萝卜ALMT基因家族的鉴定与表达

doi:10.3969/j.issn.1004-1524.2022.04.11

浙江农业学报 ›› 2022, Vol. 34 ›› Issue (4): 746-755.DOI: 10.3969/j.issn.1004-1524.2022.04.11

萝卜ALMT基因家族的鉴定与表达

刘同金¹(), 徐铭婕¹, 汪精磊², 刘良峰³, 崔群香¹, 包崇来²^,^*(), 王长义¹^,^*()

1.金陵科技学院园艺园林学院,江苏南京 210038
2.浙江省农业科学院蔬菜研究所,浙江杭州 310021
3.江宁区农业农村局,江苏南京 211100

收稿日期:2021-07-30 出版日期:2022-04-25 发布日期:2022-04-28
通讯作者: 包崇来,王长义
作者简介:包崇来,E-mail: baocl@mail.zaas.ac.cn
*王长义,E-mail: cywang@jit.edu.cn;
刘同金(1985—),男,山东德州人,博士,讲师,研究方向为蔬菜种质资源与分子生物学。E-mail: tongjinliu@163.com
基金资助:
国家自然科学基金(31801858);国家级大学生创新训练计划(202113573014Z);金陵科技学院高层次人才科研启动项目(jit-b-202009);国家现代农业产业技术体系(CARS-23-A-14)

Genome-wide identification and expression analysis of ALMT gene family in radish

LIU Tongjin¹(), XU Mingjie¹, WANG Jinglei², LIU Liangfeng³, CUI Qunxiang¹, BAO Chonglai²^,^*(), WANG Changyi¹^,^*()

1. College of Horticulture, Jinling Institute of Technology, Nanjing 210038, China
2. Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
3. Agricultural and Rural Affairs Bureau of Jiangning District, Nanjing 211100, China

Received:2021-07-30 Online:2022-04-25 Published:2022-04-28
Contact: BAO Chonglai,WANG Changyi

摘要/Abstract

摘要：

为探究萝卜铝激活苹果酸转运蛋白(ALMT)家族成员对生物和非生物胁迫的响应,本研究通过生物信息学方法对萝卜ALMT家族成员进行鉴定,并利用转录组数据对其进行表达分析。结果显示,萝卜基因组中包含17个ALMT基因,分布于8条染色体。该家族成员外显子数量为5~7个,预测N-端含有5~6个跨膜结构,在染色体上的分布不均匀。萝卜ALMT基因家族成员启动子上有多种激素响应、胁迫响应、组织和器官生长发育与环境响应的顺式作用元件,表明萝卜ALMT基因家族成员的表达受多种条件的调控。对它们在不同组织和发育时期,以及对Agrobacterium tumefaciens的侵染和重金属(铅、镉和铬)胁迫的响应研究发现,RsALMT1和RsALMT13可能参与抵抗A. tumefaciens的侵染;RsALMT3可能调控叶片气孔的开放,而RsALMT7、RsALMT11和RsALMT14可能调控叶片气孔的关闭;RsALMT15可能参与绿肉萝卜根肉中叶绿素的积累;RsALMT16在抵御铅胁迫过程中发挥重要作用。以上结果将为进一步研究萝卜ALMT家族成员在生物和非生物胁迫响应中的功能与分子机制奠定基础。

关键词: 萝卜, ALMT基因家族, 系统进化, 基因表达

Abstract:

In order to explore the response of aluminium activated malate transporter (ALMT) genes to biotic and abiotic stress in radish,ALMT genes of radish were genome-wide identified by bioinformatics method and expression patterns were analyzed based on RNA-seq data. The results showed that there were 17 ALMT genes in radish genome, and distributed on eight chromosomes. Exon number of these genes ranged from 5 to 7, and 5-6 transmembrane domains were predicted in their N-terminal region. Number of RsALMT genes on chromosomes was different. Expression analysis of RsALMT genes in different tissues and developments stages,treatment with Agrobacterium tumefaciens and heavy metal (cadmium, chromium and lead) showed that RsALMT1 and RsALMT13 might be involved in resistance to the infection of A. tumefaciens, RsALMT3 might control stomatal open, while RsALMT7, RsALMT11 and RsALMT14 mightbe involved in stomatal closure.RsALMT15 might regulate the accumulation of chlorophyll in flesh of radish and RsALMT16 might be involved in resistance to leadstress.Therefore, the above results would provide a theoretical basis for further study on the functions and molecular mechanisms of radish ALMT family members in response to biotic and abiotic stress.

