Identification and Phylogenetic Analysis of Gibberellin Oxidase Gene Family and Its Expression Pattern in Main Vine Growth in Cucurbita maxima

doi:10.16420/j.issn.0513-353x.2023-0974

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (3): 603-622.doi: 10.16420/j.issn.0513-353x.2023-0974

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Identification and Phylogenetic Analysis of Gibberellin Oxidase Gene Family and Its Expression Pattern in Main Vine Growth in Cucurbita maxima

SUN Tingzhen¹, SHU Qin¹, MA Wei¹, SHI Yuzi¹, ZHANG Meng¹, XIANG Chenggang², BO Kailiang¹, DUAN Ying¹^,^*(), WANG Changlin¹^,^*()

¹ State Key Laboratory of Vegetable Biobreeding，Institute of Vegetables and Flowers，Chinese Academy of Agricultural Sciences，Beijing 100081，China
² College of Biological & Agricultural Sciences，Honghe University，Mengzi，Yunnan 661100，China

Received:2024-10-10 Revised:2025-01-09 Online:2025-03-25 Published:2025-03-25
Contact: DUAN Ying, WANG Changlin

Abstract

Abstract:

GA2ox，GA3ox，and GA20ox are pivotal enzymes in the late stage of gibberellin synthesis，playing crucial roles in regulating plant stem elongation. In this study，the GA2ox，GA3ox，and GA20ox gene family were identified utilizing reference genomic data from Cucurbita maxima. Their physicochemical properties，gene structure，chromosome localization，phylogeny，and genomic collinearity with near-origin species were analyzed. Additionally，tissue-specific expression levels of GA2ox genes were investigated in Cucurbita maxima with varying main vine lengths. A total of 13 GA2ox，9 GA3ox，and 12 GA20ox genes were identified in the Cucurbita maxima genome. Phylogenetic analysis based on multiple amino acid sequence alignments showed these gibberellin oxidase gene family forming four major clustered branches. Promoter analysis identified numerous light-responsive，adversity stress-responsive，and hormone-responsive elements. Intragenomic analysis of GAox genes in Cucurbita maxima revealed 9 pairs of tandem duplicated genes and 10 pairs of large replicating genes. Only one gene pair（CmaGA3ox5 and CmaGA3ox6）exhibited positive selection（K_a/K_s > 1），while the rest underwent purifying selection. Genome collinearity analysis with near-origin species Cucurbita pepo and Cucurbita moschata unveiled 47 and 48 pairs of collinearity genes，respectively，between Cucurbita maxima，Cucurbita pepo，and Cucurbita moschata. CmaGAox genes were more specifically expressed in fruit，but CmaGA2ox1 and CmaGA2ox4 were more highly expressed in the main stem. The expression patterns of these two genes were significantly higher in the dwarf inbred line Cma0806 than that in the long vine inbred line Cma0807，indicates their potential roles in vine length regulation in Cucurbita maxima.

Key words: Cucurbita maxima, gibberellin oxidase, gene family, evolution analysis, main vine length, gene expression analysis

SUN Tingzhen, SHU Qin, MA Wei, SHI Yuzi, ZHANG Meng, XIANG Chenggang, BO Kailiang, DUAN Ying, WANG Changlin. Identification and Phylogenetic Analysis of Gibberellin Oxidase Gene Family and Its Expression Pattern in Main Vine Growth in Cucurbita maxima[J]. Acta Horticulturae Sinica, 2025, 52(3): 603-622.

