亚麻PLA1基因家族的鉴定及表达分析

doi:10.3724/SP.J.1006.2023.24224

作物学报 ›› 2023, Vol. 49 ›› Issue (11): 2949-3295.doi: 10.3724/SP.J.1006.2023.24224

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

亚麻PLA1基因家族的鉴定及表达分析

赵丽蓉(), 李雯, 王利民, 齐燕妮, 李闻娟, 谢亚萍, 党照, 赵玮, 张建平()

甘肃省农业科学院作物研究所, 甘肃兰州 730070

收稿日期:2022-10-09 接受日期:2023-04-17 出版日期:2023-11-12 网络出版日期:2023-05-23
通讯作者: 张建平, E-mail: zhangJPzw3@gsagr.ac.cn
作者简介:E-mail: 1744245723@qq.com
基金资助:
甘肃省农业科学院现代生物育种项目(2020GAAS08);甘肃省农业科学院现代生物育种项目(2022GAAS04);财政部和农业农村部国家现代农业产业技术体系建设专项(油料), 甘肃省科技计划项目(21JR7RA722);财政部和农业农村部国家现代农业产业技术体系建设专项(油料), 甘肃省科技计划项目(21JR1RA354);甘肃省重大科技项目(21ZD4NA022-02);安宁区科技计划项目(2022-JB-10)

Identification and relative expression pattern of PLA1 gene family in flax

ZHAO Li-Rong(), LI Wen, WANG Li-Min, QI Yan-Ni, LI Wen-Juan, XIE Ya-Ping, DANG Zhao, ZHAO Wei, ZHANG Jian-Ping()

Institute of Crops, Gansu Academy of Agricultural Sciences, Lanzhou 730070, Gansu, China

Received:2022-10-09 Accepted:2023-04-17 Published:2023-11-12 Published online:2023-05-23
Supported by:
Modern Biology Breeding Project of Gansu Academy of Agricultural Sciences(2020GAAS08);Modern Biology Breeding Project of Gansu Academy of Agricultural Sciences(2022GAAS04);China Agriculture Research System (Oil) of MOF and MARA, the Science and Technology Project of Gansu Province(21JR7RA722);China Agriculture Research System (Oil) of MOF and MARA, the Science and Technology Project of Gansu Province(21JR1RA354);Major Science and Technology Project of Gansu Province(21ZD4NA022-02);Science and Technology Planing Project of Anning District(2022-JB-10)

摘要/Abstract

摘要：

磷脂酶A1 (Phospholipase A1, PLA1)在植物生长发育及胁迫反应中发挥着重要作用, 但目前关于PLA1在亚麻中的鉴定与表达特征尚未见报道。本研究利用生物信息学方法对包括亚麻在内的7个物种PLA1基因家族进行鉴定, 分析了亚麻PLA1 (LuPLA1)的序列特征、系统进化关系、顺式作用元件、共线性关系及其复制事件, 并利用转录组数据分析了其在不同遗传背景、不同器官中的表达模式, 利用qRT-PCR分析了其在不同组织、不同发育时期及胁迫处理下的表达模式。结果表明, 在亚麻、拟南芥、玉米、水稻、大豆、蓖麻及木薯基因组中分别鉴定到14、21、15、20、41、18和35个PLA1成员; LuPLA1基因分布于8条染色体上。序列特征分析发现, 除LuPLA1-7和LuPLA1-10外, 其他家族成员都具有内含子且多数含有1个内含子; LuPLA1蛋白序列长度为388~1759 aa, 等电点为5.99~9.19, 分子量为41.55~192.61 kD, 均为亲水性蛋白, 大多数定位于液泡, 含有4~25个Motif。系统进化分析将PLA1蛋白分为4个分支, 其中第IV分支PLA1成员数量最多。共线性分析表明, LuPLA1在拟南芥、玉米、水稻、木薯及大豆中均具有同源基因且与大豆、木薯的同源基因最多。LuPLA1家族成员中共有2对基因发生串联复制, 7对基因发生片段复制, 且都经历了纯化选择。转录组分析发现大多LuPLA1成员表现为器官特异性表达。LuPLA1启动子区含大量激素与逆境响应相关元件, qRT-PCR分析进一步证实LuPLA1基因受激素、干旱、高盐、低温及高温诱导表达。其中LuPLA1-1受IAA诱导表达; LuPLA1-1和LuPLA1-6受NAA诱导表达; LuPLA1-1、LuPLA1-5和LuPLA1-6受GA₃诱导表达; LuPLA1-12/14受NaCl和PEG诱导表达; 除LuPLA1-2/4外, 其余基因均受高温诱导表达; 所有LuPLA1受低温诱导表达, 对低温的响应最为明显。本研究为进一步解析LuPLA1基因家族的功能奠定了基础。