Key words: radish, ALMT gene family, phylogenetic evolution, gene expression

中图分类号:

S631.1

刘同金, 徐铭婕, 汪精磊, 刘良峰, 崔群香, 包崇来, 王长义. 萝卜ALMT基因家族的鉴定与表达[J]. 浙江农业学报, 2022, 34(4): 746-755.

LIU Tongjin, XU Mingjie, WANG Jinglei, LIU Liangfeng, CUI Qunxiang, BAO Chonglai, WANG Changyi. Genome-wide identification and expression analysis of ALMT gene family in radish[J]. Acta Agriculturae Zhejiangensis, 2022, 34(4): 746-755.

图/表 9

表1 萝卜ALMT家族成员基本信息

Table 1 Information of ALMT gene family members in radish

基因名称 Gene name	登录号 Accession No.	氨基酸数量 Number of amino acids/aa	分子量 Molecular weight/u	等电点 Isoeletric point	不稳定指数 Instability index	亲水性 GRAVY	脂肪指数 Aliphatic index	跨膜结构 Transmembrane domain	拟南芥同源基因 Homologue of AtALMT
RsALMT1	Rsa10013723	525	58 320.75	6.40	36.07	0.010	91.22	5	AT2G17470
RsALMT2	Rsa10016259	542	60 681.27	8.99	42.72	-0.072	96.88	5	AT5G46600
RsALMT3	Rsa10035068	621	70 102.62	6.18	36.65	-0.043	89.98	5	AT3G18440
RsALMT4	Rsa10034640	491	54 643.38	8.77	32.83	-0.027	99.61	5	AT3G11680
RsALMT5	Rsa10021670	479	53 569.17	8.30	36.44	0.014	89.37	5	AT4G00910
RsALMT6	Rsa10022591	481	53 733.47	9.04	32.19	-0.020	90.58	6	AT4G00910
RsALMT7	Rsa10025402	543	60 482.70	8.84	40.46	-0.071	95.91	6	AT4G17970
RsALMT8	Rsa10010851	618	68 136.96	7.59	38.48	-0.174	90.95	5	AT5G46610
RsALMT9	Rsa10020182	404	45 923.80	8.41	30.84	-0.125	94.03	6	AT2G27240
RsALMT10	Rsa10011190	489	54 469.32	9.10	32.90	0.032	104.03	5	AT3G11680
RsALMT11	Rsa10039953	580	65 364.87	7.21	40.72	-0.098	86.60	6	AT1G25480
RsALMT12	Rsa10038217	603	67 587.76	6.32	46.06	-0.036	90.10	6	AT1G18420
RsALMT13	Rsa10037498	505	56 082.17	6.53	40.90	-0.049	97.84	5	AT1G08440
RsALMT14	Rsa10040558	515	58 157.37	6.11	41.97	-0.104	88.62	5	AT1G25480
RsALMT15	Rsa10041290	510	56 863.94	6.69	38.69	-0.123	94.43	5	AT1G08440
RsALMT16	Rsa10041291	471	52 544.32	6.11	42.05	-0.020	98.09	5	AT1G08430
RsALMT17	Rsa10003573	484	54 188.99	8.59	31.96	0.067	93.22	6	AT4G00910

