Identification of PG Gene Family and Their Roles in Papaya Fruit Softening

doi:10.13560/j.cnki.biotech.bull.1985.2025-0437

Abstract

Abstract:

Objective Polygalacturonase (PG) plays a pivotal role in the regulation of fruit softening. This study is aimed to identify the PG gene family members in papaya (Carica papaya L.) and analyze their functions, providing a theoretical framework for understanding the molecular mechanisms behind postharvest softening in papaya. Method Based on the genome data of ‘Zihui’ papaya, the CpPG family members were systematically identified,and their protein properties, evolutionary relationships, conserved motifs, gene structures, gene duplication events, cis-acting elements, and expression patterns were thoroughly investigated. Additionally, transient overexpression experiments in papaya fruit were conducted to assess the roles of CpPG1, CpPG2, and CpPG28 in fruit softening. Result A total of 38 PG genes were identified in the ‘Zihui’ papaya genome, named as CpPG1 to CpPG38, and they were distributed unevenly across 8 chromosomes. Phylogenetic analysis grouped the CpPG genes into subgroup A-F, with relatively conserved exon/intron structures within each group. However, significant differences in conserved domains and protein motifs were observed among subgroups. Collinearity analysis revealed the evidence of gene duplication and tandem repeat events within the papaya CpPG family. Promoter regions of CpPG genes contained diverse cis-elements associated with light responsiveness, plant development, stress adaptation, and hormone signaling, indicating their involvement in various developmental processes. Expression pattern analysis identified three key genes, CpPG1, CpPG2, and CpPG28, which were highly expressed in ripe papaya fruit and responsive to ethylene. Transient overexpression experiments confirmed that these genes significantly decreased fruit firmness, highlighting their critical roles in fruit softening. Conclusion This study identified 38 CpPG genes in the papaya genome and highlighted CpPG1, CpPG2, and CpPG28 as key regulators of papaya fruit softening.

Key words: papaya, fruit, ripening and softening, polygalacturonase, gene family, gene expression pattern, evolutionary relationship, functional analysis

XU Ze, ZHOU Chen-ping, KUANG Rui-bin, WU Xia-ming, YANG Min, LIU Chuan-he, HE Han, WEI Yue-rong. Identification of PG Gene Family and Their Roles in Papaya Fruit Softening[J]. Biotechnology Bulletin, 2026, 42(3): 349-361.