关键词: 亚麻, LuPLA1, 基因家族, 表达分析

Abstract:

Phospholipase A1 (PLA1) plays an important role in plant growth and development and stress responses. However, there is no function study of PLA1 in flax. In this study, we identified the PLA1 gene family in seven species including flax by bioinformatics, and analyzed the sequence characteristics, phylogenetic evolution, cis-acting elements, collinearity, and replication events of PLA1 (LuPLA1) genes in flax. Transcriptome data were used to analyze the relative expression patterns in different genetic backgrounds and organs, and qRT-PCR was used to analyze the relative expression patterns in different tissues and developmental stages, and under different stress treatments. The results showed that there were 14, 21, 15, 20, 41, 18, and 35 PLA1 members identified in flax, Arabidopsis, maize, rice, soybean, castor, and cassava, respectively. LuPLA1 were distributed on 8 chromosomes. Sequence analysis showed that except for LuPLA1-7 and LuPLA1-10, all the other members had introns and most of them had one intron, with protein length of 388-1759 aa, isoelectric point of 5.99-9.19, and molecular weight of 41.55-192.61 kD. All the LuPLA1 proteins were hydrophilic, and most of them localized in vacuoles and contained 4-25 motifs. Phylogenetic analysis revealed that the PLA1 proteins were divided into four clades, and clade IV had the largest number of PLA1 members. Collinearity analysis indicated that LuPLA1 had homologous genes in Arabidopsis, maize, rice, cassava, and soybean, and had the most homologous genes with soybean and cassava. There were two tandem duplicated gene pairs and seven segment duplicated genes pairs of LuPLA1 family members, and all the duplicated genes underwent purification selection. Transcriptome analysis showed that most LuPLA1 members exhibited organ-specific expression patterns. The promoter regions of LuPLA1 contained a large number of hormone and stress response elements. The qRT-PCR further confirmed that the relative expression of LuPLA1 genes were induced by hormone, drought, high salt, low temperature, and high temperature. LuPLA1-1 was induced by IAA. LuPLA1-1 and LuPLA1-6 were induced by NAA. LuPLA1-1, LuPLA1-5, and LuPLA1-6 were induced by GA₃. LuPLA1-12/14 was induced by NaCl and PEG. Except for LuPLA1-2/4, the other genes were induced by high temperature. All LuPLA1 members were induced by low temperature, and the response to low temperature was the most obvious. This study laid a foundation for further analysis of the function of LuPLA1 gene family.

Key words: flax, LuPLA1, gene family, the relative expression pattern

赵丽蓉, 李雯, 王利民, 齐燕妮, 李闻娟, 谢亚萍, 党照, 赵玮, 张建平. 亚麻PLA1基因家族的鉴定及表达分析[J]. 作物学报, 2023, 49(11): 2949-3295.

ZHAO Li-Rong, LI Wen, WANG Li-Min, QI Yan-Ni, LI Wen-Juan, XIE Ya-Ping, DANG Zhao, ZHAO Wei, ZHANG Jian-Ping. Identification and relative expression pattern of PLA1 gene family in flax[J]. Acta Agronomica Sinica, 2023, 49(11): 2949-3295.

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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′)
GAPDH	CTTTACCCTCAGCAAATCCG	AGGTTCTTCCCGCTCTCAAT
PLA1-1	TCTTCCCTCAGAACAGAGGTGTATTT	AGTCTTGTTGGACCCTGTCCCTAG
PLA1-2/4	CCTCTTCTCGTCCCTTGCTTTGA	GGAGAAGAGCAGGGAACGAAACT
PLA1-3/11	ATTTCCGTTTATGGGAGGTTTGCC	TAAAGGCAAATACCCTCCAAACGG
PLA1-5	CTTGATGGGGAGAATGTGAGGA	GTTGGAGCTGCGGAAGTTGATA
PLA1-6	GCTTGATGGGAAGGATGTGAGGAT	AGAGGGCGTTTGTTGTCATTTGGT
PLA1-7/10	CGAATTGACCCTAAAGGACACG	GCTTAACTGGGATTTCCTGTGC
PLA1-8/9	GAACAGCGACGAATAATCCAACG	CTTGTCGCTGCTTATTAGGTTGC
PLA1-12/14	ATGGGAGGTTTGCCGGGCTAC	TACCCTCCAAACGGCCCGATG

