油莎豆块茎特异性表达基因鉴定及分析
- 河南省农业科学院经济作物研究所, 郑州 450002
收稿日期: 2024-06-28
录用日期: 2024-08-20
网络出版日期: 2024-08-27
基金资助
河南省重大科技专项(211100110100);河南省重点研发与推广专项(科技攻关)(242102110305);河南省重点研发与推广专项(科技攻关)(242102110290)
Identification and Analysis of Tuber-specific Expression Genes in Cyperus esculentus
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
Received date: 2024-06-28
Accepted date: 2024-08-20
Online published: 2024-08-27
摘要
块茎是油莎豆(Cyperus esculentus)独特且极其重要的器官, 富含油脂且具有与种子类似的繁殖能力, 研究油莎豆块茎特异性表达基因对于解析其块茎特异性生长发育(尤其是油脂积累)的调控机理具有重要意义。通过对油莎豆主要器官(根、叶、分蘖节、匍匐茎和块茎)进行转录组测序, 全面筛选块茎特异性表达基因, 并分析相关基因的功能。结果表明, 分别以根、叶、分蘖节和匍匐茎为对照, 经过多组比对分析后共鉴定出155个块茎特异性表达基因; GO富集分析显示, 与种子发育、种子油体合成、油脂储存、脱落酸响应、非生物刺激响应和蛋白折叠相关的7个GO条目显著富集, 这些GO条目涉及的基因恰好反映出油莎豆块茎独特的类似种子的发育特性。其中, CESC_00080和CESC_16572编码油体钙蛋白, CESC_08636、CESC_12549和CESC_17828编码油体蛋白, 均参与植物油体的形成, 而油体形成是植物完成油脂储存的关键步骤, 表明这些油体形成相关基因在块茎中的特异性表达可能是油莎豆在块茎中储存大量油脂的关键所在。此外, 还筛选出8个块茎特异性表达转录因子编码基因, 如CESC_00448 (编码abscisic acid insensitive 5-like protein ABI5)和CESC_03736 (编码heat stress transcription factor C), 而在鉴定到的块茎特异性表达基因中发现一些潜在的靶基因, 表明这些转录因子可能调控各自靶基因的特异性表达。综上, 研究结果可为油莎豆块茎发育相关基因调控网络的构建以及块茎特异性基因表达的分子机制解析提供重要参考。
本文引用格式
张向歌 , 陈晨 , 程珊 , 李春鑫 , 朱雅婧 , 许欣然 , 王会伟 . 油莎豆块茎特异性表达基因鉴定及分析[J]. 植物学报, 2025 , 60(1) : 33 -48 . DOI: 10.11983/CBB24097
Abstract
Tuber is a unique and extremely important organ of Cyperus esculentus, which is rich in oil and has the reproduction ability similar to seed. It is of great significance to study the specific expression genes in the tubers of C. esculentus for analyzing the regulation mechanism of tuber-specific growth and development (especially oil accumulation). Through transcriptome sequencing of the main organs (root, leaf, tillering node, stolon and tuber) of C. esculentus, the genes specifically expressed in tubers were comprehensively screened and the functions of related genes were analyzed. The results showed that a total of 155 tuber-specific expression genes were identified after multiple sets of comparative analysis by taking root, leaf, tillering node and stolon as reference, respectively. GO enrichment analysis showed that 7 GO terms including seed development, seed oilbody biogenesis, oil storage, abscisic acid response, response to abiotic stimulus and protein folding were significantly enriched, and some of the genes involved in these GO terms just reflected the unique development characteristics similar to seed of C. esculentus tubers. Among them, CESC_00080 and CESC_16572 encode caleosin, and meanwhile, CESC_08636, CESC_12549 and CESC_17828 encode oleosin, all of which are involved in the formation of plant oil bodies. Since oil body formation is a key step for plants to complete oil storage, it is indicated that the specific expression of these oil body formation-related genes in tubers may be the key to the storage of large amounts of oil in the tubers of C. esculentus. In addition, this study also screened eight tuber-specific expression transcription factor genes, such as CESC_00448 (abscisic acid insensitive 5-like protein ABI5) and CESC_03736 (heat stress transcription factor C), some of whose potential target genes were found in identified tuber-specific expression genes, indicating that these transcription factor genes may regulate the specific expression of their respective target genes. In summary, the results of this study can provide an important reference for the construction of gene regulatory networks related to tuber development of C. esculentus and the molecular mechanism analysis of tuber-specific gene expression.
