Identification and analysis of PAT gene family in three kinds of Apiaceae vegetable crops

doi:10.3969/j.issn.1004-1524.2023.06.09

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (6): 1315-1327.DOI: 10.3969/j.issn.1004-1524.2023.06.09

• Horticultural Science • Previous Articles Next Articles

Identification and analysis of PAT gene family in three kinds of Apiaceae vegetable crops

ZHANG Xinye¹^,²^,³(), LI Wenjing¹^,²^,³, ZHU Shu¹, SUN Yanxiang¹, WANG Congyan¹, YAN Xunyou¹, ZHOU Zhiguo¹^,^*()

1. College of Life Science, Langfang Normal University, Langfang 065000, Hebei, China
2. Hebei Key Laboratory of Animal Diversity, Langfang 065000, Hebei, China
3. Langfang Key Laboratory of Cell Engineering and Application, Langfang 065000, Hebei, China

Received:2022-06-06 Online:2023-06-25 Published:2023-07-04

Abstract

Abstract:

The objective of this study was to identify the PAT gene family in three kinds of Apiaceae vegetable crops (Daucus carota, Apium graveolens, Coriandrum sativum) at genome scale and provide a reference for further exploration of their roles in plant growth, development and stress tolerance. The PAT proteins were identified from genomes of the three species by BLAST and hmmsearch. TBtools was used to depict chromosome locations of PAT genes. The isoelectric point and molecular weight were analyzed by Expasy. TMHMM-2.0, CELLO v.2.5 and WoLF PSORT were used to predict transmembrane regions and subcellular localization of PAT. MEGA6 was used to construct the phylogenetic tree, and MEME was used to analyze conserved motifs of PAT proteins. Based on real time quantitative PCR results and transcriptome data, TBtools was used to draw gene expression heat map, and tissue expression characteristics and responses to stress of PAT genes were analyzed. The results showed that 27, 25, 27 PAT gene family members were identified in Daucus carota, Apium graveolens, Coriandrum sativum respectively, which were named as DcPAT1-27, AgPAT1-25, CsPAT1-27. These members with transmembrane regions distributed unevenly on chromosomes of three species, and they had different physical and chemical properties. According to phylogenetic analysis, PAT proteins from Apiaceae and other species were divided into 7 groups, and Apiaceae PAT proteins were distributed throughout all groups. Structural analysis showed that all PAT proteins had DHHC-CRD domain, and conserved amino acid residues in this domain had varied among different species. Gene expression analysis showed that the expression levels of PAT genes were different across different tissues of Daucus carota, Apium graveolens, Coriandrum sativum. Some members showed high or low expression levels in all tissues, and the expression levels of some DcPAT genes had changed after salt stress or low temperature stress.

Key words: Apiaceae, protein S-acyltransferase, gene family, bioinformatic analysis, expression analysis

CLC Number:

ZHANG Xinye, LI Wenjing, ZHU Shu, SUN Yanxiang, WANG Congyan, YAN Xunyou, ZHOU Zhiguo. Identification and analysis of PAT gene family in three kinds of Apiaceae vegetable crops[J]. Acta Agriculturae Zhejiangensis, 2023, 35(6): 1315-1327.

Figures/Tables 7

References 42

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基因名称 Gene ID	正向引物 Sequence of forward primer (5'→3')	反向引物 Sequence of revere primer (5'→3')	退火温度 Annealing temperature/℃
DcPAT10	CATGTATGGATATCAGGCAACACA	TGGAACGTCTGGATCTGCAT	60
DcPAT13	CACTTGCATGCTTTACCGCC	AGTACCGGTAGTTGCGCTGT	60
DcPAT17	CATGGAAGGGCAGCAATGTTT	GCCACAAAAGATGGCTACAGG	60
DcPAT20	ACAAGTGTCCTTTGGCTCCT	TGCAAATGGAGCACGAGAGA	63
DcPAT25	ATGCAGGCACAAAGGAGGAA	ATGCTGCGCTCTAAGAAGGA	60
DcActin	CGGTATTGTGTTGGACTCTGGTGAT	CAGCAAGGTCAAGACGGAGTATGG	60/63