Figures/Tables 14

References 48

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引物名称 Primer name	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
CmaGA2ox1	GGCGATAAGGGCTGGATCGAATATCTC	ACCACTTCGCCGCTCAATTTCTTC
CmaGA2ox2	CTACAGGCTTGGAGCAACGA	GGCAACTCCCGATTCCAGAA
CmaGA2ox3	TGGCGTTCCCATGGAA TTCA	TATTCAACCCAGCCCACGTC
CmaGA2ox4	AGCACGGAATTGGGGTTTCT	CACCGGTAAGTTCCACCCAA
CmaGA2ox5	TGAAGAAGCTGAGCTGCGAA	AGCTTGGAGTTCCGGACATG
CmaGA2ox6	GTTGTGGACACCTGTTTGCC	ATTCAATGGTGGTGCCCCAA
CmaGA2ox7	TCCCGAGATTTTCCGGTGTG	ACAGCCTACTCAATGCGCTT
CmaGA2ox8	ACAGCCGTTTGAGCGTAAGA	ATCATCGGAGCCGTTGGA TC
CmaGA2ox9	ATGGCTGAGGGGTTAGGGAT	ACCCAAGCTTATTGGAGGGC
CmaGA2ox10	AAAACAGAGAGCTGGCCCTC	ATGGAGAGGAACCCATCGGA
CmaGA2ox11	TGGCTGGAACTTACCGATGG	GTGGGTCTGAGGGTGACATG
CmaGA2ox12	TTTGGGGAGCATTCTGACCC	ACGTAGAATGCAGACGGGTC
CmaGA2ox13	CCAGCCGACCCATTTGGATA	TCCACCGCACACCTGAAAAT
CmaGA20ox1	GTGTTCGTCGACAACCAATGGAGAC	TCTGAGTGAACCGGAGGAGCATC
CmaGA20ox2	CGACCCAACATCCCTCACCATTCT	ATCAGGGTACTGTCTTGGCCCTT
CmaGA20ox5	GTAGACAACCAATGGCGTCTCATTGC	ATGTCAGCTCTGTAATGGTTGAGAGTG
CmaGA20ox10	GGCTTTCAAGTGTGCGTCGATGATC	TCAAGCAACGTTCCCCATGTGTAATC
CmaGA20ox12	CATCGCATGACAAAGTGGTGAGAGC	ATGGCAAGATCTCGGAAACTGGGTTC
CmaGA3ox1	GATCCTCCGCAGAACATGCTTCTCA	TGCTGCTTTGGTGGAGGATTGTC
CmaGA3ox4	GATTCAACGTCATAGGTTCTCCGGTTG	GTGTCTGGTGAAGCATGGTGAAGA
CmEF1a	ACGGTGATGCTGGTATGGTTA	CATTGTTGTTGGTTGGCTTATT

引物名称 Primer name	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
CmaGA2ox1	GGCGATAAGGGCTGGATCGAATATCTC	ACCACTTCGCCGCTCAATTTCTTC
CmaGA2ox2	CTACAGGCTTGGAGCAACGA	GGCAACTCCCGATTCCAGAA
CmaGA2ox3	TGGCGTTCCCATGGAA TTCA	TATTCAACCCAGCCCACGTC
CmaGA2ox4	AGCACGGAATTGGGGTTTCT	CACCGGTAAGTTCCACCCAA
CmaGA2ox5	TGAAGAAGCTGAGCTGCGAA	AGCTTGGAGTTCCGGACATG
CmaGA2ox6	GTTGTGGACACCTGTTTGCC	ATTCAATGGTGGTGCCCCAA
CmaGA2ox7	TCCCGAGATTTTCCGGTGTG	ACAGCCTACTCAATGCGCTT
CmaGA2ox8	ACAGCCGTTTGAGCGTAAGA	ATCATCGGAGCCGTTGGA TC
CmaGA2ox9	ATGGCTGAGGGGTTAGGGAT	ACCCAAGCTTATTGGAGGGC
CmaGA2ox10	AAAACAGAGAGCTGGCCCTC	ATGGAGAGGAACCCATCGGA
CmaGA2ox11	TGGCTGGAACTTACCGATGG	GTGGGTCTGAGGGTGACATG
CmaGA2ox12	TTTGGGGAGCATTCTGACCC	ACGTAGAATGCAGACGGGTC
CmaGA2ox13	CCAGCCGACCCATTTGGATA	TCCACCGCACACCTGAAAAT
CmaGA20ox1	GTGTTCGTCGACAACCAATGGAGAC	TCTGAGTGAACCGGAGGAGCATC
CmaGA20ox2	CGACCCAACATCCCTCACCATTCT	ATCAGGGTACTGTCTTGGCCCTT
CmaGA20ox5	GTAGACAACCAATGGCGTCTCATTGC	ATGTCAGCTCTGTAATGGTTGAGAGTG
CmaGA20ox10	GGCTTTCAAGTGTGCGTCGATGATC	TCAAGCAACGTTCCCCATGTGTAATC
CmaGA20ox12	CATCGCATGACAAAGTGGTGAGAGC	ATGGCAAGATCTCGGAAACTGGGTTC
CmaGA3ox1	GATCCTCCGCAGAACATGCTTCTCA	TGCTGCTTTGGTGGAGGATTGTC
CmaGA3ox4	GATTCAACGTCATAGGTTCTCCGGTTG	GTGTCTGGTGAAGCATGGTGAAGA
CmEF1a	ACGGTGATGCTGGTATGGTTA	CATTGTTGTTGGTTGGCTTATT