Figures/Tables 10

References 43

[1]	Wang WH, Wang YY, Chen T, et al. Current insights into posttranscriptional regulation of fleshy fruit ripening [J]. Plant Physiol, 2023, 192(3): 1785-1798.
[2]	Brummell DA, Bowen JK, Gapper NE. Biotechnological approaches for controlling postharvest fruit softening [J]. Curr Opin Biotechnol, 2022, 78: 102786.
[3]	张芮宁, 袁舟宇, 陈萍. 番木瓜采后保鲜技术研究进展 [J]. 园艺与种苗, 2021, 41(2): 47-52.
	Zhang RN, Yuan ZY, Chen P. Research progress on postharvest preservation technology of Carica papaya [J]. Hortic Seed, 2021, 41(2): 47-52.
[4]	葛廷, 黄雪, 谢让金. 多聚半乳糖醛酸基因在果树中的研究进展 [J]. 植物生理学报, 2019, 55(8): 1075-1088.
	Ge T, Huang X, Xie RJ. Recent advances in polygalacturonase gene in fruit tree species [J]. Plant Physiol J, 2019, 55(8): 1075-1088.
[5]	Nie HM, Shi Y, Geng XQ, et al. CRISRP/Cas9-mediated targeted mutagenesis of tomato polygalacturonase gene (SlPG) delays fruit softening [J]. Front Plant Sci, 2022, 13: 729128.
[6]	Niture SK. Comparative biochemical and structural characterizations of fungal polygalacturonases [J]. Biologia, 2008, 63(1): 1-19.
[7]	Zou QW, Tu RR, Wu JJ, et al. A polygalacturonase gene OsPG1 modulates water homeostasis in rice [J]. Crop J, 2024, 12(1): 79-91.
[8]	Fei YC, Mo Y, Xu JJ, et al. Genome-wide analysis of the polygalacturonase gene family in Macadamia and identification of members involved in fruit abscission [J]. Plants, 2025, 14(11): 1610.
[9]	Mahmood U, Li XD, Qian MC, et al. Comparative transcriptome and co-expression network analysis revealed the genes associated with senescence and polygalacturonase activity involved in pod shattering of rapeseed [J]. Biotechnol Biofuels Bioprod, 2023, 16(1): 20.
[10]	Liao YX, Xiang B, Xue ZZ, et al. HCC1, a polygalacturonase, regulates chlorophyll degradation via the ethylene synthesis pathway [J]. Rice, 2023, 16(1): 57.
[11]	Rhee SY, Osborne E, Poindexter PD, et al. Microspore separation in the quartet 3 mutants of Arabidopsis is impaired by a defect in a developmentally regulated polygalacturonase required for pollen mother cell wall degradation [J]. Plant Physiol, 2003, 133(3): 1170-1180.
[12]	Gu C, Wang L, Wang W, et al. Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach [J]. J Exp Bot, 2016, 67(6): 1993-2005.
[13]	Atkinson RG, Sutherland PW, Johnston SL, et al. Down-regulation of POLYGALACTURONASE1 alters firmness, tensile strength and water loss in apple (Malus × domestica) fruit [J]. BMC Plant Biol, 2012, 12: 129.
[14]	Fabi JP, Broetto SG, da Silva SLGL, et al. Analysis of Papaya cell wall-related genes during fruit ripening indicates a central role of polygalacturonases during pulp softening [J]. PLoS One, 2014, 9(8): e105685.
[15]	Fu CC, Chen HJ, Gao HY, et al. Histone deacetylase CpHDA3 is functionally associated with CpERF9 in suppression of CpPME1/2 and CpPG5 genes during papaya fruit ripening [J]. J Agric Food Chem, 2019, 67(32): 8919-8925.
[16]	Yang M, Kong XD, Zhou CP, et al. Genomic insights into the domestication and genetic basis of yield in papaya [J]. Hortic Res, 2025, 12(5): uhaf045.
[17]	Torki M, Mandaron P, Mache R, et al. Characterization of a ubiquitous expressed gene family encoding polygalacturonase in Arabidopsis thaliana [J]. Gene, 2000, 242(1/2): 427-436.
[18]	Ke XB, Wang HS, Li Y, et al. Genome-wide identification and analysis of polygalacturonase genes in Solanum lycopersicum [J]. Int J Mol Sci, 2018, 19(8): 2290.
[19]	Lu L, Hou QC, Wang LL, et al. Genome-wide identification and characterization of polygalacturonase gene family in maize (Zea mays L.) [J]. Int J Mol Sci, 2021, 22(19): 10722.
[20]	Zhao MT, Hu RX, Lin YX, et al. Genome-wide analysis of polygalacturonase gene family reveals its role in strawberry softening [J]. Plants, 2024, 13(13): 1838.
[21]	Huang WJ, Chen MY, Zhao TT, et al. Genome-wide identification and expression analysis of polygalacturonase gene family in kiwifruit (Actinidia chinensis) during fruit softening [J]. Plants, 2020, 9(3): 327.
[22]	Qian M, Zhang YK, Yan XY, et al. Identification and expression analysis of polygalacturonase family members during peach fruit softening [J]. Int J Mol Sci, 2016, 17(11): 1933.
[23]	Chen HF, Shao HX, Fan S, et al. Identification and phylogenetic analysis of the POLYGALACTURONASE gene family in apple [J]. Hortic Plant J, 2016, 2(5): 241-252.
[24]	Khan N, Fatima F, Haider MS, et al. Genome-wide identification and expression profiling of the polygalacturonase (PG) and pectin methylesterase (PME) genes in grapevine (Vitis vinifera L.) [J]. Int J Mol Sci, 2019, 20(13): 3180.
[25]	Wang Y, Fan ZY, Zhai YL, et al. Polygalacturonase gene family analysis identifies FcPG12 as a key player in fig (Ficus carica L.) fruit softening [J]. BMC Plant Biol, 2023, 23(1): 320.
[26]	Zhai ZF, Feng C, Wang YY, et al. Genome-wide identification of the xyloglucan endotransglucosylase/hydrolase (XTH) and polygalacturonase (PG) genes and characterization of their role in fruit softening of sweet cherry [J]. Int J Mol Sci, 2021, 22(22): 12331.
[27]	黄少鹏, 符栩, 任正恺, 等. 基于转录组的荔枝PG基因家族鉴定及表达分析 [J]. 分子植物育种, 2022, 20(20): 6687-6695.
	Huang SP, Fu X, Ren ZK, et al. Identification and expression analysis of litchi PG gene family based on transcriptome [J]. Mol Plant Breed, 2022, 20(20): 6687-6695.
[28]	刘若南, 刘林婷, 周秋蓉, 等. 柚多聚半乳糖醛酸酶基因家族的鉴定和分析 [J]. 热带作物学报, 2022, 43(4): 666-674.
	Liu RN, Liu LT, Zhou QR, et al. Identification and analysis of polygalacturonase genes family in pomelo [J]. Chin J Trop Crops, 2022, 43(4): 666-674.
[29]	Mahmood U, Fan YH, Wei SY, et al. Comprehensive analysis of polygalacturonase genes offers new insights into their origin and functional evolution in land plants [J]. Genomics, 2021, 113(1): 1096-1108.
[30]	Liu J, Sharma A, Niewiara MJ, et al. Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion [J]. BMC Genomics, 2018, 19(1): 26.
[31]	Sun MY, Zhang MY, Chen XN, et al. Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity [J]. BMC Biol, 2022, 20(1): 181.
[32]	Peng G, Wu JY, Lu WJ, et al. A polygalacturonase gene clustered into clade E involved in lychee fruitlet abscission [J]. Sci Hortic, 2013, 150: 244-250.
[33]	Paniagua C, Ric-Varas P, García-Gago JA, et al. Elucidating the role of polygalacturonase genes in strawberry fruit softening [J]. J Exp Bot, 2020, 71(22): 7103-7117.
[34]	Li WQ, Xu LA, Xia R, et al. Cloning and functional identification of SlPG49 in Solanum lycopersicum [J]. Appl Sci, 2021, 11(23): 11450.
[35]	Ohashi T, Sari N, Misaki R, et al. Biochemical characterization of Arabidopsis clade F polygalacturonase shows a substrate preference toward oligogalacturonic acids [J]. J Biosci Bioeng, 2022, 133(1): 1-7.
[36]	Önder S, Tonguç M, Önder D, et al. Dynamic changes occur in the cell wall composition and related enzyme activities during flower development in Rosa damascena [J]. Front Plant Sci, 2023, 14: 1120098.
[37]	Qian M, Xu Z, Zhang ZH, et al. The downregulation of PpPG21 and PpPG22 influences peach fruit texture and softening [J]. Planta, 2021, 254(2): 22.
[38]	Deytieux-Belleau C, Vallet A, Donèche B, et al. Pectin methylesterase and polygalacturonase in the developing grape skin [J]. Plant Physiol Biochem, 2008, 46(7): 638-646.
[39]	Wang ZY, MacRae EA, Wright MA, et al. Polygalacturonase gene expression in kiwifruit: relationship to fruit softening and ethylene production [J]. Plant Mol Biol, 2000, 42(2): 317-328.
[40]	Liu YZ, Dong T, Lei Y, et al. Isolation of a polygalacturonase gene from Citrus sinensis fruit and its expression relative to fruit mastication trait, fruit development, and calcium or boron treatments [J]. Plant Mol Biol Report, 2011, 29(1): 51-59.
[41]	Shi YN, Li BJ, Grierson D, et al. Insights into cell wall changes during fruit softening from transgenic and naturally occurring mutants [J]. Plant Physiol, 2023, 192(3): 1671-1683.
[42]	Peng ZZ, Liu GS, Li HL, et al. Molecular and genetic events determining the softening of fleshy fruits: a comprehensive review [J]. Int J Mol Sci, 2022, 23(20): 12482.
[43]	邵远志, 高毫杰, 贾志伟, 等. 1-MCP和乙烯利处理对番木瓜果实软化生理的影响 [J]. 中国食品学报, 2013, 13(2): 143-148.
	Shao YZ, Gao HJ, Jia ZW, et al. The effects of 1-MCP and ethephon on softening physiology of Papaya fruit [J]. J Chin Inst Food Sci Technol, 2013, 13(2): 143-148.

