Genome-wide Identification and Expressional Analysis of Carotenoid Cleavage Dioxygenases(CCD) Gene Family in Populus trichocarpa under Drought and Salt Stress

doi:10.7525/j.issn.1673-5102.2021.06.018

Abstract

Abstract:

Carotenoid cleavage dioxygenases（CCD） specifically catalyzed the cleavage of conjugated double bonds of carotenoids to form various apocarotenoids and their derivatives， which played various important roles in plant growth and development and stress response. However， no research has been reported on PtrCCD in the woody model plant Populus trichocarpa. This study found that its expression level was significantly different under salt stress and drought stress. Based on this， it was planned to reveal the function of PtrCCD family at the molecular level.. The number of PtrCCD family members， evolutionary relationship， chromosome location， gene structure， basic characteristics of the encoded protein， promoter cis-acting elements， and response to drought and salt stress of PtrCCD gene family were analyzed at genome-level of P. trichocarpa， respectively. The results demonstrated that the PtrCCD family could be divided into two sub-families， CCD4 and CCD8， which included 9 and 2 genes， respectively. There were 5 pairs of paralogous genes， with Ka/Ks far less than 1. All proteins encoded by the PtrCCD family contained 5 common Motifs， such as Motif 1， Motif 2， Motif 3， Motif 9， and Motif 11. The promoter regions of PtrCCD gene family contained a large number of abiotic stress and hormone response cis-elements， among which the PtrCCD8a promoter contained 5 types and 16 elements. Analysis of the expression characteristics of the PtrCCD family showed that the PtrCCD family genes exhibited tissue-specified expression patterns and mainly expressed in stems compared with in roots and leaves， respectively. Moreover， there were significant differences of expression levels of PtrCCD family genes among roots， stems， and leaves of poplar in response to drought and salt stress during different times. The PtrCCD gene family had different response to drought and salt stress， which further indicated that this gene family played an important role in abiotic stress.

Key words: Populus trichocarpa, CCD gene family, genome wide, drought stress, salt stress, response characteristics

CLC Number:

S792.11

Shuang-Hui TIAN, He CHENG, Yang ZHANG, Cong LIU, De-An XIA, Zhi-Gang WEI. Genome-wide Identification and Expressional Analysis of Carotenoid Cleavage Dioxygenases(CCD) Gene Family in Populus trichocarpa under Drought and Salt Stress[J]. Bulletin of Botanical Research, 2021, 41(6): 993-1005.

Figures/Tables 12

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定量引物名称 qRT-PCR primer name	F端引物序列 F-terminal primer sequence（5′—3′）	R端引物序列 R-terminal primer sequence（5′—3′）
PtrCCD4a	AGAGAGACCAAAATGGCGGAG	AGTTTCGTCGAGAACCGGAG
PtrCCD4b	CAACTTCGCTCCCGTTCCT	GGTTTGGACCCACCCTCAC
PtrCCD4c	CATTTCGGCATGAGATGGCAG	TCTCTGGTAGATGAGGGGGT
PtrCCD4d	CAACCAGAAGCAGACGGACA	CCTTCCAAATCACGGTTGCT
PtrCCD4e	AAGCAGGCTGCAGGACATAC	GATAACAAGCGGGTTCTTAGGT
PtrCCD4f	GCTTTGTCGTGACTTGTGGC	CCCATGGAACACGTCTAGGAA
PtrCCD4g	AGCAAATGCTGTGAAATCTGATG	GGAGACTTGGCATCCATAACAGT
PtrCCD4h	TTGAATCATGAGCTGTCCCGT	TATGGGTTTTGGGTGCGTGT
PtrCCD4i	GCATGATGAGAACTCCGGTC	AAGAGAGGCTACGAGTCCGAT
PtrCCD8a	GGATGCTGGGTGCCAAAGAA	AAAAGATGGACAAGCCAACAAAAA
PtrCCD8b	TCACCAGTTCAACGCTGCT	ATGACTGCAACTCCTCAAGACA
PtrActin	AGGCAGGTTTCGCAGGAGATGA	TCCATCACCAGAATCCAGCACA

