Genome-Wide Identification and Expression Analysis of CCO Gene Family in Dendrobium officinale During Flower Development

doi:10.16420/j.issn.0513-353x.2023-0566

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (9): 2075-2088.doi: 10.16420/j.issn.0513-353x.2023-0566

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

Genome-Wide Identification and Expression Analysis of CCO Gene Family in Dendrobium officinale During Flower Development

ZHAO Jiaying¹, ZENG Zhouting¹, CEN Xinying¹, SHI Jiaoqi¹, LI Xiaoxian¹, SHEN Xiaoxia¹, YU Zhenming¹^,²^,^*()

¹ School of Pharmaceutical Sciences，Zhejiang Chinese Medical University，Hangzhou 311402，China
² Academy of Chinese Medical Sciences，Zhejiang Chinese Medical University，Hangzhou 310053，China

Received:2024-06-06 Revised:2024-08-22 Online:2024-09-25 Published:2024-09-19
Contact: YU Zhenming

Abstract

Abstract:

To investigate the functions of carotenoid cleavage oxygenase（CCO）gene family in Dendrobium officinale Kimura et Migo，bioinformatics methods were employed to identify the CCO family members in D. officinale. Simultaneously，their expression levels in different tissues，different stages of flower development，and after the application of methyl jasmonate（MeJA）. The results revealed that a total of 12 CCO family members were excavated，with ten belonging to the carotenoid cleavage dioxygenase（CCD）subfamily and two belonging to the 9-cis-epoxycarotenoid dioxygenase（NCED）subfamily. They were unevenly distributed on 7 chromosomes，and harbored tandem duplications. The promoter regions of these DoCCO genes contained numerous hormone and stress response elements. The expression of DoCCO genes varied across different tissues of D. officinale，with higher expression observed in pollen and roots. They were differentially expressed during flower development and in response to MeJA treatment，suggesting that their potential roles in growth，development and the MeJA response. Specifically，DoCCD1b，may play a crucial role during flower development.

Key words: Dendrobium officinale, carotenoid cleavage oxygenase, gene family, flower development, expression analysis

ZHAO Jiaying, ZENG Zhouting, CEN Xinying, SHI Jiaoqi, LI Xiaoxian, SHEN Xiaoxia, YU Zhenming. Genome-Wide Identification and Expression Analysis of CCO Gene Family in Dendrobium officinale During Flower Development[J]. Acta Horticulturae Sinica, 2024, 51(9): 2075-2088.

Figures/Tables 11

References 30

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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
EF-1α	GCTTGAGAAGGAGCCCAAGT	CCAACAGCCACAGTTTGTCG
DoCCD1a	CCGACGGAGCTAGCAATTTAT	CTGTTTCCTGCCAGTGTAGTT
DoCCD1b	GCACAATCCAGTGCCAATAAC	CCATTTCCTTTGGTCGGAAATAC
DoCCD4	CCTCAGACGAAGCCTCAATATC	GTGTGGTGGGTCGATGAAA
DoCCD7a	CCGGCCAAAGAAACAAGTTC	GTTGACCTTCACCACAGAGT
DoCCD7b	CCATTGGCCTCACAGACATTA	CTTAGTGATTCCGGCGATGAA
DoCCD7c	GAGCACCGGGTTTGAAATTG	GCCAATAACGTCGGCTCTAA
DoCCD7d	CTTGTGCTCCATTGTTGATTCC	GAAGTCGAGCTAGCGTACATAAA
DoCCD8a	GCTCCAACTACAGGGAGAAATC	AAAGGTGGCGGAAATAGTAGTC
DoCCD8b	ATGCCGCTGGAGATAGATTTG	TCTTGGGATGAGCCATGAAAG
DoCCD8c	CGATCCTTCCTCTCTTGGATTT	CGGAGTGAATGGAATGAGTTTG
DoNCED1	CGATACGCCTACCTTGCAATAG	CGAATTTCCCTTTCCCGTACTC
DoNCED2	CTCCAGGCCATTCAATCTCATC	GGACGGAATTAGGAGTGGTAGA