引物名称 Gene name	引物序列 Primer sequence （5′‒3′）
CpPG1-F	AATGGTGGTGCGTATAGATGGAAC
CpPG1-R	GGGAGTTGAGAAACCCGATTGAC
CpPG2-F	CACCCTTCATTTCTCAGCTCCATT
CpPG2-R	TTTCTCCCAAGCCTCCTCAAATAC
CpPG28-F	ACCATTGACGGACAAGGCTCTAT
CpPG28-R	TCAGACAAGGTGAACTCGACAAGA
OE-CpPG1-F	CCAAATCGACTCTAGTCTAGAATGACGACAATCCGCTCTCACAAC
OE-CpPG1-R	GCTCACCATCTGCAGAAGCTTCAAGCAACTATTGGGCTGAACCG
OE-CpPG2-F	CCAAATCGACTCTAGTCTAGAATGGCTGTTCTATATTATGATAATTATAATCGTACCC
OE-CpPG2-R	GCTCACCATCTGCAGAAGCTTCCAGATTATCATCTTAAACATGACGAGCTT
OE-CpPG28-F	CCAAATCGACTCTAGTCTAGAATGAAGATGCCAGTAGCATTTTTCTTGC
OE-CpPG28-R	GCTCACCATCTGCAGAAGCTTTACCGGGACAGCCACAGTTTCA
EIF4A-F	AGGCAGGCAAGAGAAGAT
EIF4A-R	TTCATACCGAGTAGCGATTC

