Genome-wide Identification and Expression Analysis of SRO Gene Family in Camellia sinensis

GUO Yongchun; WANG Pengjie; CHEN Di; ZHENG Yucheng; CHEN Xuejin; YE Naixing

doi:10.13305/j.cnki.jts.2019.04.004

PDF(858 KB)

Journal of Tea Science ›› 2019, Vol. 39 ›› Issue (4) : 392-402. DOI: 10.13305/j.cnki.jts.2019.04.004

Genome-wide Identification and Expression Analysis of SRO Gene Family in Camellia sinensis

GUO Yongchun, WANG Pengjie, CHEN Di, ZHENG Yucheng, CHEN Xuejin, YE Naixing^*

Author information +

History +

Abstract

SROs (Similar to rcd one) are plant-specific gene families. In this study, 9 CsSRO gene family members were identified from tea tree genome by bioinformatics method and named as CsRCD1—4 and CsSRO1—5 respectively. All coding proteins of the 9 CsSRO genes have characteristic structural domains PARP and RST, and have similar conserved motifs. The CsSRO genes were divided into 3 groups based on phylogenetic tree analysis, with the group Ι containing CsRCD1—4, the group Ⅱ containing CsSRO1, CsSRO2 and the group Ⅲ containing CsSRO3—5. Gene structure analysis shows that this gene family contained 4 to 9 exons. Analysis of transcriptome data from 8 tea tree tissues shows that CsRCD1/CsRCD3/CsRCD4 might play an important role in different developmental stages of tea plants. Most CsSRO genes were highly expressed in roots and mature leaves. Upstream promoter region analysis found a large number of cis-acting elements closely related to plant development, hormones and stress response. Further expression analysis shows that 9 CsSRO genes were induced by drought and abscission acid treatments, suggesting CsSRO genes may be closely related to drought resistance.

Key words

SRO / Camellia sinensis / phylogeny analysis / stress

Cite this article

EndNote

Ris (Procite)

Bibtex

Download Citations

GUO Yongchun, WANG Pengjie, CHEN Di, ZHENG Yucheng, CHEN Xuejin, YE Naixing. Genome-wide Identification and Expression Analysis of SRO Gene Family in Camellia sinensis[J]. Journal of Tea Science. 2019, 39(4): 392-402 https://doi.org/10.13305/j.cnki.jts.2019.04.004