基因名称 Gene ID	正向引物 Sequence of forward primer (5'→3')	反向引物 Sequence of revere primer (5'→3')	退火温度 Annealing temperature/℃
DcPAT10	CATGTATGGATATCAGGCAACACA	TGGAACGTCTGGATCTGCAT	60
DcPAT13	CACTTGCATGCTTTACCGCC	AGTACCGGTAGTTGCGCTGT	60
DcPAT17	CATGGAAGGGCAGCAATGTTT	GCCACAAAAGATGGCTACAGG	60
DcPAT20	ACAAGTGTCCTTTGGCTCCT	TGCAAATGGAGCACGAGAGA	63
DcPAT25	ATGCAGGCACAAAGGAGGAA	ATGCTGCGCTCTAAGAAGGA	60
DcActin	CGGTATTGTGTTGGACTCTGGTGAT	CAGCAAGGTCAAGACGGAGTATGG	60/63

基因名称 Gene ID	蛋白ID Protein ID	基因长度 Gene length/bp	外显子数目 Number of exon	氨基酸数目 Number of amino acids/aa	蛋白分子量 Molecular weight/ku	等电点 Isoelectric point	跨膜区个数 Number of TMD	亚细胞定位 Subcellular localization
DcPAT1	XP_017231957.1	5 544	10	391	44.78	8.91	6	质膜Plasma membrane
DcPAT2	XP_017232727.1	3 079	9	505	57.64	9.40	5	质膜Plasma membrane
DcPAT3	XP_017234967.1	5 170	7	281	31.97	9.12	4	质膜Plasma membrane
DcPAT4	XP_017231515.1	5 299	7	307	34.39	6.65	4	质膜Plasma membrane
DcPAT5	XP_017235454.1	5 088	9	627	69.43	8.92	4	质膜Plasma membrane
DcPAT6	XP_017234510.1	3 110	5	418	46.43	6.88	4	质膜Plasma membrane
DcPAT7	XP_017231049.1	4 286	7	307	34.65	6.13	4	质膜Plasma membrane
DcPAT8	XP_017241016.1	4 035	5	407	46.85	9.43	4	质膜Plasma membrane
DcPAT9	XP_017237722.1	5 752	5	413	47.87	6.17	4	质膜Plasma membrane
DcPAT10	XP_017242796.1	12 229	13	624	68.66	6.64	4	质膜Plasma membrane
DcPAT11	XP_017242953.1	8 840	11	346	39.90	8.79	4	质膜Plasma membrane
DcPAT12	XP_017248113.1	6 759	13	632	69.45	6.41	4	质膜Plasma membrane
DcPAT13	XP_017247520.1	6 889	5	424	48.71	7.57	4	质膜Plasma membrane
DcPAT14	XP_017246994.1	6 851	10	633	69.33	6.80	4	质膜Plasma membrane
DcPAT15	XP_017245764.1	2 421	5	401	45.12	9.47	4	质膜Plasma membrane
DcPAT16	XP_017246280.1	6 834	9	653	71.33	8.10	2	质膜Plasma membrane
DcPAT17	XP_017253762.1	5 261	5	441	49.57	8.22	4	质膜Plasma membrane
DcPAT18	XP_017252794.1	4 594	4	345	39.35	8.99	3	质膜Plasma membrane
DcPAT19	XP_017249993.1	4 864	12	344	38.59	8.60	6	质膜Plasma membrane