图1 萝卜ALMT基因家族成员的染色体定位

Fig.1 Chromosomal position of the ALMT gene family members in radish

图2 萝卜ALMT基因家族成员进化树与基因结构

Fig.2 Phylogenetic tree and exon distribution of ALMT family members in radish

图3 萝卜(Rs)、拟南芥(AT)与甘蓝型油菜(Bna)ALMT基因家族成员编码的蛋白质进化树

Fig.3 Phylogenetic tree of proteins coded by ALMT gene family members in Raphanus sativus(Rs), Arabidopsis(AT) and Brassica napus(Bna)

图4 萝卜ALMT基因家族成员启动子顺式作用元件预测

Fig.4 Predicted cis-elements in RsALMT promoters

图5 萝卜ALMT基因家族成员的组织表达模式 ESS、SS、EES、RES和MS分别为芽期、破肚期、膨大前期、膨大盛期和成熟期。

Fig.5 Expression profiles of RsALMT genes in various tissues ESS, seedling stage; SS, splitting stage; EES, early expanding stage; RES, rapid expanding stage; MS, mature stage.

图6 绿肉萝卜与白肉萝卜不同发育时期肉质根ALMT基因家族成员的表达 S1,9月25日,S2,10月2日,S3,10月9日,S4,10月16日,S5,10月23日。

Fig.6 Expression profiles of RsALMT genes in different growing stage of taproot of white and green flesh S1, September 25th; S2, October 2nd; S3, October 9th; S4, October 16th; S5, October 23th.

图7 抗和感根癌病萝卜接种A. tumefaciens 7 d后下胚轴ALMT基因家族成员的表达 Line_18和Line_19分别为抗和感根癌病萝卜株系;CK为接种LB培养基7 d,T为接种A. tumefaciens处理7 d。

Fig.7 Expression profiles of ALMT gene family members in 7 d after incubated with A. tumefaciens of hypocotyls Line_18 and Line_19 was resistance and susceptible radish inbred lines to A. tumefaciens, respectively. CK, 7 d after incubated with LB medium; T, 7 d after incubated with A. tumefaciens.

图8 重金属(铅、镉和铬)胁迫萝卜根中ALMT基因家族成员的表达

Fig.8 Expression profiles of ALMT gene family members in radish root with heavy metal (lead, cadmium and chromium) stress treatment

