Genome-wide Identification and Expression Analysis of the CAMTA Family in Rubber Tree (Hevea brasiliensis)

doi:10.3969/j.issn.1000-2561.2021.10.015

Abstract

Abstract:

Calmodulin-binding transcription activators (CAMTAs) are important proteins with a conserved calmodulin- binding domain, which are widely involved in biological processes such as stress response, growth and development, and hormone signalling in plant. In this study, we identified eight HbCAMTAs screening the genome-wide of the rubber tree and analyzed physicochemical properties, gene structures, regulatory elements, gene expression patterns, and so on. The results showed that all HbCAMTAs were located in the nucleus, and predicted as hydrophilic proteins with molecular weight from 104.34 to 121.99 kD and isoelectric points between 5.32 and 7.83. The sequence homology analysis showed that HbCAMTAs could be divided into four subclades, and each one had similar gene structure, conserved domains. Furthermore, each HbCAMTA was potentially regulated by at least three miRNAs. Expression analysis indicated that the expression of HbCAMTAs differed significantly in different tissues, and the expression was continuously up-regulated in leaves with the development of leaves and reached the highest expression level at mature or palegreen. Except for HbCAMTA2, ethylene stimulation failed to significantly induce the expression of other CAMTA genes in rubber tree while low-temperature could significantly induce the up-regulated expression of HbCAMTAs. HbCAMTA1 was constitutively expressed in all samples, and also mostly expressed in latex, leaves, roots, bark, male and female flowers, and four different leaf developmental stages (Bronzite, Changecolor, Palegreen, and Mature), which suggesting its fundamental function in rubber tree. HbCAMTA3 was expressed at the highest level in the seeds and was significantly up-regulated by low temperature stress, indicating its important role in response to low temperature stress. HbCAMTA7 was undetectably express in all investigated samples including different tissues, leaf developments, and treatments. Finally, this study would provide important information for further revealing the function of HbCAMTAs in rubber tree.

Key words: Hevea brasiliensis, transcription factor, CAMTA, gene expression

CLC Number:

S794.1

LIN Xianzu, XIAO Xiaohu, YANG Jianghua, QIN Yunxia, LONG Xiangyu, FANG Yongjun. Genome-wide Identification and Expression Analysis of the CAMTA Family in Rubber Tree (Hevea brasiliensis)[J]. Chinese Journal of Tropical Crops, 2021, 42(10): 2859-2868.

Figures/Tables 8

References 39

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基因名称 Gene name	基因ID Gene ID	内含子数目 Intron number	蛋白序列长度 Protein length/aa	分子量 Molecular weigh/kD	等电点 Isoelectric point	结构域预测 Predicted pfam domain	亚细胞定位 Subcellular prediction	总平均疏水性 Grand average of hydropathicity	信号肽预测 Singal petides
HbCAMTA1	scaffold0625_117727	12	923	104.34	6.45	CG-1 domain	Nucleus	?0.439	NA
HbCAMTA2	scaffold0703_610088	11	991	111.30	7.83	CG-1 domain	Nucleus	?0.522	NA
HbCAMTA3	scaffold0010_4040802	12	1069	120.85	5.63	CG-1 domain	Nucleus	?0.546	NA
HbCAMTA4	scaffold0824_240435	12	983	110.41	5.32	CG-1 domain	Nucleus	?0.574	NA
HbCAMTA5	scaffold0444_896392	12	1086	121.99	5.92	CG-1 domain	Nucleus	?0.53	NA
HbCAMTA6	scaffold0711_36887	12	974	109.51	5.92	CG-1 domain	Nucleus	?0.533	NA
HbCAMTA7	scaffold0624_160516	12	928	104.70	6.42	CG-1 domain	Nucleus	?0.384	NA
HbCAMTA8	scaffold0909_393686	12	1068	119.94	5.46	CG-1 domain	Nucleus	?0.502	NA