基因名称 Gene name	基因ID Gene ID	位置 Location	氨基酸长 Number of amino acids	正负链 Strand	等电点 pI	分子量/kD Molecular weight	疏水性 Hydro- phobicity	亚细胞定位 Subcellular localization
CmaGA20ox1	CmaCh02G010210	6058004 ~ 6060196	378	-	6.17	43.18	-0.42	Mb
CmaGA20ox2	CmaCh03G011090	7574527 ~ 7576330	364	-	7.10	41.07	-0.31	Mb
CmaGA20ox3	CmaCh07G008110	3735328 ~ 3737605	369	-	6.57	42.00	-0.41	Mb
CmaGA20ox4	CmaCh15G006420	3035007 ~ 3036820	351	+	6.73	39.48	-0.20	Mb
CmaGA20ox5	CmaCh15G013930	8764141 ~ 8766571	361	-	5.85	40.96	-0.28	Mb
CmaGA20ox6	CmaCh16G001620	703878 ~ 705410	386	-	6.25	44.19	-0.43	Nu
CmaGA20ox7	CmaCh17G000020	9087 ~ 10692	336	+	5.45	38.17	-0.36	Mb
CmaGA20ox8	CmaCh18G012060	9561682 ~ 9563098	385	+	5.36	43.50	-0.32	Chl
CmaGA20ox9	CmaCh18G012070	9565859 ~ 9567931	295	+	6.12	33.49	-0.43	Chl
CmaGA20ox10	CmaCh18G012080	9570626 ~ 9572255	384	+	5.33	43.27	-0.42	Cy
CmaGA20ox11	CmaCh18G012090	9574376 ~ 9575714	386	+	5.47	43.32	-0.39	Cy
CmaGA20ox12	CmaCh18G012100	9579614 ~ 9583282	427	+	5.82	48.00	-0.31	Cy
CmaGA3ox1	CmaCh05G006480	3289026 ~ 3290688	370	+	6.75	41.32	-0.10	Er
CmaGA3ox2	CmaCh05G006490	3293066 ~ 3294672	367	+	6.03	41.37	-0.13	Cy
CmaGA3ox3	CmaCh05G006500	3297430 ~ 3298596	346	+	6.67	38.94	-0.20	Mb
CmaGA3ox4	CmaCh05G006510	3304268 ~ 3307142	383	+	6.13	43.31	-0.19	Cy
CmaGA3ox5	CmaCh05G006520	3320084 ~ 3321250	344	+	6.50	38.77	-0.21	Cy
CmaGA3ox6	CmaCh05G006530	3325577 ~ 3326736	348	+	6.22	39.53	-0.22	Cy
CmaGA3ox7	CmaCh08G006320	3573502 ~ 3574908	377	+	6.62	41.73	-0.21	Mb
CmaGA3ox8	CmaCh12G003100	1581698 ~ 1584654	348	+	5.72	39.17	-0.23	Cy
CmaGA3ox9	CmaCh17G008310	6527065 ~ 6528927	342	+	7.27	38.55	-0.26	Mb
CmaGA2ox1	CmaCh03G013990	8817543 ~ 8818816	331	+	6.27	36.85	-0.31	Cy
CmaGA2ox2	CmaCh04G000330	191407 ~ 194668	374	-	6.70	41.93	-0.30	Cy
CmaGA2ox3	CmaCh04G006490	3321297 ~ 3322998	340	-	8.31	37.75	-0.20	Chl
CmaGA2ox4	CmaCh04G009310	4804076 ~ 4807014	360	+	5.70	41.35	-0.31	Cy
CmaGA2ox5	CmaCh07G001050	581638 ~ 582804	332	-	5.76	36.82	-0.21	Mit
CmaGA2ox6	CmaCh08G004850	2762847 ~ 2764115	331	+	8.75	36.59	-0.22	Mb
CmaGA2ox7	CmaCh13G005360	5582531 ~ 5584247	336	-	5.96	37.73	-0.16	Cy
CmaGA2ox8	CmaCh13G007180	6423868 ~ 6426404	341	-	5.96	38.51	-0.28	Mb
CmaGA2ox9	CmaCh14G009480	4909702 ~ 4911273	335	+	5.89	37.09	-0.10	Chl
CmaGA2ox10	CmaCh16G004530	2269857 ~ 2271606	327	+	7.02	36.21	-0.23	Chl
CmaGA2ox11	CmaCh16G008420	4911602 ~ 4915537	349	+	6.07	40.10	-0.44	Cy
CmaGA2ox12	CmaCh17G010160	7383663 ~ 7385904	329	-	8.70	36.45	-0.26	Mb
CmaGA2ox13	CmaCh18G004710	2653034 ~ 2655073	336	+	6.14	37.85	-0.20	Cy

