灵宝杜鹃bZIP家族全基因组鉴定及表达特征分析

doi:10.13560/j.cnki.biotech.bull.1985.2023-0822

摘要/Abstract

摘要：

【目的】鉴定灵宝杜鹃（Rhododendron henanense subsp. lngbaoense）基因组的碱性亮氨酸拉链转录因子（basic leucine zipper, bZIP）家族成员，研究其非生物胁迫下的表达模式。【方法】鉴定RhlbZIP家族成员，构建系统发育树，进行基因结构、保守基序、顺势作用元件和表达模式分析。采用实时荧光定量PCR（RT-qPCR）技术，分析RhlbZIP基因在非生物胁迫中的表达。【结果】共鉴定出57个RhlbZIP基因，划分为11个亚家族，同一亚族成员有相似的结构和基序；不均匀地分布在13条染色体中，共线性分析发现共发生45次复制事件（3对串联复制，42对片段复制）；顺式作用元件分析表明，RhlbZIP家族成员可能响应转录、发育、激素调控、生物与非生物胁迫等生物学过程；GO注释分析表明，RhlbZIP基因家族与转录调节、代谢、生物学过程等相关。转录组结果显示，87.72%的WRKY家族基因在根、茎、叶、花和下胚轴5种组织中均表达，但表达水平存在明显差异。RT-qPCR表达模式表明，RhlbZIP4低温处理下显著上调表达；RhlbZIP24在干旱和ABA处理下显著上调；RhlbZIP16在高盐和MeJA处理下显著上调。【结论】灵宝杜鹃基因组中共鉴定出57个RhlbZIP基因，所选的基因在不同处理下均有表达，其中低温、干旱、高盐、ABA与MeJA胁迫处理中的主效基因分别是RhlbZIP4、RhlbZIP24、RhlbZIP16、RhlbZIP24与RhlbZIP16。

关键词: 灵宝杜鹃, bZIP基因家族, 非生物胁迫，实时定量PCR

Abstract:

【Objective】To identify the members of the basic leucine zipper（bZIP）family of Rhododendron henanense subsp. lingbaoense genome, and to explore their expression patterns under abiotic stress.【Method】We identified the RhlbZIPs（bZIP TFs in R. henanense subsp. lingbaoense）using bioinformatic methods, and investigated their physical and chemical properties, gene structures, conserved motifs, evolutionary relationships, cis-acting elements, and expression patterns. In addition, real-time quantitative fluorescent PCR（RT-qPCR）was used to analyze the expression of RhlbZIP gene in abiotic stress.【Result】A total of 57 RhlbZIP genes were identified and divided into 11 subfamilies, and the same subfamily members having similar gene structure and conserved motifs. RhlbZIP genes were unevenly distributed in 13 chromosomes, and collinearity analysis revealed 45 replication events（3 pairs of tandem replications and 42 pairs of fragment replication）. Cis-acting elements in the promoter region of RhlbZIP genes included four categories responding to transcription, development, abiotic or biological stress and hormone. GO annotation analysis showed that RhlbZIP gene family was associated with transcriptional regulation, metabolism, and biological processes. Transcriptome data showed that most bZIP family genes（82.46%）were expressed in 5 tissues of root, stem, leaf, flower, and hypocotyl, but there were significant differences in expressions. RT-qPCR analyses demonstrated that RhlbZIP4 was significantly up-regulated under low temperature treatment. RhlbZIP24 was significantly upregulated under drought and ABA treatment. RhlbZIP16 was significantly upregulated under high salt and MeJA treatment. 【Conclusion】A total of 57 RhlbZIP genes have been identified in the R. henanense subsp. lingbaoense genome, and all selected genes are expressed under different treatments, and the major genes showing increase in expression in response to low temperature, drought, high salt, ABA and MeJA stress are RhlbZIP4, RhlbZIP24, RhlbZIP16, RhlbZIP24 and RhlbZIP16, respectively.

Key words: Rhododendron henanense subsp. lingbaoense, bZIP gene family, abiotic stress, RT-qPCR

李勇慧, 鲍星星, 段一珂, 赵运霞, 于相丽, 陈尧, 张延召. 灵宝杜鹃bZIP家族全基因组鉴定及表达特征分析[J]. 生物技术通报, 2024, 40(8): 186-198.

LI Yong-hui, BAO Xing-xing, DUAN Yi-ke, ZHAO Yun-xia, YU Xiang-li, CHEN Yao, ZHANG Yan-zhao. Genome-wide Identification and Expression Features Analysis of the bZIP Family in Rhododendron henanense subsp. lingbaoense[J]. Biotechnology Bulletin, 2024, 40(8): 186-198.