References

[1] 岳川, 曹红利, 郝心愿, 等. 茶树CsASR基因的克隆及其表达分析[J]. 茶叶科学, 2017, 37(4): 399-410.
[2] Liu S, Liu S, Wang M, et al.A wheat SIMILAR TO RCD-ONE gene enhances seedling growth and abiotic stress resistance by modulating redox homeostasis and maintaining genomic integrity[J]. The Plant Cell, 2014, 26(1): 164-180.
[3] You J, Zong W, Du H, et al.A special member of the rice SRO family, OsSRO1c, mediates responses to multiple abiotic stresses through interaction with various transcription factors[J]. Plant Molecular Biology, 2014, 84(6): 693-705.
[4] 吕有军, 杨卫军, 赵兰杰, 等. 陆地棉SRO基因家族的鉴定及表达分析[J]. 作物学报, 2017, 43(10): 1468-1479.
[5] 赵秋芳, 马海洋, 贾利强, 等. 玉米SRO基因家族的鉴定及表达分析[J]. 中国农业科学, 2018, 51(15): 196-206.
[6] Jaspers P, Overmyer K, Wrzaczek M, et al.The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants[J]. BMC Genomics, 2010, 11: 170. DOI: 10.1186/1471-2164-11-170.
[7] Katiyar-Agarwal S, Zhu J, Kim K, et al.The plasma membrane Na+/H+ antiporter SOS1 interacts with RCD1 and functions in oxidative stress tolerance in Arabidopsis[J]. Proceedings of the National Academy of Sciences, 2007, 103(49): 18816-18821.
[8] Ahlfors R, Overmyer K, Jaspers P, et al.Arabidopsis radical-induced cell death 1 belongs to the WWE protein-protein interaction domain protein family and modulates abscisic acid, ethylene and methyl jasmonate responses[J]. Plant Cell, 2004, 16(7): 1925-1937.
[9] Vainonen J P, Jaspers P, Wrzaczek M, et al.RCD1-DREB2A interaction in leaf senescence and stress responses in Arabidopsis thaliana[J]. Biochemical Journal, 2012, 442(3): 573-581.
[10] Teotia S, Lamb RS.The paralogous genes RADICAL-INDUCED CELL DEATH and SIMILAR TO RCD ONE1 have partially redundant functions during Arabidopsis development[J]. Plant Physiology, 2009, 151(1): 180-198.
[11] Jaspers P, Blomster T, Brosche M, et al.Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors[J]. The Plant Journal, 2009, 60(2): 268-279.
[12] Zhao X, Gao L, Jin P, et al.The similar to RCD-one 1 protein SRO1 interacts with GPX3 and functions in plant tolerance of mercury stress[J]. Bioscience Biotechnology and Biochemistry, 2017, 82(1): 1-7.
[13] Babajani G, Effendy J, Plant AL.Sl-SROl1 increases salt tolerance and is a member of the radical-induced cell death 1—similar to RCD1 gene family of tomato[J]. Plant Science, 2009, 176(2): 214-222.
[14] 李保珠, 赵翔, 赵孝亮, 等. 拟南芥SRO蛋白家族的结构及功能分析[J]. 遗传, 2013, 35(10): 1189-1197.
[15] Li H, Li R, Qu F, et al.Identification of the SRO gene family in apples (Malus×domestica) with a functional characterization of MdRCD1[J]. Tree Genetics & Genomes, 2017, 13(5): 94. DOI: 10.1007/s11295-018-1242-4.
[16] You J, Zong W, Li X, et al.The SNAC1-targeted gene OsSRO1c modulates stomatal closure and oxidative stress tolerance by regulating hydrogen peroxide in rice[J]. Journal of Experimental Botany, 2013, 64(2): 569-583.
[17] Wang W, Xin H, Wang M, et al.Transcriptomic analysis reveals the molecular mechanisms of drought-stress-induced decreases in Camellia sinensis leaf quality[J]. Frontiers in Plant Science, 2016, 7: 385. DOI: 10.3389/fpls.2016.00385.
[18] Zhou Y, Liu Y, Wang S, et al.Molecular cloning and characterization of galactinol synthases in Camellia sinensis with different responses to biotic and abiotic stressors[J]. Journal of Agricultural and Food Chemistry, 2017, 65(13): 2751-2759.
[19] Hou Y, Wu A, He Y, et al.Genome-wide characterization of the basic leucine zipper transcription factors in Camellia sinensis[J]. Tree Genetics & Genomes, 2018, 14(2): 27. DOI: 10.1007/s11295-018-1242-4.
[20] Liu L, Li Y, She G, et al.Metabolite profiling and transcriptomic analyses reveal an essential role of UVR8-mediated signal transduction pathway in regulating flavonoid biosynthesis in tea plants (Camellia sinensis) in response to shading[J]. BMC Plant Biology, 2018, 18(1): 233. DOI: 10.1186/s12870-018-1440-0.
[21] Zhang Q, Cai M, Yu X, et al.Transcriptome dynamics of Camellia sinensis in response to continuous salinity and drought stress[J]. Tree Genetics & Genomes, 2017, 13(4): 1-17.
[22] Wei C, Yang H, Wang S, et al.Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality[J]. Proceedings of the National Academy of Sciences, 2018, 115(18): 4151-4158.
[23] Xia EH, Zhang HB, Sheng J, et al.The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis[J]. Mol Plant, 2017, 10(6): 866-877.
[24] Bailey TL, Boden M, Buske FA, et al.MEME SUITE: tools for motif discovery and searching[J]. Nucleic Acids Research, 2009, 37: 202-208.
[25] Hu B, Jin J, Guo A, et al.GSDS 2.0: an upgraded gene feature visualization server[J]. Bioinformatics, 2015, 31(8): 1296-1297.
[26] Hall B G.Building phylogenetic trees from molecular data with MEGA[J]. Molecular Biology and Evolution, 2013, 30(5): 1229-1235.
[27] Lescot M.PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences[J]. Nucleic Acids Research, 2002, 30(1): 325-327.
[28] Trapnell C, Roberts A, Goff L, et al.Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks[J]. Nature Protocols, 2012, 7(3): 562-578.
[29] Anders S, Pyl P T, Huber W.HTSeq—a Python framework to work with high-throughput sequencing data[J]. Bioinformatics, 2015, 31(2): 166-169.
[30] Livak K J, Schmittgen T D.Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method[J]. Methods, 2001, 25(4): 402-408.
[31] 魏瑞敏, 郑井元, 刘峰, 等. 辣椒bZIP家族基因的鉴定与表达分析[J]. 园艺学报, 2018, 45(8): 1535-1550.
[32] Wang YX, Liu ZW, Wu ZJ, et al.Genome-wide identification and expression analysis of GRAS family transcription factors in tea plant (Camellia sinensis)[J]. Scientific Reports, 2018, 8(1): 3949. DOI: 10.1038/s41598-018-22275-z.
[33] Xu G, Guo C, Shan H, et al.Divergence of duplicate genes in exon-intron structure[J]. Proceedings of the National Academy of Sciences, 2012, 109(4): 1187-1192.
[34] 岳川, 曹红利, 王赞, 等. 茶树水通道蛋白基因的克隆与表达分析[J]. 西北植物学报, 2018, 38(8): 1419-1427.