DcPAT20	XP_017258526.1	9 185	10	731	79.22	8.58	4	质膜Plasma membrane
DcPAT21	XP_017214813.1	5 759	5	447	49.99	8.91	4	质膜Plasma membrane
DcPAT22	XP_017254573.1	5 903	5	439	49.30	8.78	4	质膜Plasma membrane
DcPAT23	XP_017216415.1	4 688	4	356	39.87	9.10	4	质膜Plasma membrane
DcPAT24	XP_017220920.1	3 730	7	277	31.20	8.25	4	质膜Plasma membrane
DcPAT25	XP_017226581.1	10 201	13	538	59.90	6.30	4	质膜Plasma membrane
DcPAT26	XP_017224127.1	5 827	4	364	40.54	7.46	4	质膜Plasma membrane
DcPAT27	XP_017224090.1	5 681	9	627	69.16	8.56	4	质膜Plasma membrane
AgPAT1	Ag1G00678.1	16 983	14	566	63.21	6.48	4	质膜Plasma membrane
AgPAT2	Ag1G01444.1	5 264	9	627	69.42	8.56	4	质膜Plasma membrane
AgPAT3	Ag2G01570.1	1 651	3	330	37.67	8.41	2	质膜Plasma membrane
AgPAT4	Ag3G00580.1	5 851	9	725	79.76	8.66	4	质膜Plasma membrane
AgPAT5	Ag3G01929.1	6 092	5	424	48.77	8.35	4	质膜Plasma membrane
AgPAT6	Ag3G02080.1	9 965	11	348	40.26	8.80	4	质膜Plasma membrane
AgPAT7	Ag3G02578.1	6 182	10	631	69.41	7.54	4	质膜Plasma membrane
AgPAT8	Ag3G02732.1	11 809	13	631	69.47	6.31	4	质膜Plasma membrane
AgPAT9	Ag4G00005.1	5 085	5	441	49.62	7.53	4	质膜Plasma membrane
AgPAT10	Ag4G01427.1	5 150	5	398	45.72	9.20	4	质膜Plasma membrane
AgPAT11	Ag4G01428.1	6 853	6	413	48.01	6.02	4	质膜Plasma membrane
AgPAT12	Ag4G01654.1	19 854	13	625	68.63	6.49	4	质膜Plasma membrane
AgPAT13	Ag5G01814.1	4 227	3	230	25.85	9.29	2	质膜Plasma membrane
AgPAT14	Ag6G00122.1	4 968	7	307	34.52	5.98	4	质膜Plasma membrane
AgPAT15	Ag6G00420.1	5 916	10	626	69.17	9.00	4	质膜Plasma membrane
AgPAT16	Ag6G01499.1	3 608	5	384	43.87	8.36	4	质膜Plasma membrane
AgPAT17	Ag6G01663.1	6 690	7	307	34.59	6.65	4	质膜Plasma membrane
AgPAT18	Ag6G02949.1	11 924	10	392	45.05	9.08	6	质膜Plasma membrane
AgPAT19	Ag8G00168.1	3 545	7	277	31.27	8.38	4	质膜Plasma membrane
AgPAT20	Ag9G01243.1	5 048	5	437	49.33	8.68	4	质膜Plasma membrane
AgPAT21	Ag11G03538.1	11 445	9	727	78.74	8.74	4	质膜Plasma membrane
AgPAT22	Ag11G03938.1	2 801	9	500	57.00	9.55	5	质膜Plasma membrane