图/表 10

表1 RT-qPCR引物序列

Table 1 Primer sequences for RT-qPCR

引物名称Primer name	引物序列Primer sequence（5'-3'）
EF1α-F	TGTCATCGATGCTCCTGGAC
EF1α-R	TCTCGGGTCTGACCATCCTT
RhlbZIP4-F	GCAATTTCGGCTCTGTGAGT
RhlbZIP4-R	AAGTGGACGGTGAGATTGGT
RhlbZIP7-F	GGCCATGGCATCTCATCAAG
RhlbZIP7-R	ACGTTGGGATGTCTCCCATT
RhlbZIP41-F	GAAAGCACACACGGCTTACT
RhlbZIP41-R	TCGAGATTTCGGCTTCGAGA

图1 灵宝杜鹃和拟南芥的bZIP转录因子进化关系

Fig. 1 Evolutionary relationship of bZIP transcription factors in R. henanense subsp. lingbaoense and A. thaliana

图2 灵宝杜鹃bZIP家族成员系统发育关系（A）、基序组成（B）和基因结构（C）

Fig. 2 Phylogenetic relationship（A）, motif composition（B）, and gene structure combination（C）of members of the bZIP family of R. henanense subsp. lingbaoense

图3 灵宝杜鹃bZIP基因家族染色体定位红色基因为串联重复基因

Fig. 3 Chromosomal localization of bZIP family genes in R. henanense subsp. Lingbaoense The red genes are repeated in series

图4 灵宝杜鹃bZIP转录因子共线性分析

Fig. 4 Collinearity analysis of bZIP transcription factors in R. henanense subsp. lingbaoense

表2 16个基因对的Ks、Ka和Ka/Ks的比值

Table 2 Ks, Ka and Ka/Ks ratios of the sixteen gene pairs

基因对 Gene pairs	Ka	Ks	Ka/Ks值
RhlbZIP-2&RhlbZIP-52	0.965 8	1.110 4	0.869 8
RhlbZIP-3&RhlbZIP-54	5.273 6	2.352 6	2.241 6
RhlbZIP-4&RhlbZIP-25	2.243 5	3.787 2	0.592 4
RhlbZIP-7&RhlbZIP-18	4.907 7	2.147 5	2.285 3
RhlbZIP-12&RhlbZIP-21	1.765 8	3.384 7	0.521 7
RhlbZIP-13&RhlbZIP-14	1.047 2	1.365 0	0.767 1
RhlbZIP-15&RhlbZIP-38	1.438 8	2.038 5	0.705 8
RhlbZIP-19&RhlbZIP-33	0.970 8	1.108 9	0.875 5
RhlbZIP-20&RhlbZIP-32	1.027 2	0.905 2	1.134 8
RhlbZIP-26&RhlbZIP-53	2.080 5	3.975 9	0.523 3
RhlbZIP-28&RhlbZIP-46	1.047 1	0.846 9	1.236 5
RhlbZIP-30&RhlbZIP-43	0.962 8	1.134 1	0.849 0
RhlbZIP-31&RhlbZIP-34	0.931 3	1.280 4	0.727 4
RhlbZIP-36&RhlbZIP-48	2.289 1	4.049 4	0.565 3
RhlbZIP-37&RhlbZIP-40	1.020 4	0.936 5	1.089 6
RhlbZIP-44&RhlbZIP-55	0.976 2	1.078 6	0.905 1

图5 RhlbZIP启动子中顺式元件的数量

Fig. 5 Number of homeopathic elements in the RhlbZIP promoter

图6 灵宝杜鹃bZIP转录因子GO注释

Fig. 6 GO annotation of bZIP transcription factor in R. henanense subsp. lingbaoense

图7 RhlbZIP基因在不同组织（根、茎、叶、花和下胚轴）中表达谱的热图根据色码显示log10（FPKM）值（右上）

Fig. 7 Hierarchical clustering of expression profiles of RhlbZIP genes in different tissues（root, stem, leaf, flower, and hypocotyl） log10（FPKM）values showed according to the color code（Top right）

图8 灵宝杜鹃基因在不同处理下表达量分析与0 h对照相比，* P < 0.05，**P < 0.01，***P<0.001

Fig. 8 Expression analysis of three genes of in R. henanense subsp. lingbaoense under different treatments Compared with 0 h control, * P< 0.05, **P< 0.01, ***P<0. 001

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