 2 PatCASPL2D6/PatCASPL2A3
A13 3 PatCASPL4B8/PatCASP7/PatCASPL2B6
A14 3 PatCASPL4B5/PatCASP7/PatCASPL2B6
A15 5 PatCASPL1A9/PatCASPL5B6/PatCASPL4D3/PatCASPL4D1/PatCASPL4D6
A16 1 PatCASPL1A11
A17 5 PatCASP9/PatCASPL5B9/PatCASPL5A1/PatCASPL5A5/PatCASP3
A18 5 PatCASPL5B10/PatCASPL4B2/PatCASPL5A2/PatCASPL5A6/PatCASP2
A19 1 PatCASPL1D5
A20 1 PatCASPL1D7
A21 5 PatCASPL4A2/PatCASPL1A7/PatCASPL1A2/PatCASPL5C6/PatCASPL1C2
A22 5 PatCASPL4A1/PatCASPL1A6/PatCASPL1A1/PatCASPL5C8/PatCASPL1C1
A23 2 PatCASPL5B3/PatCASPL1F4
A24 2 PatCASPL5B1/PatCASPL1F1
A25 1 PatCASPL4A10
A26 2 PatCASPL4A12/PatCASPL4A13
A27 0
A28 0
A29 2 PatCASPL1E1/PatCASPL1D2
A30 2 PatCASPL1E3/PatCASPL1D3
A31 1 PatCASPL2C2
A32 1 PatCASPL2C3
A33 1 PatCASPL5C1
A34 1 PatCASPL5C4
A35 4 PatCASPL1C7/PatCASPL2B4/PatCASPL4D9/PatCASPL4A14
A36 4 PatCASPL1C5/PatCASPL2B3/PatCASPL4D12/PatCASPL4A16
A37 6 PatCASPL3A2/PatCASPL4A8/PatCASPL4D8/PatCASPL1F8/PatCASPL1B2/PatCASPL2D2
A38 5 PatCASPL3A1/PatCASPL4A5/PatCASPL1F5/PatCASPL1B4/PatCASPL2D4
A39 2 PatCASPL5A11/PatCASPL1F11
A40 2 PatCASPL5A10/PatCASPL1F10
A41 0
A42 1 PatCASPL4D14
A43 2 PatCASPL2D7/PatCASPL2A4
A44 2 PatCASPL2D5/PatCASPL2A1
A45 3 PatCASPL4B6/PatCASP8/PatCASPL2B5
A46 3 PatCASPL4B7/PatCASP5/PatCASPL2B7
A47 5 PatCASPL1A10/PatCASPL5B7/PatCASPL4D4/PatCASPL4D2/PatCASPL4D5
A48 1 PatCASPL1A12
A49 6 PatCASP11/PatCASPL5B11/PatCASPL4B3/PatCASPL5A3/PatCASPL5A7/PatCASP1
A50 6 PatCASP10/PatCASPL5B8/PatCASPL4B1/PatCASPL5A4/PatCASPL5A8/PatCASP4
A51 1 PatCASPL1D8
A52 1 PatCASPL1D6
A53 5 PatCASPL4A4/PatCASPL1A5/PatCASPL1A4/PatCASPL5C5/PatCASPL1C3
A54 5 PatCASPL4A3/PatCASPL1A8/PatCASPL1A3/PatCASPL5C7/PatCASPL1C4
A55 2 PatCASPL5B2/PatCASPL1F3
A56 2 PatCASPL5B4/PatCASPL1F2
A57 1 PatCASPL4A9
A58 1 PatCASPL4A11
A59 0
A60 0
A61 2 PatCASPL1E2/PatCASPL1D1
A62 1 PatCASPL1D4
A63 1 PatCASPL2C1
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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.

Figure 5.

Figure 5

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Expression of PatCASPL gene in P. cablin at different treatment stages of p-HBA.

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.

Conflicts of Interest

The authors declare no conflict of interest.

Funding Statement

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).

Footnotes

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