Genome-wide Identification and Expression Analysis of CCDs Family in Brassia rapa L.

doi:10.13560/j.cnki.biotech.bull.1985.2024-0722

Abstract

Abstract:

Objective The members of the carotenoid cleavage dioxygenase gene family in Brassia rapa L. were identified to gain insight into the function and tissue expression characteristics of the BrCCD family genes. Method Bioinformatics methods were used to identify the CCDs gene family in B.rapa L., construct a phylogenetic tree, and analyze the chromosome distribution, gene structure, conserved motif, intraspecific collinearity and promoter cis elements. Combined with transcriptome data and RT-qPCR technology, the expression of CCDs genes in different tissues was analyzed. Result Total 16 BrCCD genes were identified in B.rapa L., which were divided into six subgroups and distributed unevenly on eight chromosomes. Colinearity analysis showed that there was a collinearity between seven pairs of CCDs genes. Cis element analysis showed that CCDs family members may respond to various regulatory processes such as growth and development, hormone regulation, and abiotic stress. Transcriptome and quantitative PCR data analysis showed that the expression of BrCCD was tissue-specific, and the expression of BrCCD-L gene was higher in flowers, leaves and seeds, BrCCD1b was higher in flowers, and the rest was higher in seeds and leaves. Result Total 16 CCDs genes were identified in the genome of B.rapa L., which showed different expression patterns in different tissues. The BrCCD-L gene was highly similar to the CCD2 gene with saffron genus, and was significantly expressed in different tissues.

Key words: Brassia rapa L., bioinformatics analysis, CCDs gene family, expression analysis, tissue specificity

WANG Chen, LIU Guo-mei, CHEN Chang, ZHANG Jin-long, YAO Lin, SUN Xuan, DU Chun-fang. Genome-wide Identification and Expression Analysis of CCDs Family in Brassia rapa L.[J]. Biotechnology Bulletin, 2025, 41(3): 161-170.

Figures/Tables 10

References 42

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引物名称 Primer name	上游引物 Upstream primer（5′-3′）	下游引物 Downstream primer（5′-3′）	产物长度 Product length/bp
BrCCD8	CATTGCAGATTGTTGCGAACAC	CCACTCCATCATCTTCATGG	170
BrCCD7	TCCGGTTATCAACTCATCATGG	AACGTTAAATTCCTCGGGACC	169
BrCCD4a	CCATGGACTATTTGTCAAGGAG	TTTGTTGCCGAAGAAAGTAAGAAGC	256
BrCCD4b	TTAAGGGTTTTAGCGGGACAG	ACGATCGGAACGTCTCTTTG	320
BrCCD-L	GCGGAGAACTGCATAGTTTC	GGACCAACCCTCACAAATTC	403
BrCCD1a	GGCTCTGCAGCATTTTTCTC	GTACCCATCTCCATCAAACC	376
BrCCD1b	TCTCTGTCAATCCTAAACCCTC	GTGAGGGGATCAAACATAACC	292
BrNCED9b	ACGTCGAGATTCCACTTGATG	GAGATGGAAACAGAAGCAATCAGG	236
BrNCED3c	AACAAACCGGTTTATCCAAGAGC	GAGTGATCCTGACTTGGTAAGG	236
BrNCED6	TTACCACGTGAAGATCAACGG	GTCAAGGTCACGTGTCTTTTTC	208
Brassia rapa-Actin	CATTGCAGATTGTTGCGAACAC	CCACTCCATCATCTTCATGG	91

引物名称 Primer name	上游引物 Upstream primer（5′-3′）	下游引物 Downstream primer（5′-3′）	产物长度 Product length/bp
BrCCD8	CATTGCAGATTGTTGCGAACAC	CCACTCCATCATCTTCATGG	170
BrCCD7	TCCGGTTATCAACTCATCATGG	AACGTTAAATTCCTCGGGACC	169
BrCCD4a	CCATGGACTATTTGTCAAGGAG	TTTGTTGCCGAAGAAAGTAAGAAGC	256
BrCCD4b	TTAAGGGTTTTAGCGGGACAG	ACGATCGGAACGTCTCTTTG	320
BrCCD-L	GCGGAGAACTGCATAGTTTC	GGACCAACCCTCACAAATTC	403
BrCCD1a	GGCTCTGCAGCATTTTTCTC	GTACCCATCTCCATCAAACC	376
BrCCD1b	TCTCTGTCAATCCTAAACCCTC	GTGAGGGGATCAAACATAACC	292
BrNCED9b	ACGTCGAGATTCCACTTGATG	GAGATGGAAACAGAAGCAATCAGG	236
BrNCED3c	AACAAACCGGTTTATCCAAGAGC	GAGTGATCCTGACTTGGTAAGG	236
BrNCED6	TTACCACGTGAAGATCAACGG	GTCAAGGTCACGTGTCTTTTTC	208
Brassia rapa-Actin	CATTGCAGATTGTTGCGAACAC	CCACTCCATCATCTTCATGG	91

