Study on the Fragrance Metabolic Genes of Rosa odorata Based on Transcriptome Sequencing

doi:10.16420/j.issn.0513-353x.2020-0944

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (11): 2262-2274.doi: 10.16420/j.issn.0513-353x.2020-0944

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Study on the Fragrance Metabolic Genes of Rosa odorata Based on Transcriptome Sequencing

ZHUANG Yueying, ZHOU Lijun, CHENG Bixuan, YU Chao(), LUO Le, PAN Huitang, ZHANG Qixiang

School of Landscape Architecture,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding,National Engineering Research Center for Floriculture,Beijing Laboratory of Urban and Rural Ecological Environment,Engineering Research Center of Landscape Environment of Ministry of Education,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education,Beijing Forestry University,Beijing 100083,China

Received:2021-04-09 Revised:2021-08-06 Published:2021-12-02

Abstract

Abstract:

By using the technique of transcriptome sequencing,floral fragrance metabolic pathways and genes related to the unique floral fragrance of Rosa odorata var. gigantea and R. odorata var. odorata were investigated. The results showed that 8 339,8 849,and 7 572 differentially expressed genes were detected in these two plant species at the flower budding stage,early flowering stage,and blooming stage, including 3 762 differentially expressed genes that were detected in all three stages. Cluster analysis of GO and KEGG showed that the differentially expressed genes were mainly involved in the terms of metabolic process,cell process,single organism process,catalytic activity,and other biological processes. They were also largely enriched in the metabolic pathway,secondary metabolites biosynthesis,carbon metabolism,and other pathways. A total of 27 differentially expressed genes were predicted to be associated with six important floral fragrance biosynthesis pathways（terpenoid backbone biosynthesis,phenylpropanoid biosynthesis,fatty acid biosynthesis,monoterpenoid biosynthesis,diterpenoid biosynthesis,sesquiterpene,and triterpene biosynthesis）. The results showed that these 27 genes had a significant effect on the difference of floral fragrance emission between the two species,and the difference was consistent in the three stages. Furthermore,the expression of Rc_0128091 and Rc_0119291,which are the characteristic floral substance synthetase genes,were investigated. It was found that the expression of Rc_0128091 and Rc_0119291 in the transcriptional data was consistent with the emission of 3,5-dimethoxybenzene and 1,3,5-trimethoxybenzene,suggesting that they are decisive for the synthesis of the characteristic aroma compounds. By randomly selecting 10 differentially expressed genes,the correlation between qRT-PCR and RNA-seq results was verified. The highly correlated results indicate that the RNA-seq results are of high accuracy.

Key words: Rosa odorata, floral, RNA-Seq, differentially expression genes, metabolic pathway

CLC Number:

S685.12

ZHUANG Yueying, ZHOU Lijun, CHENG Bixuan, YU Chao, LUO Le, PAN Huitang, ZHANG Qixiang. Study on the Fragrance Metabolic Genes of Rosa odorata Based on Transcriptome Sequencing[J]. Acta Horticulturae Sinica, 2021, 48(11): 2262-2274.

Figures/Tables 12

References 28

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基因ID Gene ID	正向引物序列（5′-3′） Forward primer sequence	反向引物序列（5′-3′） Reverse primer sequence
GAPDH	ATCCATTCATCACCACCGACTACA	GCATCCTTACTTGGGGCAGAGA
Rc 0174951	TGGTTTCCCTAGGAGTCACG	GGAAGTGGTGCATAAGGGAT
Rc 0121071	AGAAAGGCCATCCATAGTGC	TTGGCCTTCTTGATTGTCTC
Rc 0059511	TGGATTTCAACCTGCTGCA	TCTCACGTCCAAGTCCTTCC
Rc 0412071	TGAAACTTGATTCAGGCAAGC	TTCTGGGGTGGAGGACCTT
Rc 0241141	ATGGCATTTAACACTGCTGGT	CGGCTCCTGCTTAAGAACCT
Rc 0083751	TCAGTGGCTATGTTGGTGGT	ACCAATCAGCCTAAAATGCC
Rc 0392511	CTCCTCCAGTCTGGCCAAAT	TGACATGTATGTTTTCCGCGT
Rc 0110711	ACTCAACATTCCTGCAACGA	AGCGGACAGGTAGTTTTTGA
Rc 0214071	CTGCTGGGGAAGAGAAGAGT	ATGGAGGACGAAACATTTGC