引物名称 Gene name	引物序列 Primer sequence （5′‒3′）
CpPG1-F	AATGGTGGTGCGTATAGATGGAAC
CpPG1-R	GGGAGTTGAGAAACCCGATTGAC
CpPG2-F	CACCCTTCATTTCTCAGCTCCATT
CpPG2-R	TTTCTCCCAAGCCTCCTCAAATAC
CpPG28-F	ACCATTGACGGACAAGGCTCTAT
CpPG28-R	TCAGACAAGGTGAACTCGACAAGA
OE-CpPG1-F	CCAAATCGACTCTAGTCTAGAATGACGACAATCCGCTCTCACAAC
OE-CpPG1-R	GCTCACCATCTGCAGAAGCTTCAAGCAACTATTGGGCTGAACCG
OE-CpPG2-F	CCAAATCGACTCTAGTCTAGAATGGCTGTTCTATATTATGATAATTATAATCGTACCC
OE-CpPG2-R	GCTCACCATCTGCAGAAGCTTCCAGATTATCATCTTAAACATGACGAGCTT
OE-CpPG28-F	CCAAATCGACTCTAGTCTAGAATGAAGATGCCAGTAGCATTTTTCTTGC
OE-CpPG28-R	GCTCACCATCTGCAGAAGCTTTACCGGGACAGCCACAGTTTCA
EIF4A-F	AGGCAGGCAAGAGAAGAT
EIF4A-R	TTCATACCGAGTAGCGATTC