基因名称 Gene name	基因ID Gene ID	位置 Location	氨基酸长 Number of amino acids	正负链 Strand	等电点 pI	分子量/kD Molecular weight	疏水性 Hydro- phobicity	亚细胞定位 Subcellular localization
CmaGA20ox1	CmaCh02G010210	6058004 ~ 6060196	378	-	6.17	43.18	-0.42	Mb
CmaGA20ox2	CmaCh03G011090	7574527 ~ 7576330	364	-	7.10	41.07	-0.31	Mb
CmaGA20ox3	CmaCh07G008110	3735328 ~ 3737605	369	-	6.57	42.00	-0.41	Mb
CmaGA20ox4	CmaCh15G006420	3035007 ~ 3036820	351	+	6.73	39.48	-0.20	Mb
CmaGA20ox5	CmaCh15G013930	8764141 ~ 8766571	361	-	5.85	40.96	-0.28	Mb
CmaGA20ox6	CmaCh16G001620	703878 ~ 705410	386	-	6.25	44.19	-0.43	Nu
CmaGA20ox7	CmaCh17G000020	9087 ~ 10692	336	+	5.45	38.17	-0.36	Mb
CmaGA20ox8	CmaCh18G012060	9561682 ~ 9563098	385	+	5.36	43.50	-0.32	Chl
CmaGA20ox9	CmaCh18G012070	9565859 ~ 9567931	295	+	6.12	33.49	-0.43	Chl
CmaGA20ox10	CmaCh18G012080	9570626 ~ 9572255	384	+	5.33	43.27	-0.42	Cy
CmaGA20ox11	CmaCh18G012090	9574376 ~ 9575714	386	+	5.47	43.32	-0.39	Cy
CmaGA20ox12	CmaCh18G012100	9579614 ~ 9583282	427	+	5.82	48.00	-0.31	Cy
CmaGA3ox1	CmaCh05G006480	3289026 ~ 3290688	370	+	6.75	41.32	-0.10	Er
CmaGA3ox2	CmaCh05G006490	3293066 ~ 3294672	367	+	6.03	41.37	-0.13	Cy
CmaGA3ox3	CmaCh05G006500	3297430 ~ 3298596	346	+	6.67	38.94	-0.20	Mb
CmaGA3ox4	CmaCh05G006510	3304268 ~ 3307142	383	+	6.13	43.31	-0.19	Cy
CmaGA3ox5	CmaCh05G006520	3320084 ~ 3321250	344	+	6.50	38.77	-0.21	Cy
CmaGA3ox6	CmaCh05G006530	3325577 ~ 3326736	348	+	6.22	39.53	-0.22	Cy
CmaGA3ox7	CmaCh08G006320	3573502 ~ 3574908	377	+	6.62	41.73	-0.21	Mb
CmaGA3ox8	CmaCh12G003100	1581698 ~ 1584654	348	+	5.72	39.17	-0.23	Cy
CmaGA3ox9	CmaCh17G008310	6527065 ~ 6528927	342	+	7.27	38.55	-0.26	Mb
CmaGA2ox1	CmaCh03G013990	8817543 ~ 8818816	331	+	6.27	36.85	-0.31	Cy
CmaGA2ox2	CmaCh04G000330	191407 ~ 194668	374	-	6.70	41.93	-0.30	Cy
CmaGA2ox3	CmaCh04G006490	3321297 ~ 3322998	340	-	8.31	37.75	-0.20	Chl
CmaGA2ox4	CmaCh04G009310	4804076 ~ 4807014	360	+	5.70	41.35	-0.31	Cy
CmaGA2ox5	CmaCh07G001050	581638 ~ 582804	332	-	5.76	36.82	-0.21	Mit
CmaGA2ox6	CmaCh08G004850	2762847 ~ 2764115	331	+	8.75	36.59	-0.22	Mb
CmaGA2ox7	CmaCh13G005360	5582531 ~ 5584247	336	-	5.96	37.73	-0.16	Cy
CmaGA2ox8	CmaCh13G007180	6423868 ~ 6426404	341	-	5.96	38.51	-0.28	Mb
CmaGA2ox9	CmaCh14G009480	4909702 ~ 4911273	335	+	5.89	37.09	-0.10	Chl
CmaGA2ox10	CmaCh16G004530	2269857 ~ 2271606	327	+	7.02	36.21	-0.23	Chl
CmaGA2ox11	CmaCh16G008420	4911602 ~ 4915537	349	+	6.07	40.10	-0.44	Cy
CmaGA2ox12	CmaCh17G010160	7383663 ~ 7385904	329	-	8.70	36.45	-0.26	Mb
CmaGA2ox13	CmaCh18G004710	2653034 ~ 2655073	336	+	6.14	37.85	-0.20	Cy