名称 Name	登录号 Accession number	名称 Name	登录号 Accession number
Longya-10-fruit-1	SRR8281918	Heiya-14-fruit-1	SRR8281912
Longya-10-fruit-2	SRR8281919	Heiya-14-fruit-2	SRR8281913
Longya-10-stem-1	SRR8281920	Heiya-14-stem-1	SRR8281916
Longya-10-stemt-2	SRR8281921	Heiya-14-stem-2	SRR8281917

基因对 Gene pairs	复制事件 Duplication events	同义替换率 K_s	非同义替换率 K_a	K_a/K_s	选择类型 Selection type	分歧时间 Divergence time (Mya)
LuPLA1-7/LuPLA1-8	串联复制 Tandem duplication	0.5411	0.1419	0.2622	纯化选择 Purifying selection	44.3525
LuPLA1-9/LuPLA1-10	串联复制 Tandem duplication	0.5093	0.1448	0.2843	纯化选择 Purifying selection	41.7459
LuPLA1-2/LuPLA1-4	片段复制 Segmental duplication	0.1189	0.0213	0.1791	纯化选择 Purifying selection	9.7459
LuPLA1-3/LuPLA1-11	片段复制 Segmental duplication	0.1217	0.0061	0.0501	纯化选择 Purifying selection	9.9754
LuPLA1-3/LuPLA1-12	片段复制 Segmental duplication	1.0065	0.0692	0.0687	纯化选择 Purifying selection	82.5000
LuPLA1-7/LuPLA1-9	片段复制 Segmental duplication	0.5776	0.1400	0.2424	纯化选择 Purifying selection	47.3443
LuPLA1-11/LuPLA1-12	片段复制 Segmental duplication	0.9443	0.0758	0.0803	纯化选择 Purifying selection	77.4016
LuPLA1-11/LuPLA1-14	片段复制 Segmental duplication	0.9403	0.0770	0.0819	纯化选择 Purifying selection	77.0738
LuPLA1-12/LuPLA1-14	片段复制 Segmental duplication	0.0845	0.0135	0.1598	纯化选择 Purifying selection	6.9262

基因名称 Gene name	基因号 Gene ID	染色体位置 Chromosome location	外显子数量 No. of exons	蛋白序列长度 Protein length (aa)	分子量 Molecular weight (kD)	等电点 Isoelectric point	亚细胞定位 Subcellular location
LuPLA1-1	L.us.o.m.scaffold73.66	Chr1:21780419- 21783081(-)	7	459	50.96	5.99	液泡 Vacuole
LuPLA1-2	L.us.o.m.scaffold17.61	Chr5:5454111- 5456030(-)	2	388	41.55	8.08	液泡 Vacuole
LuPLA1-3	L.us.o.m.scaffold255.68	Chr5:17092681- 17095829(-)	2	463	50.92	8.00	液泡 Vacuole
LuPLA1-4	L.us.o.m.scaffold11.49	Chr6:4217828- 4219482(+)	2	390	41.81	7.52	液泡 Vacuole
LuPLA1-5	L.us.o.m.scaffold100.2	Chr7:7572800- 7576425(+)	7	400	44.50	6.97	液泡 Vacuole
LuPLA1-6	L.us.o.m.scaffold284.7	Chr7:7630026- 7633875(+)	7	391	43.23	6.92	液泡 Vacuole
LuPLA1-7	L.us.o.m.scaffold219.29	Chr8:17228540- 17230314(+)	1	483	52.59	9.19	细胞膜, 液泡 Cell membrane, vacuole
LuPLA1-8	L.us.o.m.scaffold219.27	Chr8:17242561- 17243859(+)	2	421	45.31	8.99	液泡 Vacuole
LuPLA1-9	L.us.o.m.scaffold253.44	Chr11:1866126- 1867424(-)	2	421	45.30	8.99	液泡 Vacuole
LuPLA1-10	L.us.o.m.scaffold253.45	Chr11:1884093- 1885373(-)	1	426	45.90	9.15	叶绿体, 液泡 Chloroplast, vacuole
LuPLA1-11	L.us.o.m.scaffold144.142	Chr11:13906282- 13908918(-)	2	463	50.94	7.55	叶绿体, 液泡 Chloroplast, vacuole
LuPLA1-12	L.us.o.m.scaffold263.24	Chr12:5589259- 5592930(+)	2	453	49.49	7.01	液泡 Vacuole
LuPLA1-13	L.us.o.m.scaffold220.83	Chr15:8920678- 8929774(-)	28	1759	192.61	6.80	液泡 Vacuole
LuPLA1-14	L.us.o.m.scaffold0.620	Chr15:11287238- 11289213(-)	2	452	49.43	6.97	叶绿体, 液泡 Chloroplast, vacuole

亚麻PLA1基因家族的鉴定及表达分析

Identification and relative expression pattern of PLA1 gene family in flax

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