参考文献 38

[1]	SHARMA T, DREYER I, KOCHIAN L, et al. The ALMT family of organic acid transporters in plants and their involvement in detoxification and nutrient security[J]. Frontiers in Plant Science, 2016, 7: 1488.
[2]	BARBIER-BRYGOO H, DE ANGELI A, FILLEUR S, et al. Anion channels/transporters in plants: from molecular bases to regulatory networks[J]. Annual Review of Plant Biology, 2011, 62: 25-51. DOI URL
[3]	LIU J, ZHOU M X. The ALMT gene family performs multiple functions in plants[J]. Agronomy, 2018, 8(2): 20. DOI URL
[4]	XU M Y, GRUBER B D, DELHAIZE E, et al. The barley anion channel, HvALMT 1, has multiple roles in guard cell physiology and grain metabolism[J]. Physiologia Plantarum, 2015, 153(1): 183-193. DOI URL
[5]	MOTODA H, SASAKI T, KANO Y, et al. The membrane topology of ALMT1, an aluminum-activated malate transport protein in wheat (Triticum aestivum)[J]. Plant Signaling & Behavior, 2007, 2(6): 467-472.
[6]	PENG W T, WU W W, PENG J C, et al. Characterization of the soybean GmALMT family genes and the function of GmALMT5 in response to phosphate starvation[J]. Journal of Integrative Plant Biology, 2018, 60(3): 216-231. DOI URL
[7]	SASAKI T, YAMAMOTO Y, EZAKI B, et al. A wheat gene encoding an aluminum-activated malate transporter[J]. The Plant Journal, 2004, 37(5): 645-653. DOI URL
[8]	KOVERMANN P, MEYER S, HÖRTENSTEINER S, et al. The Arabidopsis vacuolar malate channel is a member of the ALMT family[J]. The Plant Journal, 2007, 52(6): 1169-1180. DOI URL
[9]	KOBAYASHI Y, KOBAYASHI Y, SUGIMOTO M, et al. Characterization of the complex regulation of AtALMT1 expression in response to phytohormones and other inducers[J]. Plant Physiology, 2013, 162(2): 732-740. DOI URL
[10]	HOEKENGA O A, MARON L G, PIÑEROS M A, et al. AtALMT1, which encodes a malate transporter, is identified as one of several genes critical for aluminum tolerance in Arabidopsis[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(25): 9738-9743.
[11]	LIGABA A, MARON L, SHAFF J, et al. Maize ZmALMT2 is a is a root anion transporter that mediates constitutive root malate efflux[J]. Plant, Cell & Environment, 2012, 35(7): 1185-1200.
[12]	CHEN Z C, YOKOSHO K, KASHINO M, et al. Adaptation to acidic soil is achieved by increased numbers of cis-acting elements regulating ALMT1 expression in Holcus lanatus[J]. The Plant Journal, 2013, 76(1): 10-23.
[13]	LIANG C Y, PIÑEROS M A, TIAN J, et al. Low pH, aluminum, and phosphorus coordinately regulate malate exudation through GmALMT1 to improve soybean adaptation to acid soils[J]. Plant Physiology, 2013, 161(3): 1347-1361. DOI URL
[14]	LIGABA A, KATSUHARA M, RYAN P R, et al. The BnALMT1 and BnALMT2 genes from rape encode aluminum-activated malate transporters that enhance the aluminum resistance of plant cells[J]. Plant Physiology, 2006, 142(3): 1294-1303. DOI URL
[15]	CHEN Q, WU K H, WANG P, et al. Overexpression of MsALMT1, from the aluminum-sensitive Medicago sativa, enhances malate exudation and aluminum resistance in tobacco[J]. Plant Molecular Biology Reporter, 2013, 31(3): 769-774. DOI URL
[16]	EISENACH C, BAETZ U, HUCK N V, et al. ABA-induced stomatal closure involves ALMT4, a phosphorylation-dependent vacuolar anion channel of Arabidopsis[J]. The Plant Cell, 2017, 29(10): 2552-2569. DOI URL
[17]	DE ANGELI A, ZHANG J, MEYER S, et al. AtALMT9 is a malate-activated vacuolar chloride channel required for stomatal opening in Arabidopsis[J]. Nature Communications, 2013, 4: 1804. DOI URL
[18]	MEYER S, SCHOLZ-STARKE J, DE ANGELI A, et al. Malate transport by the vacuolar AtALMT6 channel in guard cells is subject to multiple regulation[J]. The Plant Journal, 2011, 67(2): 247-257. DOI URL
[19]	SASAKI T, MORI I C, FURUICHI T, et al. Closing plant stomata requires a homolog of an aluminum-activated malate transporter[J]. Plant & Cell Physiology, 2010, 51(3): 354-365.
[20]	DE ANGELI A, BAETZ U, FRANCISCO R, et al. The vacuolar channel VvALMT9 mediates malate and tartrate accumulation in berries of Vitis vinifera[J]. Planta, 2013, 238(2): 283-291. DOI URL