基因名称 Gene name	基因ID Gene ID	亚组 Subgroup	染色体 Chromosome	基因长度 Gene length/bp	外显子数目 Numbei of exons	蛋白长度 Protein length/aa	分子量 Molecular wt./kD	等电点 pI	亲水性 GRAVY	亚细胞定位 Subcellular location
BrCCD1a	BraA09g055140.3.5C.2	CCD1	A09	6 077	7	273	31.35	5.27	-0.342	细胞质Cytoplasm
BrCCD1b	BraA09g055150.3.5C.8	CCD1	A09	5 488	8	333	38.12	5.27	-0.272	细胞质Cytoplasm
BrCCD4a	BraA01g010600.3.5C.1	CCD4	A01	2 099	1	595	65.60	6.19	-0.230	叶绿体Chloroplasts
BrCCD4b	BraA08g013940.3.5C.1	CCD4	A08	3 734	4	633	69.71	7.65	-0.132	过氧化物酶体Peroxisome
BrCCD7	BraA04g031980.3.5C.1	CCD7	A04	5 466	10	668	74.77	5.86	-0.381	叶绿体Chloroplasts
BrCCD8	BraA01g005270.3.5C.1	CCD8	A01	3 320	6	568	63.89	7.12	-0.345	叶绿体Chloroplasts
BrCCD-L	BraA04g000030.3.5C.6	CCD-L	A04	3 242	12	536	60.77	5.91	-0.235	细胞质Cytoplasm
BrNCED2a	BraA03g048870.3.5C.1	NCED	A03	1 734	1	577	64.31	5.50	-0.261	细胞骨架Cytoskeleton
BrNCED2b	BraA01g009860.3.5C.1	NCED	A01	1 746	1	581	64.50	5.37	-0.214	叶绿体Chloroplasts
BrNCED3a	BraA05g033680.3.5C.1	NCED	A05	2 324	1	597	65.76	5.81	-0.287	线粒体Mitochondria
BrNCED3b	BraA01g038580.3.5C.1	NCED	A01	2 305	1	598	65.76	5.57	-0.275	叶绿体Chloroplasts
BrNCED3c	BraA03g036960.3.5C.1	NCED	A03	2 363	1	592	65.45	5.56	-0.305	叶绿体Chloroplasts
BrNCED5	BraA09g036480.3.5C.1	NCED	A09	1 767	1	588	65.28	5.42	-0.315	叶绿体Chloroplasts
BrNCED6	BraA07g009270.3.5C.1	NCED	A07	1 815	1	604	67.20	6.16	-0.312	叶绿体Chloroplasts
BrNCED9a	BraA07g042490.3.5C.1	NCED	A07	2 840	2	618	68.50	5.84	-0.307	叶绿体Chloroplasts
BrNCED9b	BraA02g025460.3.5C.1	NCED	A02	1 764	1	587	65.28	6.30	-0.225	叶绿体Chloroplasts

基因名称 Gene name	基因ID Gene ID	亚组 Subgroup	染色体 Chromosome	基因长度 Gene length/bp	外显子数目 Numbei of exons	蛋白长度 Protein length/aa	分子量 Molecular wt./kD	等电点 pI	亲水性 GRAVY	亚细胞定位 Subcellular location
BrCCD1a	BraA09g055140.3.5C.2	CCD1	A09	6 077	7	273	31.35	5.27	-0.342	细胞质Cytoplasm
BrCCD1b	BraA09g055150.3.5C.8	CCD1	A09	5 488	8	333	38.12	5.27	-0.272	细胞质Cytoplasm
BrCCD4a	BraA01g010600.3.5C.1	CCD4	A01	2 099	1	595	65.60	6.19	-0.230	叶绿体Chloroplasts
BrCCD4b	BraA08g013940.3.5C.1	CCD4	A08	3 734	4	633	69.71	7.65	-0.132	过氧化物酶体Peroxisome
BrCCD7	BraA04g031980.3.5C.1	CCD7	A04	5 466	10	668	74.77	5.86	-0.381	叶绿体Chloroplasts
BrCCD8	BraA01g005270.3.5C.1	CCD8	A01	3 320	6	568	63.89	7.12	-0.345	叶绿体Chloroplasts
BrCCD-L	BraA04g000030.3.5C.6	CCD-L	A04	3 242	12	536	60.77	5.91	-0.235	细胞质Cytoplasm
BrNCED2a	BraA03g048870.3.5C.1	NCED	A03	1 734	1	577	64.31	5.50	-0.261	细胞骨架Cytoskeleton
BrNCED2b	BraA01g009860.3.5C.1	NCED	A01	1 746	1	581	64.50	5.37	-0.214	叶绿体Chloroplasts
BrNCED3a	BraA05g033680.3.5C.1	NCED	A05	2 324	1	597	65.76	5.81	-0.287	线粒体Mitochondria
BrNCED3b	BraA01g038580.3.5C.1	NCED	A01	2 305	1	598	65.76	5.57	-0.275	叶绿体Chloroplasts
BrNCED3c	BraA03g036960.3.5C.1	NCED	A03	2 363	1	592	65.45	5.56	-0.305	叶绿体Chloroplasts
BrNCED5	BraA09g036480.3.5C.1	NCED	A09	1 767	1	588	65.28	5.42	-0.315	叶绿体Chloroplasts
BrNCED6	BraA07g009270.3.5C.1	NCED	A07	1 815	1	604	67.20	6.16	-0.312	叶绿体Chloroplasts
BrNCED9a	BraA07g042490.3.5C.1	NCED	A07	2 840	2	618	68.50	5.84	-0.307	叶绿体Chloroplasts
BrNCED9b	BraA02g025460.3.5C.1	NCED	A02	1 764	1	587	65.28	6.30	-0.225	叶绿体Chloroplasts

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