AgPAT23	AgUnG00368.1	5 493	5	443	49.67	8.83	4	质膜Plasma membrane
AgPAT24	AgUnG01143.1	11 544	13	631	69.42	6.31	4	质膜Plasma membrane
AgPAT25	AgUnG01289.1	4 578	7	283	32.37	9.15	4	质膜Plasma membrane
CsPAT1	Cs01G00487.1	3 053	9	504	57.63	9.45	4	质膜Plasma membrane
CsPAT2	Cs01G01377.1	4 658	5	441	49.57	7.95	4	质膜Plasma membrane
CsPAT3	Cs02G01000.1	5 130	10	250	27.89	8.68	3	质膜Plasma membrane
CsPAT4	Cs03G02877.1	4 546	5	413	48.07	6.47	4	质膜Plasma membrane
CsPAT5	Cs03G02879.1	3 500	5	408	47.25	9.36	4	质膜Plasma membrane
CsPAT6	Cs04G00058.1	6 781	9	720	78.10	8.68	4	质膜Plasma membrane
CsPAT7	Cs05G00045.1	4 286	9	277	31.19	8.56	4	质膜Plasma membrane
CsPAT8	Cs07G02759.1	4 664	4	361	40.52	8.80	5	质膜Plasma membrane
CsPAT9	Cs09G00033.1	9 462	10	392	44.93	9.08	6	质膜Plasma membrane
CsPAT10	Cs09G01589.1	6 526	7	307	34.43	7.02	4	质膜Plasma membrane
CsPAT11	Cs09G02975.1	4 906	9	625	68.98	9.02	4	质膜Plasma membrane
CsPAT12	Cs09G03315.1	4 262	7	305	34.25	6.44	4	质膜Plasma membrane
CsPAT13	Cs09G04864.1	6 143	9	431	47.63	8.77	4	质膜Plasma membrane
CsPAT14	Cs09G05377.1	5 760	9	627	69.60	8.64	4	质膜Plasma membrane
CsPAT15	Cs10G00189.1	3 010	5	401	45.75	8.91	4	质膜Plasma membrane
CsPAT16	Cs10G00720.1	8 155	5	371	43.08	6.82	3	质膜Plasma membrane
CsPAT17	Cs10G01251.1	13 537	11	350	40.41	8.67	4	质膜Plasma membrane
CsPAT18	Cs10G01544.1	6 303	10	631	69.68	8.03	4	质膜Plasma membrane
CsPAT19	Cs10G01658.1	7 185	13	630	69.20	6.44	4	质膜Plasma membrane
CsPAT20	Cs10G01915.1	5 199	5	438	49.44	8.79	4	质膜Plasma membrane
CsPAT21	Cs10G02331.1	5 362	5	446	49.85	8.82	4	质膜Plasma membrane
CsPAT22	Cs10G03215.1	3 461	5	308	35.43	8.81	4	质膜Plasma membrane
CsPAT23	Cs11G00778.1	7 628	13	538	59.78	6.27	4	质膜Plasma membrane
CsPAT24	Cs11G01042.1	4 192	4	364	40.58	6.77	5	质膜Plasma membrane
CsPAT25	CsUnG00290.1	2 050	4	358	41.33	8.66	3	质膜Plasma membrane
CsPAT26	CsUnG01718.1	3 463	5	308	35.42	8.81	4	质膜Plasma membrane
CsPAT27	CsUnG03874.1	3 495	5	411	47.34	8.98	4	质膜Plasma membrane