串联复制基因对 Tandem duplication	K_a	K_s	K_a/K_s	纯化选择 Purifying selection	分化时间/Mya Divergence time
CmaGA20ox8/CmaGA20ox9	0.092	0.231	0.402	是 Yes	7.70
CmaGA20ox9/CmaGA20ox10	0.101	0.171	0.594	是 Yes	5.69
CmaGA20ox10/CmaGA20ox11	0.177	0.210	0.846	是 Yes	6.99
CmaGA20ox11/CmaGA20ox12	0.024	0.056	0.424	是 Yes	1.87
CmaGA3ox1/CmaGA3ox2	0.516	1.760	0.293	是 Yes	58.65
CmaGA3ox2/CmaGA3ox3	0.120	0.165	0.727	是 Yes	5.50
CmaGA3ox3/CmaGA3ox4	0.051	0.073	0.700	是 Yes	2.45
CmaGA3ox4/CmaGA3ox5	0.054	0.079	0.693	是 Yes	2.62
CmaGA3ox5/CmaGA3ox6	0.117	0.107	1.086	否 No	3.58

Identification and Phylogenetic Analysis of Gibberellin Oxidase Gene Family and Its Expression Pattern in Main Vine Growth in Cucurbita maxima

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References 48

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大片段复制基因对 Segmental duplication	K_a	K_s	K_a/K_s	纯化选择 Purifying selection	分化时间/Mya Divergence ime
CmaGA20ox1/CmaGA20ox5	0.085	0.553	0.154	是 Yes	18.45
CmaGA20ox2/CmaGA20ox3	0.082	0.872	0.094	是 Yes	29.08
CmaGA20ox6/CmaGA20ox8	0.185	0.462	0.400	是 Yes	15.40
CmaGA2ox1/CmaGA2ox13	0.262	1.876	0.140	是 Yes	62.54
CmaGA2ox1/CmaGA2ox6	0.515	NaN	NaN	否 No	—
CmaGA2ox6/CmaGA2ox13	0.448	2.994	0.149	是 Yes	99.80
CmaGA2ox3/CmaGA2ox10	0.047	0.533	0.089	是 Yes	17.77
CmaGA2ox4/CmaGA2ox11	0.116	0.416	0.280	是 Yes	13.87
CmaGA2ox12/CmaGA2ox5	0.538	NaN	NaN	否 No	—
CmaGA3ox1/CmaGA3ox8	0.429	1.563	0.274	是 Yes	52.10

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