引物名称 Primer name	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
EF-1α	GCTTGAGAAGGAGCCCAAGT	CCAACAGCCACAGTTTGTCG
DoCCD1a	CCGACGGAGCTAGCAATTTAT	CTGTTTCCTGCCAGTGTAGTT
DoCCD1b	GCACAATCCAGTGCCAATAAC	CCATTTCCTTTGGTCGGAAATAC
DoCCD4	CCTCAGACGAAGCCTCAATATC	GTGTGGTGGGTCGATGAAA
DoCCD7a	CCGGCCAAAGAAACAAGTTC	GTTGACCTTCACCACAGAGT
DoCCD7b	CCATTGGCCTCACAGACATTA	CTTAGTGATTCCGGCGATGAA
DoCCD7c	GAGCACCGGGTTTGAAATTG	GCCAATAACGTCGGCTCTAA
DoCCD7d	CTTGTGCTCCATTGTTGATTCC	GAAGTCGAGCTAGCGTACATAAA
DoCCD8a	GCTCCAACTACAGGGAGAAATC	AAAGGTGGCGGAAATAGTAGTC
DoCCD8b	ATGCCGCTGGAGATAGATTTG	TCTTGGGATGAGCCATGAAAG
DoCCD8c	CGATCCTTCCTCTCTTGGATTT	CGGAGTGAATGGAATGAGTTTG
DoNCED1	CGATACGCCTACCTTGCAATAG	CGAATTTCCCTTTCCCGTACTC
DoNCED2	CTCCAGGCCATTCAATCTCATC	GGACGGAATTAGGAGTGGTAGA

基因ID Gene ID	氨基酸数 Number of amino acid	分子量/kD Molecular weight	等电点 pI	不稳定系数 Instability index	脂肪系数 Aliphatic index	总平均亲水系数 Grand average of hydropathicity	RPE65保守域 RPE65 domain	亚细胞定位 Subcellular localization
DoCCD1a	512	57.63	9.12	30.53	89.30	0	1 ~ 319	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD1b	501	56.47	9.19	35.52	83.05	-0.278	17 ~ 384	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD4	633	68.58	6.30	45.29	81.39	-0.163	148 ~ 622	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD7a	194	21.94	9.25	51.25	68.81	-0.236	26 ~ 167	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD7b	261	28.58	7.72	41.14	96.82	0.153	66 ~ 216	叶绿体 Chloroplast
DoCCD7c	600	67.57	6.65	37.66	79.65	-0.218	65 ~ 597	细胞质 Cytoplasm
DoCCD7d	296	33.84	8.10	50.41	85.30	-0.136	112 ~ 222	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD8a	769	85.68	5.05	42.49	80.01	-0.332	298 ~ 764	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD8b	559	61.50	6.04	36.29	87.73	-0.110	88 ~ 394；424 ~ 554	细胞质 Cytoplasm
DoCCD8c	333	37.94	6.42	48.06	67.39	-0.425	195 ~ 281	叶绿体、细胞质、细胞核Chloroplast，cytoplasm，nucleus
DoNCED1	592	65.40	5.98	42.95	79.71	-0.279	121 ~ 584	细胞质 Cytoplasm
DoNCED2	610	67.31	6.27	50.40	79.26	-0.300	137 ~ 600	细胞质 Cytoplasm

基因ID Gene ID	氨基酸数 Number of amino acid	分子量/kD Molecular weight	等电点 pI	不稳定系数 Instability index	脂肪系数 Aliphatic index	总平均亲水系数 Grand average of hydropathicity	RPE65保守域 RPE65 domain	亚细胞定位 Subcellular localization
DoCCD1a	512	57.63	9.12	30.53	89.30	0	1 ~ 319	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD1b	501	56.47	9.19	35.52	83.05	-0.278	17 ~ 384	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD4	633	68.58	6.30	45.29	81.39	-0.163	148 ~ 622	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD7a	194	21.94	9.25	51.25	68.81	-0.236	26 ~ 167	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD7b	261	28.58	7.72	41.14	96.82	0.153	66 ~ 216	叶绿体 Chloroplast
DoCCD7c	600	67.57	6.65	37.66	79.65	-0.218	65 ~ 597	细胞质 Cytoplasm
DoCCD7d	296	33.84	8.10	50.41	85.30	-0.136	112 ~ 222	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD8a	769	85.68	5.05	42.49	80.01	-0.332	298 ~ 764	叶绿体、细胞质 Chloroplast，cytoplasm
DoCCD8b	559	61.50	6.04	36.29	87.73	-0.110	88 ~ 394；424 ~ 554	细胞质 Cytoplasm
DoCCD8c	333	37.94	6.42	48.06	67.39	-0.425	195 ~ 281	叶绿体、细胞质、细胞核Chloroplast，cytoplasm，nucleus
DoNCED1	592	65.40	5.98	42.95	79.71	-0.279	121 ~ 584	细胞质 Cytoplasm
DoNCED2	610	67.31	6.27	50.40	79.26	-0.300	137 ~ 600	细胞质 Cytoplasm

Genome-Wide Identification and Expression Analysis of CCO Gene Family in Dendrobium officinale During Flower Development

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