基因名称 Gene ID	蛋白ID Protein ID	基因长度 Gene length/bp	外显子数目 Number of exon	氨基酸数目 Number of amino acids/aa	蛋白分子量 Molecular weight/ku	等电点 Isoelectric point	跨膜区个数 Number of TMD	亚细胞定位 Subcellular localization
DcPAT1	XP_017231957.1	5 544	10	391	44.78	8.91	6	质膜Plasma membrane
DcPAT2	XP_017232727.1	3 079	9	505	57.64	9.40	5	质膜Plasma membrane
DcPAT3	XP_017234967.1	5 170	7	281	31.97	9.12	4	质膜Plasma membrane
DcPAT4	XP_017231515.1	5 299	7	307	34.39	6.65	4	质膜Plasma membrane
DcPAT5	XP_017235454.1	5 088	9	627	69.43	8.92	4	质膜Plasma membrane
DcPAT6	XP_017234510.1	3 110	5	418	46.43	6.88	4	质膜Plasma membrane
DcPAT7	XP_017231049.1	4 286	7	307	34.65	6.13	4	质膜Plasma membrane
DcPAT8	XP_017241016.1	4 035	5	407	46.85	9.43	4	质膜Plasma membrane
DcPAT9	XP_017237722.1	5 752	5	413	47.87	6.17	4	质膜Plasma membrane
DcPAT10	XP_017242796.1	12 229	13	624	68.66	6.64	4	质膜Plasma membrane
DcPAT11	XP_017242953.1	8 840	11	346	39.90	8.79	4	质膜Plasma membrane
DcPAT12	XP_017248113.1	6 759	13	632	69.45	6.41	4	质膜Plasma membrane
DcPAT13	XP_017247520.1	6 889	5	424	48.71	7.57	4	质膜Plasma membrane
DcPAT14	XP_017246994.1	6 851	10	633	69.33	6.80	4	质膜Plasma membrane
DcPAT15	XP_017245764.1	2 421	5	401	45.12	9.47	4	质膜Plasma membrane
DcPAT16	XP_017246280.1	6 834	9	653	71.33	8.10	2	质膜Plasma membrane
DcPAT17	XP_017253762.1	5 261	5	441	49.57	8.22	4	质膜Plasma membrane
DcPAT18	XP_017252794.1	4 594	4	345	39.35	8.99	3	质膜Plasma membrane
DcPAT19	XP_017249993.1	4 864	12	344	38.59	8.60	6	质膜Plasma membrane
DcPAT20	XP_017258526.1	9 185	10	731	79.22	8.58	4	质膜Plasma membrane
DcPAT21	XP_017214813.1	5 759	5	447	49.99	8.91	4	质膜Plasma membrane
DcPAT22	XP_017254573.1	5 903	5	439	49.30	8.78	4	质膜Plasma membrane
DcPAT23	XP_017216415.1	4 688	4	356	39.87	9.10	4	质膜Plasma membrane
DcPAT24	XP_017220920.1	3 730	7	277	31.20	8.25	4	质膜Plasma membrane
DcPAT25	XP_017226581.1	10 201	13	538	59.90	6.30	4	质膜Plasma membrane
DcPAT26	XP_017224127.1	5 827	4	364	40.54	7.46	4	质膜Plasma membrane
DcPAT27	XP_017224090.1	5 681	9	627	69.16	8.56	4	质膜Plasma membrane
AgPAT1	Ag1G00678.1	16 983	14	566	63.21	6.48	4	质膜Plasma membrane
AgPAT2	Ag1G01444.1	5 264	9	627	69.42	8.56	4	质膜Plasma membrane
AgPAT3	Ag2G01570.1	1 651	3	330	37.67	8.41	2	质膜Plasma membrane
AgPAT4	Ag3G00580.1	5 851	9	725	79.76	8.66	4	质膜Plasma membrane
AgPAT5	Ag3G01929.1	6 092	5	424	48.77	8.35	4	质膜Plasma membrane
AgPAT6	Ag3G02080.1	9 965	11	348	40.26	8.80	4	质膜Plasma membrane
AgPAT7	Ag3G02578.1	6 182	10	631	69.41	7.54	4	质膜Plasma membrane
AgPAT8	Ag3G02732.1	11 809	13	631	69.47	6.31	4	质膜Plasma membrane
AgPAT9	Ag4G00005.1	5 085	5	441	49.62	7.53	4	质膜Plasma membrane
AgPAT10	Ag4G01427.1	5 150	5	398	45.72	9.20	4	质膜Plasma membrane
AgPAT11	Ag4G01428.1	6 853	6	413	48.01	6.02	4	质膜Plasma membrane
AgPAT12	Ag4G01654.1	19 854	13	625	68.63	6.49	4	质膜Plasma membrane