Key words： Cyperus esculentus; tuber; transcriptome sequencing; specific expression
参考文献
| [1] | Alexa A, Rahnenfuhrer J (2010). topGO: enrichment analysis for gene ontology. R Package Version 2.0. 2010. |
| [2] | Alonso R, On?ate-Sa?nchez L, Weltmeier F, Ehlert A, Diaz I, Dietrich K, Vicente-Carbajosa J, Dro?ge-Laser W (2009). A pivotal role of the basic leucine zipper transcription factor bZIP53 in the regulation of Arabidopsis seed maturation gene expression based on heterodimerization and protein complex formation. Plant Cell 21, 1747-1761. |
| [3] | Bolger AM, Lohse M, Usadel B (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120. |
| [4] | Cai ZQ, Cai ZP, Huang JL, Wang AQ, Ntambiyukuri A, Chen BM, Zheng GH, Li HF, Huang YM, Zhan J, Xiao D, He LF (2022). Transcriptomic analysis of tuberous root in two sweet potato varieties reveals the important genes and regulatory pathways in tuberous root development. BMC Genomics 23, 473. |
| [5] | Chen AM (2012). Research progress on stem/leaf-specific promoters in rice. Mod Agric Sci Technol (17), 16-17, 19. (in Chinese) |
| 陈爱敏 (2012). 水稻茎叶特异性启动子研究进展. 现代农业科技 (17), 16-17, 19. | |
| [6] | Chen JQ, Zhao MZ, Wang Y, Zhang MP (2023). Research progress on tissue specific promoters in plant. North Hortic (19), 128-134. (in Chinese) |
| 陈建琦, 赵明珠, 王义, 张美萍 (2023). 植物中组织特异性启动子的研究进展. 北方园艺 (19), 128-134. | |
| [7] | Chitnis PR, Morishige DT, Nechushtai R, Thornber JP (1988). Assembly of the barley light-harvesting chlorophyll a/b proteins in barley etiochloroplasts involves processing of the precursor on thylakoids. Plant Mol Biol 11, 95-107. |
| [8] | Clevenger J, Chu Y, Scheffler B, Ozias-Akins P (2016). A developmental transcriptome map for allotetraploid Arachis hypogaea. Front Plant Sci 7, 1446. |
| [9] | Collin A, Daszkowska-Golec A, Szarejko I (2021). Updates on the role of ABSCISIC ACID INSENSITIVE 5 (ABI5) and ABSCISIC ACID-RESPONSIVE ELEMENT BINDING FACTORs (ABFs) in ABA signaling in different developmental stages in plants. Cells 10, 1996. |
| [10] | Cui P, Zhao YR, Yao ZP, Pang LJ, Lu GQ (2022). Starch physicochemical properties and expression levels of anabolism key genes in sweetpotato under low temperature. Sci Agric Sin 55, 3831-3840. (in Chinese) |
| 崔鹏, 赵逸人, 姚志鹏, 庞林江, 陆国权 (2022). 低温对甘薯淀粉理化特性及代谢关键基因表达量的影响. 中国农业科学 55, 3831-3840. | |
| [11] | Fan SH, Liu N, Hua W (2021). Research advances in the biosynthesis and regulation of lipid in oil crops. Chin J Oil Crop Sci 43, 361-375. (in Chinese) |
| 范世航, 刘念, 华玮 (2021). 油料作物油脂合成调控研究进展. 中国油料作物学报 43, 361-375. | |
| [12] | Hodge A, Berta G, Doussan C, Merchan F, Crespi M (2009). Plant root growth, architecture and function. Plant Soil 321, 153-187. |
| [13] | Izadi-Darbandi A, Alameldin H, Namjoo N, Ahmad K (2023). Introducing sorghum DREB2 gene in maize (Zea mays L.) to improve drought and salinity tolerance. Biotechnol Appl Biochem 4, 1480-1488. |
| [14] | Jia Y, Yao M, He X, Xiong XH, Guan M, Liu ZS, Guan CY, Qian LW (2022). Transcriptome and regional association analyses reveal the effects of oleosin genes on the accumulation of oil content in Brassica napus. Plants 11, 3140. |
| [15] | Jiao Y, Liu XQ, Jiang HY, Chen RM (2019). Research advances of plant tissue specific promoters. J Agric Sci Technol 21, 18-28. (in Chinese) |
