Genome‑wide Identification and Stress Response Analysis of Cyclic Nucleotide-gated Channels(CNGC) Gene Family in Populus trichocarpa

doi:10.7525/j.issn.1673-5102.2022.04.011

Abstract

Abstract:

The plant cyclic nucleotide-gated channels（CNGC） family has a variety of biological functions and plays an important role in the growth and development of plants and the response to stress. In this study， bioinformatics methods and qRT-PCR were used to analyze the basic physicochemical properties， structural characteristics， phylogeny， gene structure and conserved motif， cis-acting elements of the promoter and gene expression patterns of the PtrCNGC gene family members respectively. The results showed that a total of 19 PtrCNGC genes were identified in the whole genome of Populus trichocarpa. PtrCNGC gene family could be divided into four subgroups（Ⅰ， Ⅱ， Ⅲ and Ⅳ）， and subgroup Ⅳ could be divided into two subgroups（Ⅳa and Ⅳb）. The proteins encoded by the PtrCNGC genes were all basic proteins， and only one member of the PtrCNGC gene family was hydrophobic protein， while all the other members were hydrophilic proteins. A total of 19 PtrCNGCs were distributed unevenly on 11 chromosomes of P. trichocarpa， while the remaining 8 chromosomes had no members distributed. The PtrCNGC gene family contained seven pairs of homologous genes and the K_a/K_s value between them was far less than one. There was little difference in gene structure and protein conserved motif distribution among the family members. Predictive analysis of cis-acting elements in the promoter region of the PtrCNGC gene sequence showed that there were acting elements related to various hormones and stress. The qRT-PCR results showed that the expression of PtrCNGC gene family was specific in different tissues， with higher expression levels in stems and lower expression levels in roots and leaves. Under salt stress and drought stress， most members of the same branch of the PtrCNGC gene family showed similar expression patterns. The results of this study provid a reference for further study on the function of PtrCNGC family in abiotic stress.

Key words: Populus trichocarpa, CNGC gene family, bioinformatic analysis, abiotic stresses

CLC Number:

S792.11

Xueying WANG, Ruiqi WANG, Yang ZHANG, Cong LIU, Dean XIA, Zhigang WEI. Genome‑wide Identification and Stress Response Analysis of Cyclic Nucleotide-gated Channels(CNGC) Gene Family in Populus trichocarpa[J]. Bulletin of Botanical Research, 2022, 42(4): 613-625.