[21]	MA B Q, LIAO L, ZHENG H Y, et al. Genes encoding aluminum-activated malate transporter II and their association with fruit acidity in apple[J/OL]. The Plant Genome, 2015, 8(3):1-14.[2021-07-20]. https://acsess.onlinelibrary.wiley.com/doi/10.3835/plantgenome2015.03.0016.
[22]	XU M Y, GRUBER B D, DELHAIZE E, et al. The barley anion channel, HvALMT1, has multiple roles in guard cell physiology and grain metabolism[J]. Physiologia Plantarum, 2015, 153(1): 183-193. DOI URL
[23]	XU L L, QIAO X, ZHANG M Y, et al. Genome-Wide analysis of aluminum-activated malate transporter family genes in six Rosaceae species, and expression analysis and functional characterization on malate accumulation in Chinese white pear[J]. Plant Science, 2018, 274: 451-465. DOI URL
[24]	MA B Q, YUAN Y Y, GAO M, et al. Genome-wide identification, molecular evolution, and expression divergence of aluminum-activated malate transporters in apples[J]. International Journal of Molecular Sciences, 2018, 19(9): 2807. DOI URL
[25]	MA X W, AN F, WANG L F, et al. Genome-wide identification of aluminum-activated malate transporter (ALMT) gene family in rubber trees (Hevea brasiliensis) highlights their involvement in aluminum detoxification[J]. Forests, 2020, 11(2): 142. DOI URL
[26]	张慧, 李泽锋, 徐国云, 等. 普通烟草ALMT基因家族的鉴定与表达分析[J]. 烟草科技, 2020, 53(5): 1-9.
	ZHANG H, LI Z F, XU G Y, et al. Identification and expression analysis of ALMT gene family in Nicotiana tabacum[J]. Tobacco Science & Technology, 2020, 53(5): 1-9. (in Chinese with English abstract)
[27]	DIN I, ULLAH I, WANG W, et al. Genome-wide analysis, evolutionary history and response of ALMT family to phosphate starvation in Brassica napus[J]. International Journal of Molecular Sciences, 2021, 22(9): 4625. DOI URL
[28]	ZHANG X H, YUE Z, MEI S Y, et al. A de novo genome of a Chinese radish cultivar[J]. Horticultural Plant Journal, 2015, 1(3): 155-164.
[29]	HU B, JIN J P, GUO A Y, et al. GSDS 2.0: an upgraded gene feature visualization server[J]. Bioinformatics, 2014, 31(8): 1296-1297. DOI URL
[30]	CHEN C J, CHEN H, ZHANG Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 2020, 13(8): 1194-1202. DOI URL
[31]	WANG J, QIU Y, WANG X, et al. Insights into the species-specific metabolic engineering of glucosinolates in radish (Raphanus sativus L.) based on comparative genomic analysis[J]. Scientific Reports, 2017, 7: 16040. DOI URL
[32]	刘同金, 张晓雪, 张晓辉, 等. 萝卜全基因组中LBD基因家族成员的鉴定与分析[J]. 植物遗传资源学报, 2019, 20(1): 168-178.
	LIU T J, ZHANG X X, ZHANG X H, et al. Genome-wide characterization of the LBD gene family in radish[J]. Journal of Plant Genetic Resources, 2019, 20(1): 168-178. (in Chinese with English abstract)
[33]	LI Y Y, HAN M, WANG R H, et al. Comparative transcriptome analysis identifies genes associated with chlorophyll levels and reveals photosynthesis in green flesh of radish taproot[J]. PLoS One, 2021, 16(5): e0252031. DOI URL
[34]	TKACHENKO A A, GANCHEVA M S, TVOROGOVA V E, et al. Transcriptome analysis of crown gall in radish (Raphanus sativus L.) inbred lines[J]. Annals of Applied Biology, 2021, 178(3): 527-548. DOI URL
[35]	XU L, WANG Y, LIU W, et al. De novo sequencing of root transcriptome reveals complex cadmium-responsive regulatory networks in radish (Raphanus sativus L.)[J]. Plant Science, 2015, 236: 313-323. DOI URL
[36]	XIE Y, YE S, WANG Y, et al. Transcriptome-based gene profiling provides novel insights into the characteristics of radish root response to Cr stress with next-generation sequencing[J]. Frontiers in Plant Science, 2015, 6: 202.
[37]	WANG Y, XU L, CHEN Y L, et al. Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to lead (Pb) stress with next generation sequencing[J]. PLoS One, 2013, 8(6): e66539. DOI URL
[38]	LIGABA A, KOCHIAN L, PIÑEROS M. Phosphorylation at S 384 regulates the activity of the TaALMT1 malate transporter that underlies aluminum resistance in wheat[J]. The Plant Journal, 2009, 60(3): 411-423. DOI URL