AgPAT13	Ag5G01814.1	4 227	3	230	25.85	9.29	2	质膜Plasma membrane
AgPAT14	Ag6G00122.1	4 968	7	307	34.52	5.98	4	质膜Plasma membrane
AgPAT15	Ag6G00420.1	5 916	10	626	69.17	9.00	4	质膜Plasma membrane
AgPAT16	Ag6G01499.1	3 608	5	384	43.87	8.36	4	质膜Plasma membrane
AgPAT17	Ag6G01663.1	6 690	7	307	34.59	6.65	4	质膜Plasma membrane
AgPAT18	Ag6G02949.1	11 924	10	392	45.05	9.08	6	质膜Plasma membrane
AgPAT19	Ag8G00168.1	3 545	7	277	31.27	8.38	4	质膜Plasma membrane
AgPAT20	Ag9G01243.1	5 048	5	437	49.33	8.68	4	质膜Plasma membrane
AgPAT21	Ag11G03538.1	11 445	9	727	78.74	8.74	4	质膜Plasma membrane
AgPAT22	Ag11G03938.1	2 801	9	500	57.00	9.55	5	质膜Plasma membrane
AgPAT23	AgUnG00368.1	5 493	5	443	49.67	8.83	4	质膜Plasma membrane
AgPAT24	AgUnG01143.1	11 544	13	631	69.42	6.31	4	质膜Plasma membrane
AgPAT25	AgUnG01289.1	4 578	7	283	32.37	9.15	4	质膜Plasma membrane
CsPAT1	Cs01G00487.1	3 053	9	504	57.63	9.45	4	质膜Plasma membrane
CsPAT2	Cs01G01377.1	4 658	5	441	49.57	7.95	4	质膜Plasma membrane
CsPAT3	Cs02G01000.1	5 130	10	250	27.89	8.68	3	质膜Plasma membrane
CsPAT4	Cs03G02877.1	4 546	5	413	48.07	6.47	4	质膜Plasma membrane
CsPAT5	Cs03G02879.1	3 500	5	408	47.25	9.36	4	质膜Plasma membrane
CsPAT6	Cs04G00058.1	6 781	9	720	78.10	8.68	4	质膜Plasma membrane
CsPAT7	Cs05G00045.1	4 286	9	277	31.19	8.56	4	质膜Plasma membrane
CsPAT8	Cs07G02759.1	4 664	4	361	40.52	8.80	5	质膜Plasma membrane
CsPAT9	Cs09G00033.1	9 462	10	392	44.93	9.08	6	质膜Plasma membrane
CsPAT10	Cs09G01589.1	6 526	7	307	34.43	7.02	4	质膜Plasma membrane
CsPAT11	Cs09G02975.1	4 906	9	625	68.98	9.02	4	质膜Plasma membrane
CsPAT12	Cs09G03315.1	4 262	7	305	34.25	6.44	4	质膜Plasma membrane
CsPAT13	Cs09G04864.1	6 143	9	431	47.63	8.77	4	质膜Plasma membrane
CsPAT14	Cs09G05377.1	5 760	9	627	69.60	8.64	4	质膜Plasma membrane
CsPAT15	Cs10G00189.1	3 010	5	401	45.75	8.91	4	质膜Plasma membrane
CsPAT16	Cs10G00720.1	8 155	5	371	43.08	6.82	3	质膜Plasma membrane
CsPAT17	Cs10G01251.1	13 537	11	350	40.41	8.67	4	质膜Plasma membrane
CsPAT18	Cs10G01544.1	6 303	10	631	69.68	8.03	4	质膜Plasma membrane
CsPAT19	Cs10G01658.1	7 185	13	630	69.20	6.44	4	质膜Plasma membrane
CsPAT20	Cs10G01915.1	5 199	5	438	49.44	8.79	4	质膜Plasma membrane
CsPAT21	Cs10G02331.1	5 362	5	446	49.85	8.82	4	质膜Plasma membrane
CsPAT22	Cs10G03215.1	3 461	5	308	35.43	8.81	4	质膜Plasma membrane
CsPAT23	Cs11G00778.1	7 628	13	538	59.78	6.27	4	质膜Plasma membrane
CsPAT24	Cs11G01042.1	4 192	4	364	40.58	6.77	5	质膜Plasma membrane
CsPAT25	CsUnG00290.1	2 050	4	358	41.33	8.66	3	质膜Plasma membrane
CsPAT26	CsUnG01718.1	3 463	5	308	35.42	8.81	4	质膜Plasma membrane
CsPAT27	CsUnG03874.1	3 495	5	411	47.34	8.98	4	质膜Plasma membrane

Identification and analysis of PAT gene family in three kinds of Apiaceae vegetable crops

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