Figures/Tables 13

Table 1

Table 2

Fig.1

Fig.2

Fig.3

Table 3

Summary of PtrCNGC gene family

基因名称 Gene name	登录号 Gene ID	基因位置 Genomic location	cds长度 Length of cds /bp	氨基酸长度 Amino acid length /aa	等电点 pI	分子质量 Molecular weight /kDa	亲水性平均值 Grand average ofhydropathicity	亚细胞定位预测（概率） Prediction of subcellular Localization（Percentage）
PtrCNGC1.1	Potri.001G043900	3172345~3176133	2 238	745	9.15	86.026 09	-0.266	细胞质（96.82%）
PtrCNGC1.2	Potri.001G407800	43033745~43040720	2 055	684	8.77	78.532 21	-0.119	细胞质（78.01%）
PtrCNGC2.1	Potri.002G170000	12916136~12920918	2 187	728	9.15	84.103 14	-0.193	细胞质（91.63%）
PtrCNGC3.1	Potri.003G183000	18942476~18946581	2 220	739	8.98	85.236 32	-0.193	细胞质（98.00%）
PtrCNGC6.1	Potri.006G271500	27277609~27283688	2 076	691	7.53	79.603 33	-0.226	细胞质（98.27%）
PtrCNGC9.1	Potri.009G010700	1914122~1917753	2 238	745	9.27	85.463 00	-0.131	细胞质（97.11%）
PtrCNGC12.1	Potri.012G002200	206744~215632	2 130	709	9.03	82.008 80	-0.149	细胞质（91.28%）
PtrCNGC12.2	Potri.012G038700	3420369~3434999	2 310	769	9.23	88.215 84	-0.113	细胞质（95.04%）
PtrCNGC13.1	Potri.013G108200	12173969~12176818	2 055	684	9.32	79.382 80	-0.096	细胞质（55.25%）
PtrCNGC14.1	Potri.014G097900	7650920~7655559	2 172	723	9.45	83.918 28	-0.220	细胞质（90.95%）
PtrCNGC15.1	Potri.015G019100	1357777~1365061	2 127	708	9.11	81.738 42	-0.150	细胞质（87.32%）
PtrCNGC15.2	Potri.015G033900	2808538~2824047	2 346	781	9.42	89.048 90	-0.113	细胞质（95.49%）
PtrCNGC15.3	Potri.015G034000	2836520~2851182	2 358	785	9.53	89.681 54	-0.132	细胞质（95.91%）
PtrCNGC17.1	Potri.017G067000	7020102~7024372	2 067	688	9.16	79.682 99	-0.141	过氧化物酶体（50.67%）
PtrCNGC17.2	Potri.017G089800	10685838~10690733	2 157	718	9.49	82.019 61	-0.022	细胞质（54.87%）
PtrCNGC17.3	Potri.017G089900	10744470~10751288	2 118	705	9.55	81.146 94	0.035	细胞质（80.80%）
PtrCNGC18.1	Potri.018G009200	639720~644438	2 163	720	9.12	82.685 22	-0.148	细胞质（91.75%）
PtrCNGC18.2	Potri.018G097600	12595117~12608310	2 184	727	9.19	83.793 61	-0.236	细胞质（96.75%）
PtrCNGC18.3	Potri.018G106100	13287094~13300441	2 205	734	9.31	84.049 79	-0.217	细胞质（98.37%）

Table 3

Table 4

Fig.4

Fig 5

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Fig.9

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基因名称 Gene name	上游引物 Forward primer（5′→3′）	下游引物 Reverse primer（5′→3′）
PtrCNGC1.1	CAACCGAGGTGTATTGAAAGAAG	CCTGCCTACTATGAAGACGCC
PtrCNGC1.2	CTCTTGAAACCACCGAGGCT	AGCAGCCCAAGTTCTCCATC
PtrCNGC2.1	AAGGCTGGTGACTTCTGTGG	GTAATCGGCGAAACTGGGA
PtrCNGC3.1	CGGACGAGGTGAACTTGTGAT	AGCGAGCAAACCTTGGGAT
PtrCNGC6.1	GTTACAAATCCGCGTTTCGCC	TGTTGCATGACGCTCAATCG
PtrCNGC9.1	CGGAAGGAGGCGACTGAC	ACAACACTTGAATCTGAGCCG
PtrCNGC12.1	CTCGCAGCAGTGGAGAACAT	GGAACTCTATCTGGCACCCTT
PtrCNGC12.2	CCAAGGCTGTGGAGGTTTACT	TGGCAGGCATCACGGAG
PtrCNGC13.1	CTTTGCGAAATAGCATTGGAT	CAAGGTTGTGGCTACGAGATG
PtrCNGC14.1	GTAGAGGAAATGCGGGTGAAG	AGCAAAGATGGCGGTTTATGT
PtrCNGC15.1	GCTACATTGTTCGTGAGGGTG	CAGATTAGATGAGGAGTGGGGAT
PtrCNGC15.2	GCGTTTGATTAGCAGCAGGA	CAGGCAACTTGAATGTGGGTA
PtrCNGC15.3	GATTTCTGGACAGCGTTTGATTA	TTGATACCTTATGGCTCCTTGG
PtrCNGC17.1	TGACTGTAGTGCCAAGGATAACC	CGGCAAACATCCCAAACTG
PtrCNGC17.2	ACGCCAAGATGTGGAATGGT	GTCCTTCGGGCAGTTCTTCA
PtrCNGC17.3	CGCTGTCAAACCCCGAAC	CGCACGAACGAGCAACTG
PtrCNGC18.1	TCGTCAACTCCCTCAAAGTCTAC	CGTCTAACAAGGTCCAGGCAT
PtrCNGC18.2	GGAAGAATGGAGACTCAAGCG	TCCATCTGTGAGAAAAAGGGC
PtrCNGC18.3	TTCTCGGGTATTTGGGCG	AGCAGGATGATGTAAAGCAAGG
PtrActin	AGGCAGGTTTCGCAGGAGATGA	TCCATCACCAGAATCCAGCACA