基因名称 Gene name	基因ID Gene ID	内含子数目 Intron number	蛋白序列长度 Protein length/aa	分子量 Molecular weigh/kD	等电点 Isoelectric point	结构域预测 Predicted pfam domain	亚细胞定位 Subcellular prediction	总平均疏水性 Grand average of hydropathicity	信号肽预测 Singal petides
HbCAMTA1	scaffold0625_117727	12	923	104.34	6.45	CG-1 domain	Nucleus	?0.439	NA
HbCAMTA2	scaffold0703_610088	11	991	111.30	7.83	CG-1 domain	Nucleus	?0.522	NA
HbCAMTA3	scaffold0010_4040802	12	1069	120.85	5.63	CG-1 domain	Nucleus	?0.546	NA
HbCAMTA4	scaffold0824_240435	12	983	110.41	5.32	CG-1 domain	Nucleus	?0.574	NA
HbCAMTA5	scaffold0444_896392	12	1086	121.99	5.92	CG-1 domain	Nucleus	?0.53	NA
HbCAMTA6	scaffold0711_36887	12	974	109.51	5.92	CG-1 domain	Nucleus	?0.533	NA
HbCAMTA7	scaffold0624_160516	12	928	104.70	6.42	CG-1 domain	Nucleus	?0.384	NA
HbCAMTA8	scaffold0909_393686	12	1068	119.94	5.46	CG-1 domain	Nucleus	?0.502	NA

基因名Gene name	miRNA登录号miRNA_Acc.	期望值Expectation	抑制性Inhibition	多样性Multiplicity
HbCAMTA1	gma-miR4347	2.5	Cleavage	1
	hvu-miR6190	3.0	Cleavage	1
	ppt-miR1219d	2.5	Cleavage	1
	sly-miR6024	3.0	Cleavage	1
	stu-miR6024-3p	3.0	Cleavage	1
HbCAMTA2	ata-miR2275c-3p	3.0	Cleavage	1
	ata-miR9674b-3p	2.5	Cleavage	1
	ath-miR2937	3.0	Cleavage	1
	bdi-miR2275c	3.0	Cleavage	1
	mes-miR2275	3.0	Cleavage	1
	mes-miR2950	2.0	Cleavage	1
	osa-miR2275a	3.0	Cleavage	1
	osa-miR2275b	3.0	Cleavage	1
	tae-miR2275-3p	3.0	Cleavage	1
	vvi-miR2950-5p	2.0	Cleavage	1
HbCAMTA3	aly-miR4244	3.0	Cleavage	1
	aqc-miR529	3.0	Cleavage	1
	cme-miR159b	2.5	Cleavage	1
	gma-miR5371-3p	3.0	Cleavage	1
	hbr-miR6174	2.5	Translation	1
	osa-miR159c	2.5	Cleavage	1
	osa-miR159d	2.5	Cleavage	1
	osa-miR159e	2.5	Cleavage	1
	sly-miR9474-5p	3.0	Cleavage	1
HbCAMTA4	aly-miR156g-3p	2.5	Cleavage	1
	aly-miR3437-5p	3.0	Cleavage	1
	bcy-miR529	3.0	Cleavage	1
	bgy-miR529	3.0	Cleavage	1
	osa-miR2868	3.0	Translation	1
	zma-miR399e-5p	3.0	Cleavage	1
HbCAMTA5	aly-miR828-5p	3.0	Translation	1
	ath-miR828	3.0	Translation	1
	mdm-miR159c	3.0	Cleavage	1
	mtr-miR2673a	3.0	Translation	1
	mtr-miR2673b	3.0	Translation	1
HbCAMTA6	aly-miR156g-3p	2.5	Cleavage	1
	aly-miR4230	2.5	Cleavage	1
	aly-miR4238	3.0	Cleavage	2
HbCAMTA7	csi-miR3950	3.0	Cleavage	1
	gma-miR4347	2.5	Cleavage	1
	hme-miR-316	3.0	Cleavage	1
	osa-miR169q	3.0	Cleavage	1
	stu-miR8022	2.0	Cleavage	1
HbCAMTA8	aly-miR774b-5p	3.0	Cleavage	1
	gma-miR5371-3p	3.0	Cleavage	1
	mtr-miR2600b	3.0	Cleavage	1
	mtr-miR2600c	3.0	Cleavage	1
	mtr-miR2600d	3.0	Cleavage	1
	mtr-miR2600e	3.0	Cleavage	1
	stu-miR8024a-3p	2.5	Cleavage	2
	stu-miR8024a-3p	3.0	Translation	2
	stu-miR8024b	2.5	Cleavage	2
	stu-miR8024b	3.0	Translation	2