| 焦勇, 柳小庆, 江海洋, 陈茹梅 (2019). 植物组织特异性启动子研究进展. 中国农业科技导报 21, 18-28. | |
| [16] | Kim D, Langmead B, Salzberg SL (2015). HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357-360. |
| [17] | Li JS, Xue X, Xu J, Wu B (2023). Cloning and activity comparison of eight green tissue-specific promoters. Mol Plant Breed, 1-13 [2024-05-25]. http://kns.cnki.net/kcms/detail/46.1068.S.20230524.1143.006.html. (in Chinese) |
| 李姬霜, 薛旭, 徐静, 吴斌 (2023). 八个绿色组织特异性启动子的克隆及活性比较. 分子植物育种, 1-13 [2024-05-25]. http://kns.cnki.net/kcms/detail/46.1068.S.20230524.1143.006.html. | |
| [18] | Li WX, Oono Y, Zhu JH, He XJ, Wu JM, Iida K, Lu XY, Cui XP, Jin HL, Zhu JK (2008). The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell 20, 2238-2251. |
| [19] | Li YC, Li K, Wang LN, Chen X, Li YZ, Wang WQ (2023). Cloning and identification of root tissue-specific promoter from cassava (Manihot esculenta Crantz.). J South Agric 54, 1925-1932. (in Chinese) |
| 李远超, 李可, 王连南, 陈新, 李有志, 王文泉 (2023). 木薯根组织特异性启动子的克隆及鉴定. 南方农业学报 54, 1925-1932. | |
| [20] | Li ZJ, Qin Y (2021). Chromatin accessibility and the gene expression regulation in plants. Chin Bull Bot 56, 664-675. (in Chinese) |
| 李占杰, 秦源 (2021). 染色质可及性与植物基因表达调控. 植物学报 56, 664-675. | |
| [21] | Li ZX, Chen XB (2015). Research advances in plant tissue specific promoters and related cis-acting elements. J Biol 32(6), 91-95. (in Chinese) |
| 李濯雪, 陈信波 (2015). 植物组织特异性启动子及相关顺式作用元件研究进展. 生物学杂志 32(6), 91-95. | |
| [22] | Liu K, Li GJ, Yang Q (2022). Research progress in DREB/ CBF transcription factor involved in responses in plant to abiotic stress. Biotechnol Bull 38(5), 201-214. (in Chinese) |
| 刘坤, 李国婧, 杨杞 (2022). 参与植物非生物逆境响应的DREB/CBF转录因子研究进展. 生物技术通报 38(5), 201-214. | |
| [23] | Liu YH, Li YM, Liu Z, Wang L, Lin-Wang K, Zhu JY, Bi ZZ, Sun C, Zhang JL, Bai JP (2023). Integrative analysis of metabolome and transcriptome reveals a dynamic regulatory network of potato tuber pigmentation. iScience 26, 105903. |
| [24] | Livak KJ, Schmittgen TD (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods 25, 402-408. |
| [25] | Mikami K, Sakamoto A, Iwabuchi M (1994). The HBP-1 family of wheat basic/leucine zipper proteins interacts with overlapping cis-acting hexamer motifs of plant histone genes. J Biol Chem 269, 9974-9985. |
| [26] | Mudge SR, Smith FW, Richardson AE (2003). Root-specific and phosphate-regulated expression of phytase under the control of a phosphate transporter promoter enables Arabidopsis to grow on phytate as a sole P source. Plant Sci 165, 871-878. |
| [27] | Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33, 290-295. |
| [28] | Qu AL, Ding YF, Jiang Q, Zhu C (2013). Molecular mechanisms of the plant heat stress response. Biochem Biophys Res Commun 432, 203-207. |
| [29] | Ramegowda V, Gill US, Sivalingam PN, Gupta A, Gupta C, Govind G, Nataraja KN, Pereira A, Udayakumar M, Mysore KS, Senthil-Kumar M (2017). GBF3 transcription factor imparts drought tolerance in Arabidopsis thaliana. Sci Rep 7, 9148. |
| [30] | Schünmann PHD, Richardson AE, Smith FW, Delhaize E (2004). Characterization of promoter expression patterns derived from the Pht1 phosphate transporter genes of barley (Hordeum vulgare L.). J Exp Bot 55, 855-865. |