基因名字 Gene name	登录号 Accession No.	基因位置 Location（5′—3′）	cds长度 Length of cds（bp）	氨基酸 Amino acid（aa）	等电点 PI	分子量 Molecular weight（KDa）	亚细胞定位 Subcellular localization
PtrCCD4a	Potri.001G265400.1	Chr01：27349090-27356583	1 656	551	5.84	62.12	C
PtrCCD4b	Potri.009G060500.1	Chr09：6255532-6262921	1 881	626	7.66	70.42	C
PtrCCD4c	Potri.001G265900.1	Chr01：27384456-27389644	1 323	440	6.1	49.9	C
PtrCCD4d	Potri.005G069100.1	Chr05：4955113-4957530	1 836	611	6.15	66.94	C
PtrCCD4e	Potri.019G093400.1	Chr19：12358073-12360220	1 839	612	6.52	66.94	C
PtrCCD4f	Potri.004G190700.1	Chr04：20536504-20537827	996	331	8.42	37.86	C
PtrCCD4g	Potri.009G152300.1	Chr09：11947452-11949727	1 581	526	7.55	58.54	C
PtrCCD4h	Potri.009G152200.1	Chr09：11939825-11941582	1 746	581	7.27	65.10	C
PtrCCD4i	Potri.009G151900.1	chr09：11927854-11929641	1 788	595	7.95	66.73	C/Chl/E
PtrCCD8a	Potri.006G238500.1	Chr06：24740981-24746347	1 674	557	5.75	61.89	C
PtrCCD8b	Potri.018G044100.1	Chr18：3994122-3998074	1 674	557	5.87	62	C

同源基因Paralogues		非同义替换率 Ka（JC）	同义替换率 Ks（JC）	Ka/Ks	同源片段长度 Homologous fragment（bp）	同源性 Homology（%）
基因1 Gene 1	基因2 Gene 2	非同义替换率 Ka（JC）	同义替换率 Ks（JC）	Ka/Ks	同源片段长度 Homologous fragment（bp）	同源性 Homology（%）
PtrCCD4a	PtrCCD4c	0.015 876	0.055 039	0.288 454	1 291	98%
PtrCCD4b	PtrCCD4c	0.057 054	0.183 749	0.310 499	1 210	93%
PtrCCD4a	PtrCCD4b	0.051 108	0.245 111	0.208 509	1 506	93%
PtrCCD4d	PtrCCD4e	0.027 409	0.165 349	0.165 763	1 732	94%
PtrCCD8a	PtrCCD8b	0.037 764	0.260 887	0.144 752	1 540	92%

基因名称 Gene name	植物激素响应元件 Phytohormone response element					非生物胁迫响应元件 Abiotic stress response element						共计 Total amount
基因名称 Gene name	TGA element	TCA element	CGTCA motif	ABRE	TGACG motif	ARE	STRE	MBS	DRE	TC-rich repeats	LTR	共计 Total amount
PtrCCD4a	1	0	1	6	1	3	0	0	0	0	0	12
PtrCCD4b	0	0	0	0	0	0	0	0	0	0	0	0
PtrCCD4c	0	0	0	0	0	5	0	0	0	0	0	5
PtrCCD4d	0	1	0	1	0	7	0	0	0	0	0	9
PtrCCD4e	1	0	0	1	0	5	0	1	0	3	1	12
PtrCCD4f	1	1	2	5	0	2	0	0	0	1	0	12
PtrCCD4g	0	0	1	8	0	1	0	0	0	0	0	10
PtrCCD4h	0	0	0	0	0	1	1	0	0	0	0	2
PtrCCD4i	0	0	4	4	4	4	0	0	0	0	0	12
PtrCCD8a	2	2	4	4	4	0	0	0	0	0	0	16
PtrCCD8b	0	0	0	0	0	2	0	0	0	0	0	3
共计Total amount	5	4	12	29	5	30	1	1	1	4	1	93

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