基因ID Gene ID	正向引物序列（5′-3′） Forward primer sequence	反向引物序列（5′-3′） Reverse primer sequence
GAPDH	ATCCATTCATCACCACCGACTACA	GCATCCTTACTTGGGGCAGAGA
Rc 0174951	TGGTTTCCCTAGGAGTCACG	GGAAGTGGTGCATAAGGGAT
Rc 0121071	AGAAAGGCCATCCATAGTGC	TTGGCCTTCTTGATTGTCTC
Rc 0059511	TGGATTTCAACCTGCTGCA	TCTCACGTCCAAGTCCTTCC
Rc 0412071	TGAAACTTGATTCAGGCAAGC	TTCTGGGGTGGAGGACCTT
Rc 0241141	ATGGCATTTAACACTGCTGGT	CGGCTCCTGCTTAAGAACCT
Rc 0083751	TCAGTGGCTATGTTGGTGGT	ACCAATCAGCCTAAAATGCC
Rc 0392511	CTCCTCCAGTCTGGCCAAAT	TGACATGTATGTTTTCCGCGT
Rc 0110711	ACTCAACATTCCTGCAACGA	AGCGGACAGGTAGTTTTTGA
Rc 0214071	CTGCTGGGGAAGAGAAGAGT	ATGGAGGACGAAACATTTGC

样本 Sample	原始测序数据 Raw reads	过滤后测序数据 Clean reads	未比对测序数据 Unmapped reads	Q20/%	Q30/%	GC/%
T1a	62 786 040	62 674 405	60 810 922	97.83	93.80	47.62
T1b	67 274 777	67 166 924	65 797 731	98.17	94.59	47.80
T1c	61 386 237	61 283 162	60 016 880	97.85	93.82	47.71
T2a	66 064 221	65 936 595	61 819 035	97.94	94.03	47.93
T2b	65 163 741	65 017 603	61 516 931	97.48	93.01	47.94
T2c	62 902 745	62 794 761	58 409 372	98.06	94.28	48.21

样本 Sample	原始测序数据 Raw reads	过滤后测序数据 Clean reads	未比对测序数据 Unmapped reads	Q20/%	Q30/%	GC/%
T1a	62 786 040	62 674 405	60 810 922	97.83	93.80	47.62
T1b	67 274 777	67 166 924	65 797 731	98.17	94.59	47.80
T1c	61 386 237	61 283 162	60 016 880	97.85	93.82	47.71
T2a	66 064 221	65 936 595	61 819 035	97.94	94.03	47.93
T2b	65 163 741	65 017 603	61 516 931	97.48	93.01	47.94
T2c	62 902 745	62 794 761	58 409 372	98.06	94.28	48.21

样本 Sample	0 ~ 0.1（%）	0.1 ~ 1（%）	1 ~ 10（%）	10 ~ 100（%）	100 ~ 1 000（%）	> 1 000（%）
T1a	12 189（30.59）	9 640（24.21）	10 392（26.08）	6 725（16.88）	847（2.13）	48（0.12）
T1b	12 998（32.62）	9 860（24.77）	9 968（25.02）	6 144（15.42）	806（2.02）	61（0.15）
T1c	13 637（34.22）	9 464（23.75）	9 652（24.22）	6 221（15.61）	811（2.04）	61（0.15）
T2a	13 724（34.44）	8 871（22.26）	9 473（23.77）	6 755（16.95）	964（2.42）	59（0.15）
T2b	15 133（37.98）	9 288（23.31）	8 889（22.31）	5 534（13.89）	937（2.35）	65（0.16）
T2c	14 104（35.40）	9 408（23.61）	9 433（23.67）	5 816（14.60）	1 023（2.57）	62（0.16）
平均Mean	13 631（34.21）	9 422（23.65）	9 635（24.18）	6 199（15.56）	898（2.26）	59（0.15）

Study on the Fragrance Metabolic Genes of Rosa odorata Based on Transcriptome Sequencing