| [31] | Smolikova G, Leonova T, Vashurina N, Frolov A, Medvedev S (2021). Desiccation tolerance as the basis of long-term seed viability. Int J Mol Sci 22, 101. |
| [32] | S?derman E, Mattsson J, Engstr?m P (1996). The Arabidopsis homeobox gene ATHB-7 is induced by water deficit and by abscisic acid. Plant J 10, 375-381. |
| [33] | Song SQ, Liu J, Tang CF, Cheng HY, Wang WQ, Zhang Q, Zhang WH, Gao JD (2022). Research progress on the physiology and its molecular mechanism of seed desiccation tolerance. Sci Agric Sin 55, 1047-1063. (in Chinese) |
| 宋松泉, 刘军, 唐翠芳, 程红焱, 王伟青, 张琪, 张文虎, 高家东 (2022). 种子耐脱水性的生理及分子机制研究进展. 中国农业科学 55, 1047-1063. | |
| [34] | Song SQ, Tang CF, Lei HP, Fei ST, Chen HB (2023). Research progress on seed development regulated by ABA. Guihaia 43, 1553-1567. (in Chinese) |
| 宋松泉, 唐翠芳, 雷华平, 费思恬, 陈海波 (2023). ABA调控种子发育的研究进展. 广西植物 43, 1553-1567. | |
| [35] | Song Y, Zhou JH, Zhang YQ (2007). Research on plant tissue-specific promoters. Biotechnol Bull (6), 21-24. (in Chinese) |
| 宋扬, 周军会, 张永强 (2007). 植物组织特异性启动子研究. 生物技术通报 (6), 21-24. | |
| [36] | Song YH, Shi WL, Zhang J, Ding ZY, Peng HX, Jiang CY, Ma QQ, Li ZJ, Zhao Y, Tang DB, Zhang K, Wang JC, Liu X (2021). Development and application of an efficient method for the amylose/amylopectin ratio determination in potato tubers. Acta Hortic Sin 48, 600-608. (in Chinese) |
| 宋玉浩, 史伟玲, 张娇, 丁振宇, 彭洪娴, 蒋春燕, 马秋芹, 李芝静, 赵勇, 唐道彬, 张凯, 王季春, 刘勋 (2021). 马铃薯块茎淀粉组分高效检测体系的建立及应用. 园艺学报 48, 600-608. | |
| [37] | Spreitzer RJ (2003). Role of the small subunit in ribulose-1,5-bisphosphate carboxylase/oxygenase. Arch Biochem Biophys 414, 141-149. |
| [38] | Sun M, Tian K, Zhang Y, Wang H, Guan DX, Yue HT (2017). Research on leaf functional traits and their environmental adaptation. Plant Sci J 35, 940-949. (in Chinese) |
| 孙梅, 田昆, 张贇, 王行, 管东旭, 岳海涛 (2017). 植物叶片功能性状及其环境适应研究. 植物科学学报 35, 940-949. | |
| [39] | Vijaybhaskar V, Subbiah V, Kaur J, Vijayakumari P, Siddiqi I (2008). Identification of a root-specific glycosyltransferase from Arabidopsis and characterization of its promoter. J Biosci 33, 185-193. |
| [40] | Wang HW, Zhu SX, Zhang XY, Wang Y, Yang TG, Zhang XG, Wang SF, Li CX (2023). Genome size, ploidy and phylogeny of Cyperus esculentus L. J Henan Agric Sci 52, 34-41. (in Chinese) |
| 王会伟, 朱世新, 张新友, 王艳, 杨铁钢, 张向歌, 王树峰, 李春鑫 (2023). 油莎豆基因组大小、倍性和系统发育分析. 河南农业科学 52, 34-41. | |
| [41] | Wang YC, Jiang HY, Mao ZL, Liu WJ, Jiang SH, Xu HF, Su MY, Zhang J, Wang N, Zhang ZY, Chen XS (2021). Ethylene increases the cold tolerance of apple via the MdERF1B-MdCIbHLH1 regulatory module. Plant J 106, 379-393. |
| [42] | Wang YY, Bai YF, Zhang DY (2010). Application of plants pyruvate orthophosphate dikinase in genetic engineering. J Shanxi Agric Sci 38(8), 88-91. (in Chinese) |
| 王原媛, 白云凤, 张定宇 (2010). 植物PPDK基因在基因工程中的应用. 山西农业科学 38(8), 88-91. | |
| [43] | Wehmeyer N, Vierling E (2000). The expression of small heat shock proteins in seeds responds to discrete developmental signals and suggests a general protective role in desiccation tolerance. Plant Physiol 122, 1099-1108. |
| [44] | Wei H, Zhong HJ, Wang H (2004). Improvement on determination of crude oil by soxhlet extraction. China Oils Fats 29, 52-54. (in Chinese) |