基因名称	基因号	氨基酸数	分子量	等电点	不稳定指数	脂肪系数	亲疏水性	信号肽
Gene name	Gene ID	Number of amino acids （aa）	Molecular weight （kD）	pI	Instability index	Aliphatic index	Hydropathicity index	Signal peptide
CpPG1	Cp_zihui11610	359	38.0	9.24	31.42	85.46	-0.060	+
CpPG2	Cp_zihui13876	437	48.2	5.69	34.70	77.12	-0.509	-
CpPG3	Cp_zihui12587	428	47.2	8.75	28.24	79.88	-0.373	+
CpPG4	Cp_zihui01876	390	42.2	8.63	44.78	87.95	-0.046	+
CpPG5	Cp_zihui19603	482	52.9	8.34	41.88	86.72	-0.111	-
CpPG6	Cp_zihui08791	447	48.7	7.57	36.53	89.80	-0.009	+
CpPG7	Cp_zihui00474	401	43.2	7.41	26.91	86.28	-0.026	+
CpPG8	Cp_zihui00470	278	30.7	8.94	28.18	79.93	-0.251	-
CpPG9	Cp_zihui00483	461	50.0	8.34	33.67	81.58	-0.211	-
CpPG10	Cp_zihui02232	458	49.0	6.30	44.43	77.86	-0.171	+
CpPG11	Cp_zihui06380	262	29.1	5.77	58.76	84.43	-0.274	-
CpPG12	Cp_zihui07099	432	45.8	5.35	45.09	77.59	-0.076	+
CpPG13	Cp_zihui08226	374	40.8	8.64	33.01	85.78	-0.102	+
CpPG14	Cp_zihui08889	488	53.6	5.38	35.37	90.20	-0.143	+
CpPG15	Cp_zihui09177	481	52.4	8.34	34.35	88.90	-0.025	+
CpPG16	Cp_zihui10261	349	37.8	7.89	35.97	86.07	-0.200	-
CpPG17	Cp_zihui10262	371	40.4	8.71	30.26	84.88	-0.188	-
CpPG18	Cp_zihui10270	335	35.8	6.72	45.96	94.84	-0.067	+
CpPG19	Cp_zihui10273	431	47.5	8.55	44.22	88.19	-0.016	+
CpPG20	Cp_zihui10665	475	51.6	5.48	50.72	83.28	-0.080	-
CpPG21	Cp_zihui10984	498	54.8	5.12	37.87	89.22	-0.144	-
CpPG22	Cp_zihui11565	530	58.3	5.71	31.68	87.19	0.085	-
CpPG23	Cp_zihui11577	425	45.4	6.78	29.06	84.24	-0.052	+
CpPG24	Cp_zihui11602	356	37.6	9.6	28.92	87.36	0.043	+
CpPG25	Cp_zihui11601	393	42.0	9.68	36.76	80.87	-0.097	+
CpPG26	Cp_zihui11608	395	43.1	7.58	38.66	84.89	-0.072	+
CpPG27	Cp_zihui11609	403	42.8	5.40	38.28	80.77	-0.082	+
CpPG28	Cp_zihui11883	457	49.6	5.59	48.03	90.83	-0.042	+
CpPG29	Cp_zihui12006	494	53.1	4.80	53.12	73.00	-0.252	+
CpPG30	Cp_zihui13178	477	52.2	5.35	33.45	85.97	-0.203	+
CpPG31	Cp_zihui13181	454	49.9	8.72	43.42	88.41	-0.148	+
CpPG32	Cp_zihui13193	499	54.3	5.20	34.53	81.42	-0.164	+
CpPG33	Cp_zihui14064	477	52.8	6.71	44.22	88.68	-0.208	-
CpPG34	Cp_zihui14065	429	46.3	5.38	42.46	91.17	-0.078	+
CpPG35	Cp_zihui16353	240	27.3	6.11	29.48	116.88	0.202	+
CpPG36	Cp_zihui16358	277	30.2	7.21	42.86	92.82	-0.201	-
CpPG37	Cp_zihui16904	536	60.3	8.70	44.09	87.95	-0.238	-
CpPG38	Cp_zihui19689	415	45.0	4.61	39.69	77.49	-0.295	+