亚群 Group	基因名称 Gene name	登录号 Gene ID	不同蛋白数据库中的结构域 Domain architectures in different databases
亚群 Group	基因名称 Gene name	登录号 Gene ID	Pfam	SMART	CDD	PROSIT	SurperFamily
Ⅰ	PtrCNGC2.1	Potri.002G170000	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN
	PtrCNGC14.1	Potri.014G097900	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP，IQ	cAMP_bd-like，PLN
	PtrCNGC12.1	Potri.012G002200	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN
	PtrCNGC15.1	Potri.015G019100	ITP，cNMP	cNMP TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN
Ⅱ	PtrCNGC18.3	Potri.018G106100	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP，IQ	cAMP_bd-like，PLN
	PtrCNGC1.1	Potri.001G043900	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN
	PtrCNGC3.1	Potri.003G183000	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN
Ⅲ	PtrCNGC9.1	Potri.009G010700	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP，IQ	cAMP_bd-like，PLN
	PtrCNGC13.1	Potri.013G108200	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN
	PtrCNGC17.1	Potri.017G067000	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN
	PtrCNGC18.2	Potri.018G097600	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN
	PtrCNGC6.1	Potri.006G271500	ITP，cNMP	cNMP，TM	CAP-ED	cNMP	cAMP_bd-like，PLN
	PtrCNGC18.1	Potri.018G009200	ITP，cNMP	cNMP，TM	ITP，CAP-ED	cNMP	cAMP_bd-like，PLN
Ⅳa	PtrCNGC12.2	Potri.012G038700	ITP	cNMP，TM	CAP-ED，PLN，ITP	cNMP	cAMP_bd-like，PLN
	PtrCNGC15.2	Potri.015G033900	ITP，cNMP	cNMP，TM	PLN	cNMP	cAMP_bd-like，PLN
	PtrCNGC15.3	Potri.015G034000	ITP	cNMP，TM	CAP-ED，PLN，ITP	cNMP	cAMP_bd-like，PLN
Ⅳb	PtrCNGC1.2	Potri.001G407800	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN
	PtrCNGC17.2	Potri.017G089800	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN
	PtrCNGC17.3	Potri.017G089900	ITP，cNMP	cNMP，TM	CAP-ED，PLN	cNMP	cAMP_bd-like，PLN

同源基因 Paralogues		非同义替换率 K_a	同义替换率 K_s	K_a/K_s	同源片段长度 The length of homologous fragment /bp	同源性 Homology /%
基因1 Gene 1	基因2 Gene 2	非同义替换率 K_a	同义替换率 K_s	K_a/K_s	同源片段长度 The length of homologous fragment /bp	同源性 Homology /%
PtrCNGC1.1	PtrCNGC3.1	0.056 975	0.220 971	0.257 839	2 026	90.53
PtrCNGC2.1	PtrCNGC14.1	0.061 054	0.219 205	0.278 523	1 981	90.37
PtrCNGC6.1	PtrCNGC18.1	0.094 621	0.306 729	0.308 484	1 355	89.97
PtrCNGC12.1	PtrCNGC15.1	0.043 307	0.211 946	0.204 330	1 972	90.53
PtrCNGC12.2	PtrCNGC15.2	0.115 981	0.274 512	0.422 499	1 572	85.62
	PtrCNGC15.3	0.096 435	0.267 658	0.360 292	1 604	87.36
PtrCNGC15.2	PtrCNGC15.3	0.059 375	0.109 146	0.543 996	2 198	93.06

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