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基因ID Gene ID	花蕾期 Flower budding stage				初开期Early flowering stage				盛开期Blooming stage
基因ID Gene ID	T1a- FPKM	T2a- FPKM	log₂ (FC)	FDR	T1b- FPKM	T2b- FPKM	log₂ (FC)	FDR	T1c- FPKM	T2c- FPKM	log₂ (FC)	FDR
Rc_0097351	0.9	33.1	5.1	5.2E-17	1.6	61.5	5.3	2.2E-68	0.9	61.0	6.1	3.1E-08
Rc_0096771	123.6	415.8	1.8	2.7E-11	141.0	453.8	1.7	3.6E-12	74.0	223.5	1.6	2.2E-03
Rc_0199551	30.1	91.2	1.6	2.4E-02	21.0	200.4	3.3	8.6E-13	17.1	360.2	4.4	3.7E-15
Rc_0131551	9.4	2.2	-2.1	4.2E-06	12.1	0.8	-3.9	3.1E-12	7.8	0.9	-3.2	1.0E-04
Rc_0014811	30.2	1.8	-4.1	1.1E-31	24.7	1.2	-4.4	3.5E-31	29.7	1.1	-4.8	3.3E-17
Rc_0110711	541.7	227.9	-1.2	8.0E-03	753.1	235.4	-1.7	7.1E-04	676.7	152.4	-2.2	6.1E-03
Rc_0026721	0.1	32.0	8.5	9.7E-22	0.3	41.7	7.3	1.8E-42	0.3	29.5	6.8	4.8E-06
Rc_0017561	0.4	15.3	5.3	7.3E-17	0.4	29.1	6.3	4.0E-39	0	18.0	8.9	6.4E-11
Rc_0469861	23.8	55.5	1.2	6.0E-03	10.4	55.4	2.4	5.7E-04	6.7	43.4	2.7	1.3E-02
Rc_0068591	23.5	48.3	1.0	3.4E-02	12.8	60.6	2.2	5.7E-17	6.1	31.1	2.4	8.0E-03
Rc_0496721	38.6	6.2	-2.6	3.4E-06	76.1	4.8	-4.0	2.4E-09	26.2	4.4	-2.6	3.5E-04
Rc_0077971	71.6	0.1	-10.0	6.7E-05	38.8	0.2	-7.8	4.7E-09	5.3	0.6	-3.3	2.1E-02
Rc_0188031	13.7	5.7	-1.3	4.6E-04	4.8	1.8	-1.4	2.3E-02	6.4	0.8	-3.0	4.1E-03
Rc_0017641	12.6	0.7	-4.2	1.9E-04	7.8	0.3	-4.6	8.7E-05	23.9	0.4	-6.1	1.0E-07
Rc_0430481	7.6	0.1	-6.6	4.1E-07	14.4	0.3	-5.7	5.0E-14	4.4	0	-12.1	1.7E-03
Rc_0179641	372.9	0.4	-9.8	1.5E-06	197.1	0.3	-9.4	6.3E-12	26.6	1.6	-4.0	2.8E-02
Rc_0433321	565.7	0.3	-10.7	1.7E-03	318.9	0.3	-10.3	1.4E-07	41.8	2.3	-4.2	1.2E-02
Rc_0101451	62.8	22.8	-1.5	5.2E-03	66.9	8.5	-3.0	1.3E-04	33.3	2.9	-3.5	3.8E-09
Rc_0101491	154.1	57.6	-1.4	9.1E-03	156.5	25.5	-2.6	2.8E-04	95.2	10.6	-3.2	1.4E-10
Rc_0186071	33.1	68.3	1.0	2.8E-03	11.0	51.0	2.2	1.6E-09	4.9	23.7	2.3	1.3E-03
Rc_0071571	197.3	26.0	-2.9	1.0E-04	269.3	20.2	-3.7	5.0E-08	100.8	14.7	-2.8	8.0E-04
Rc_0226301	95.8	9.8	-3.3	3.4E-16	37.7	4.3	-3.1	9.2E-09	28.6	1.8	-4.0	4.8E-10
Rc_0353511	2.6	45.2	4.1	4.6E-11	2.6	24.8	3.3	1.8E-08	0.9	6.1	2.7	1.1E-02
Rc_0137231	0.2	53.2	8.0	2.2E-24	0.3	27.7	6.8	1.3E-36	0.1	12.2	7.7	4.8E-10
Rc_0283821	43.4	315.4	2.9	5.1E-03	7.6	36.7	2.3	2.9E-08	5.4	36.9	2.8	5.0E-02
Rc_0059511	91.7	2 062.3	4.5	1.1E-03	65.3	2 952.4	5.5	2.2E-10	38.8	2 143.2	5.8	1.3E-12
Rc_0212441	95.4	2.9	-5.0	3.2E-08	470.5	44.3	-3.4	8.9E-09	993.0	98.3	-3.3	8.7E-04

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[10]	YANG Mengting，XU Jing，and PANG Jiliang*. Flower Shape Changes of African Violets Caused by LjCYC1 Gene in Lotus japonicus [J]. ACTA HORTICULTURAE SINICA, 2020, 47(4): 708-716.
[11]	LI Shuaijie and CAI Xiuzhen*. Studies on Floral Syndrome and Breeding System of Primulina hunanensis [J]. ACTA HORTICULTURAE SINICA, 2020, 47(3): 492-502.
[12]	ZHOU Qin1，LU Rui1，ZHANG Shuting1，BAO Manzhu1，and LIU Guofeng1,2,*. Phenotype Characterization and Genetic Analysis of a Floral Mutant aps in Petunia [J]. ACTA HORTICULTURAE SINICA, 2019, 46(2): 317-329.
[13]	KOU Dandan，ZHANG Ye，WANG Pengfei，Li Dongdong，ZHANG Xueying，and CHEN Haijiang. Differences in Sucrose and Malic Acid Accumulation and The Related Gene Expression in‘Kurakato Wase’Peach and Its Early-ripening Mutant [J]. ACTA HORTICULTURAE SINICA, 2019, 46(12): 2286-2298.
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