基因名称	基因号	氨基酸数	分子量	等电点	不稳定指数	脂肪系数	亲疏水性	信号肽
Gene name	Gene ID	Number of amino acids （aa）	Molecular weight （kD）	pI	Instability index	Aliphatic index	Hydropathicity index	Signal peptide
CpPG1	Cp_zihui11610	359	38.0	9.24	31.42	85.46	-0.060	+
CpPG2	Cp_zihui13876	437	48.2	5.69	34.70	77.12	-0.509	-
CpPG3	Cp_zihui12587	428	47.2	8.75	28.24	79.88	-0.373	+
CpPG4	Cp_zihui01876	390	42.2	8.63	44.78	87.95	-0.046	+
CpPG5	Cp_zihui19603	482	52.9	8.34	41.88	86.72	-0.111	-
CpPG6	Cp_zihui08791	447	48.7	7.57	36.53	89.80	-0.009	+
CpPG7	Cp_zihui00474	401	43.2	7.41	26.91	86.28	-0.026	+
CpPG8	Cp_zihui00470	278	30.7	8.94	28.18	79.93	-0.251	-
CpPG9	Cp_zihui00483	461	50.0	8.34	33.67	81.58	-0.211	-
CpPG10	Cp_zihui02232	458	49.0	6.30	44.43	77.86	-0.171	+
CpPG11	Cp_zihui06380	262	29.1	5.77	58.76	84.43	-0.274	-
CpPG12	Cp_zihui07099	432	45.8	5.35	45.09	77.59	-0.076	+
CpPG13	Cp_zihui08226	374	40.8	8.64	33.01	85.78	-0.102	+
CpPG14	Cp_zihui08889	488	53.6	5.38	35.37	90.20	-0.143	+
CpPG15	Cp_zihui09177	481	52.4	8.34	34.35	88.90	-0.025	+
CpPG16	Cp_zihui10261	349	37.8	7.89	35.97	86.07	-0.200	-
CpPG17	Cp_zihui10262	371	40.4	8.71	30.26	84.88	-0.188	-
CpPG18	Cp_zihui10270	335	35.8	6.72	45.96	94.84	-0.067	+
CpPG19	Cp_zihui10273	431	47.5	8.55	44.22	88.19	-0.016	+
CpPG20	Cp_zihui10665	475	51.6	5.48	50.72	83.28	-0.080	-
CpPG21	Cp_zihui10984	498	54.8	5.12	37.87	89.22	-0.144	-
CpPG22	Cp_zihui11565	530	58.3	5.71	31.68	87.19	0.085	-
CpPG23	Cp_zihui11577	425	45.4	6.78	29.06	84.24	-0.052	+
CpPG24	Cp_zihui11602	356	37.6	9.6	28.92	87.36	0.043	+
CpPG25	Cp_zihui11601	393	42.0	9.68	36.76	80.87	-0.097	+
CpPG26	Cp_zihui11608	395	43.1	7.58	38.66	84.89	-0.072	+
CpPG27	Cp_zihui11609	403	42.8	5.40	38.28	80.77	-0.082	+
CpPG28	Cp_zihui11883	457	49.6	5.59	48.03	90.83	-0.042	+
CpPG29	Cp_zihui12006	494	53.1	4.80	53.12	73.00	-0.252	+
CpPG30	Cp_zihui13178	477	52.2	5.35	33.45	85.97	-0.203	+
CpPG31	Cp_zihui13181	454	49.9	8.72	43.42	88.41	-0.148	+
CpPG32	Cp_zihui13193	499	54.3	5.20	34.53	81.42	-0.164	+
CpPG33	Cp_zihui14064	477	52.8	6.71	44.22	88.68	-0.208	-
CpPG34	Cp_zihui14065	429	46.3	5.38	42.46	91.17	-0.078	+
CpPG35	Cp_zihui16353	240	27.3	6.11	29.48	116.88	0.202	+
CpPG36	Cp_zihui16358	277	30.2	7.21	42.86	92.82	-0.201	-
CpPG37	Cp_zihui16904	536	60.3	8.70	44.09	87.95	-0.238	-
CpPG38	Cp_zihui19689	415	45.0	4.61	39.69	77.49	-0.295	+