萝卜ALMT基因家族的鉴定与表达

Genome-wide identification and expression analysis of ALMT gene family in radish

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

图/表 9

参考文献 38

相关文章 15

编辑推荐

Metrics

本文评价

[1]	余艳玲, 罗洪林, 罗辉, 冯鹏霏, 潘传燕, 宋漫玲, 肖蕊, 张永德. 卵形鲳鲹生肌调节因子基因家族的鉴定及在胚胎中的表达[J]. 浙江农业学报, 2022, 34(4): 695-705.
[2]	王乾昆, 张小辉, 庞有志, 祁艳霞, 雷莹, 白俊艳, 户运奇, 赵毅威, 苑志文, 王涛. 基于RNA-seq技术挖掘鹌鹑羽色自别雌雄相关基因[J]. 浙江农业学报, 2022, 34(3): 498-506.
[3]	贾利强, 赵秋芳, 陈曙, 丁波. 玉米转录因子bZIP G亚家族基因的表达模式[J]. 浙江农业学报, 2022, 34(2): 221-231.
[4]	赵国富, 严亚琴, 汪精磊, 魏庆镇, 包崇来. 茄子脂氧合酶家族基因全基因组鉴定与表达分析[J]. 浙江农业学报, 2021, 33(6): 1025-1034.
[5]	杨昕霞, 张斌. 大豆LAZ1基因家族鉴定与GmLAZ1-9基因的功能研究[J]. 浙江农业学报, 2021, 33(4): 586-594.
[6]	黄咏明, 宋放, 王策, 姚京磊, 王志静, 何利刚, 吴黎明, 蒋迎春. 根系修剪对枳生长及相关基因表达的影响[J]. 浙江农业学报, 2021, 33(2): 270-277.
[7]	白皓, 李潇凡, 仲黎, 宋倩倩, 江勇, 张扬, 王志秀, 徐琪, 常国斌, 陈国宏. 连城白鸭不同组织中主要矿物元素沉积规律与关键基因表达水平研究[J]. 浙江农业学报, 2021, 33(12): 2264-2274.
[8]	胡天华, 魏庆镇, 汪精磊, 王五宏, 胡海娇, 严亚琴, 包崇来. 利用QTL-seq定位萝卜肉质根根形指数QTL[J]. 浙江农业学报, 2021, 33(12): 2313-2319.
[9]	杜金梁, 曹丽萍, 贾睿, 顾郑琰, 何勤, 徐跑, JENEYGalina, 马玉忠, 殷国俊. 甘草总黄酮对高脂条件下罗非鱼肝损伤的保护作用[J]. 浙江农业学报, 2021, 33(10): 1826-1835.
[10]	杨海健, 张云贵, 周心智, 洪林, 杨蕾, 彭芳芳, 王武. 不同PE材料遮光下血橙转色期果皮花色苷合成及其相关基因的表达分析[J]. 浙江农业学报, 2021, 33(10): 1861-1869.
[11]	徐秀红, 刘金亮, 李栋成, 刘仁祥. 不同类型烟草种质的烟碱含量变化与相关基因表达水平[J]. 浙江农业学报, 2020, 32(9): 1555-1563.
[12]	刘凯, 冯晓宇, 马恒甲, 谢楠. 钱塘江三角鲂线粒体基因组测序及其结构特征分析[J]. 浙江农业学报, 2020, 32(9): 1591-1608.
[13]	刘坤举, 张小辉, 庞有志, 赵淑娟, 祁艳霞, 王乾昆. 朝鲜鹌鹑GNAS基因表达、克隆及其多态性与羽色的相关性[J]. 浙江农业学报, 2020, 32(8): 1369-1377.
[14]	李秋玲, 齐颖, 王琛, 张一名, 王新妤, 尚校兰, 贾永红, 李美茹, 储明星. 热应激对中国荷斯坦牛乳腺组织基因表达及信号通路的影响[J]. 浙江农业学报, 2020, 32(5): 770-778.
[15]	卢祎, 高有领, 王水涛, 何盛盛. MicroRNA-499对中华鳖脂类代谢相关基因表达的影响[J]. 浙江农业学报, 2020, 32(5): 798-803.