| 魏红, 钟红舰, 汪红 (2004). 索氏抽提法测定粗脂肪含量的改进. 中国油脂 29, 52-54. | |
| [45] | Wei YX, Wang J, Li T, Liu LJ, Huang J, Zheng YQ (2021). Potassium application improved the agronomic properties and starch components of cassava. Chin J Trop Crops 42, 102-109. (in Chinese) |
| 魏云霞, 王娟, 李天, 刘丽娟, 黄洁, 郑永清 (2021). 施钾改善木薯农艺性状及淀粉组分. 热带作物学报 42, 102-109. | |
| [46] | Xu DA, Zhao CQ, Zhang CH, Chen J (2015). Expression patterns of a root-specific barley aquaporin gene HvTIP2;1 and promoter. China Biotechnol 35(7), 15-21. (in Chinese) |
| 徐登安, 赵纯钦, 张赤红, 陈静 (2015). 大麦水孔蛋白基因HvTIP2;1及其启动子的表达特性分析. 中国生物工程杂志 35(7), 15-21. | |
| [47] | Xue D, Yan Q, Hu YQ, Zhou YY, Wei YW, Yuan XX, Wang XJ, Chen X (2023). Genome-scale mining of root-preferential genes from soybean and characterization of their promoter activity. Plant Physiol J 59, 55-66. (in Chinese) |
| 薛冬, 闫强, 胡亚群, 周琰琰, 韦雅雯, 袁星星, 王学军, 陈新 (2023). 大豆根系特异表达基因全基因组水平挖掘及其启动子活性鉴定. 植物生理学报 59, 55-66. | |
| [48] | Xun HW, Zhang X, Yu JM, Pang JS, Wang SC, Liu B, Dong YS, Jiang LL, Guo DQ (2021). Analysis of expression characteristics of soybean leaf and root tissue-specific promoters in Arabidopsis and soybean. Transgenic Res 30, 799-810. |
| [49] | Yamori W (2013). Improving photosynthesis to increase food and fuel production by biotechnological strategies in crops. J Plant Biochem Physiol 1, 1000113. |
| [50] | Yan J, Du J, Li C, Chen B, Shen YH (2016). Main components analysis of Cyperus esculentus in Jingbian, Shaanxi. China Oils Fats 41(3), 85-88. (in Chinese) |
| 闫军, 杜静, 李聪, 陈邦, 申烨华 (2016). 陕西靖边油莎豆主要成分分析. 中国油脂 41(3), 85-88. | |
| [51] | Yang F, Zhu WX (2020). Research status and prospect of Cyperus esculentus. Cereals Oils 33(7),4-6. (in Chinese) |
| 杨帆, 朱文学 (2020). 油莎豆研究现状及展望. 粮食与油脂 33(7), 4-6. | |
| [52] | Yang SN, Miao L, He JB, Zhang K, Li Y, Gai JY (2019). Dynamic transcriptome changes related to oil accumulation in developing soybean seeds. Int J Mol Sci 20, 2202. |
| [53] | Zhang H, Yang YJ, Li DL, Song JK, Ma CH, Wang R (2018). RNA-Seq analysis of the tissue-specific expressed genes of Pyrus betulaefolia in root, stem and leaf. Acta Hortic Sin 45, 1881-1894. (in Chinese) |
| 张欢, 杨英杰, 李鼎立, 宋健坤, 马春晖, 王然 (2018). 杜梨根茎叶特异表达基因的RNA-Seq分析. 园艺学报 45, 1881-1894. | |
| [54] | Zhang XG, Song WX, Zhu YJ, Yu MQ, Song WX, Wang SF, Li JZ, Wang HW (2023). Content changes of endogenous hormones in Cyperus esculentus tuber during germination. Seed 42(8), 45-49. (in Chinese) |
| 张向歌, 宋万献, 朱雅婧, 于美琴, 宋雯栩, 王树峰, 李居政, 王会伟 (2023). 油莎豆茎豆萌发过程中内源激素含量的变化. 种子 42(8), 45-49. | |
| [55] | Zhang XK (2019). R & D progress report of Cyperus escu-lentus industry in China. China Rural Sci Technol (4), 67-69. (in Chinese) |
| 张学昆 (2019). 我国油莎豆产业研发进展报告. 中国农村科技 (4), 67-69. | |
| [56] | Zhao XQ, Yi LX, Ren YF, Li J, Ren W, Hou ZH, Su SF, Wang JG, Zhang YY, Dong Q, Yang XD, Cheng YC, Lu ZY (2023). Chromosome-scale genome assembly of the yellow nutsedge (Cyperus esculentus). Genome Biol Evol 15, evad027. |
| [57] | Zhou D, Zhao JZ, Bai Y, Zhang Q, Jing W, Zhang WH (2012). Research advance in triacylglycerol synthesis, metabolism, and regulation in plants. J Nanjing Agric Univ 35(5), 77-86. (in Chinese) |
| 周丹, 赵江哲, 柏杨, 张群, 井文, 章文华 (2012). 植物油脂合成代谢及调控的研究进展. 南京农业大学学报 35(5), 77-86. |