基因名Gene name	miRNA登录号miRNA_Acc.	期望值Expectation	抑制性Inhibition	多样性Multiplicity
HbCAMTA1	gma-miR4347	2.5	Cleavage	1
	hvu-miR6190	3.0	Cleavage	1
	ppt-miR1219d	2.5	Cleavage	1
	sly-miR6024	3.0	Cleavage	1
	stu-miR6024-3p	3.0	Cleavage	1
HbCAMTA2	ata-miR2275c-3p	3.0	Cleavage	1
	ata-miR9674b-3p	2.5	Cleavage	1
	ath-miR2937	3.0	Cleavage	1
	bdi-miR2275c	3.0	Cleavage	1
	mes-miR2275	3.0	Cleavage	1
	mes-miR2950	2.0	Cleavage	1
	osa-miR2275a	3.0	Cleavage	1
	osa-miR2275b	3.0	Cleavage	1
	tae-miR2275-3p	3.0	Cleavage	1
	vvi-miR2950-5p	2.0	Cleavage	1
HbCAMTA3	aly-miR4244	3.0	Cleavage	1
	aqc-miR529	3.0	Cleavage	1
	cme-miR159b	2.5	Cleavage	1
	gma-miR5371-3p	3.0	Cleavage	1
	hbr-miR6174	2.5	Translation	1
	osa-miR159c	2.5	Cleavage	1
	osa-miR159d	2.5	Cleavage	1
	osa-miR159e	2.5	Cleavage	1
	sly-miR9474-5p	3.0	Cleavage	1
HbCAMTA4	aly-miR156g-3p	2.5	Cleavage	1
	aly-miR3437-5p	3.0	Cleavage	1
	bcy-miR529	3.0	Cleavage	1
	bgy-miR529	3.0	Cleavage	1
	osa-miR2868	3.0	Translation	1
	zma-miR399e-5p	3.0	Cleavage	1
HbCAMTA5	aly-miR828-5p	3.0	Translation	1
	ath-miR828	3.0	Translation	1
	mdm-miR159c	3.0	Cleavage	1
	mtr-miR2673a	3.0	Translation	1
	mtr-miR2673b	3.0	Translation	1
HbCAMTA6	aly-miR156g-3p	2.5	Cleavage	1
	aly-miR4230	2.5	Cleavage	1
	aly-miR4238	3.0	Cleavage	2
HbCAMTA7	csi-miR3950	3.0	Cleavage	1
	gma-miR4347	2.5	Cleavage	1
	hme-miR-316	3.0	Cleavage	1
	osa-miR169q	3.0	Cleavage	1
	stu-miR8022	2.0	Cleavage	1
HbCAMTA8	aly-miR774b-5p	3.0	Cleavage	1
	gma-miR5371-3p	3.0	Cleavage	1
	mtr-miR2600b	3.0	Cleavage	1
	mtr-miR2600c	3.0	Cleavage	1
	mtr-miR2600d	3.0	Cleavage	1
	mtr-miR2600e	3.0	Cleavage	1
	stu-miR8024a-3p	2.5	Cleavage	2
	stu-miR8024a-3p	3.0	Translation	2
	stu-miR8024b	2.5	Cleavage	2
	stu-miR8024b	3.0	Translation	2