基于转录组信息的黑果枸杞MYB转录因子家族分析

doi:10.3864/j.issn.0578-1752.2017.20.013

Abstract

Abstract: 【Objective】 MYB is one of the most common transcription factor families in plants. It is widely involved in plant growth, and metabolic regulations. So far, there is no systematic analysis of the MYB transcription factor family of tree crops. Analysis of MYB family based on the transcriptome data in Lycium ruthenicum Murr. was conducted in this study, which laid a foundation for the research on biological function, and mechanism of metabolic regulations of MYB genes. 【Method】 Based on the transcriptome sequencing (RNA-Seq) data, the NR, NT, Swiss-Prot, PFAM and NCBI sites were used at the same time to screen and classify the MYB genes of L. ruthenicum Murr. The Web Logo3, Prot Comp 9.0, and MEGA5.0 were also applied to conservative structure prediction, subcellular localization, and phylogenetic analysis. The expression pattern of MYB genes related to fruit development was obtained and Real-time fluorescence quantitative PCR was used to detect the specific expression of those genes. 【Result】 Based on the transcriptome sequencing (RNA-Seq) data, 83 transcription factors of MYB family were annotated, selected, and divided into four categories (R2R3-MYB, 1R-MYB, 3R-MYB and 4R-MYB) according to their structural characteristics. The R2 MYB motif of the R2R3-MYB transcription factor contains three highly conserved tryptophan residues, and the first tryptophan residue in the R3 MYB motif is replaced by some hydrophobic amino acids. The phylogenetic trees of MYB family of L. ruthenicum Murr. and Arabidopsis thaliana were constructed, which showed that the MYB family of L. ruthenicum Murr. contained three major branches, and six evolutionary branches. The result of the subcellular localization demonstrated that 44 MYB transcription factors were located in the cytoplasm, and 37 MYB transcription factors were located in the nucleus. The analysis of differential expression of MYB genes of L. ruthenicum Murr. based on transcriptome sequencing (RNA-Seq) showed that MYB genes might be involved in the regulation of anthocyanin in three fruit development periods. Additionally, differential expression data based on fluorescence quantitative PCR confirmed that some MYB transcription factors might play a role in the regulation of anthocyanin synthesis in different fruit development periods of L. ruthenicum Murr.. 【Conclusion】 83 transcription factors of MYB family were annotated of L. ruthenicum Murr. The findings have laid a foundation for further studies of the structures and biological functions of MYB family.

Key words: Lycium ruthenicum, RNA-Seq, MYB family, hierarchical clustering analysis, expression pattern

YAN Li, WANG CuiPing, CHEN JianWei, QIAO GaiXia, LI Jian. Analysis of MYB Transcription Factor Family Based on Transcriptome Sequencing in Lycium ruthenicum Murr.[J].Scientia Agricultura Sinica, 2017, 50(20): 3991-4002.

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References

[1] ZENG S, WU M, ZOU C, LIU X, SHEN X, HAYWARD A, LIU C, WANG Y. Comparative analysis of anthocyanin biosynthesis during fruit development in two Lycium species. Physiologia Plantarum, 2014, 150(4): 505-516.

[2] 郝媛媛, 颉耀文, 张文培, 宁宝山, 路新军. 荒漠黑果枸杞研究进展. 草业科学, 2016, 33(9): 1835-1845.

HAO Y Y, JI Y W, ZHANG W P, YU B S, LU X J. The research progress on desert Lycium ruthenicum. Pratacultural Science, 2016, 33(9): 1835-1845. (in Chinese)

[3] 陈海魁, 蒲凌奎, 曹君迈, 任贤.黑果枸杞的研究现状及其开发利用. 黑龙江农业科学, 2008(5): 155-157.

CHEN H K, PU L K, CAO J M, REN X. Current research state and exploitation of Lycium ruthenicum Murr. Heilongjiang Agricultural Sciences, 2008(5): 155-157. (in Chinese)

[4] 双全, 张海霞, 卢宇, 刘燕. 野生黑果枸杞化学成分及抗氧化活性研究. 食品工业科技, 2017, 38(4): 94-100.

SHUANG Q, ZHANG H X, LU Y, LIU Y. The research on chemical component and antioxidant activity of wild Lycium ruthenicum. Science and Technology of Food Industry, 2017, 38(4): 94-100. (in Chinese)

[5] 夏园园, 莫仁楠, 曲玮, 柳文媛. 黑果枸杞化学成分研究进展. 药学进展, 2015, 32(5): 351-356.

XIA Y Y, MO R N, QU W, Liu W Y. Research progress in chemical constituents of Lycium ruthenicum Murr. Progress in Pharmaceutical Sciences, 2015, 32(5): 351-356. (in Chinese)

[6] AMBAWAT S, SHARMA P, YADAV N R, YADAV R C. MYB transcription factor genes as regulators for plant responses: an overview. Physiology and Molecular Biology of Plants, 2013, 19(3): 307-321.

[7] LAI B, DU L N, LIU R, Hu B, SU W B, QIN Y H, ZHAO J T, WANG H C, HU G B. Two LcbHLH transcription factors interacting with LcMYB1 in regulating late structural genes of anthocyanin biosynthesis in Nicotiana and Litchi chinensis during anthocyanin accumulation. Frontiers in Plant Science, 2016, 7(212): 166.

[8] SALIH H, GONG W F, HE S P, Sun G F, SUN J L, DU X M. Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum. BMC Genetics, 2016, 17(1): 129.

[9] DUBOS C, STRACKE R, GROTEWOLD E, WEISSHAAR B, MARTIN C, LEPINIEC L. MYB transcription factors in Arabidopsis. Trends in Plant Science, 2010, 15(10): 573-581.

[10] PAZ-ARES J, GHOSAL D, WIENAND U, PETERSON PA, SAEDLER H. The regulatory c1 locus of Zea mays encodes a protein with homology to MYB-related proto-oncogene products and with structural similarities to transcriptional activators. EMBO Journal, 1988, 6(12): 3553-3558.

[11] WAITES R, SELVADURAI H R, OLIVER I R, HUDSON A. The PHANTASTICA gene encodes a MYB transcription factor involved in growth and dorsoventrality of lateral organs in Antirrhinum. Cell, 1998, 93(5): 779-789.

[12] LOGUERICO L L, ZHANG J Q, WILKINS T A. Differential regulation of six novel MYB-domain genes defines two distinct expression patterns in allotetraploid cotton (Gossypium hirsutum L.). Molecular Genetics and Genomics, 1999, 261(4): 660-671.

[13] MIYAKE K, ITO T, SENDA M, ISHIKAWA R, HARADA T, NIIZEKI M, AKADA S. Isolation of a subfamily of genes for R2R3-MYB transcription factors showing up-regulated expression under nitrogen nutrient-limited conditions. Plant Molecular Biology, 2003, 53(1): 237-245.

[14] CHEN Y, YANG X, HE K, LIU M H, LI J G, GAO Z F, LIN Z Q, ZHANG Y F, WANG X X, QIU X M, SHEN Y P, ZHANG L, DENG X H, LUO J C, DENG X W, CHEN Z L, GU H Y, QU L J. The MYB transcription factor superfamily of Arabidopsis: Expression analysis and phylogenetic comparison with the rice MYB family. Plant Molecular Biology, 2006, 60(1): 107-124.

[15] TAKOS A M, JAFFE F W, JACOB S R, BOGS J, ROBINSON S P, WALKER A R. Light-induced expression of a MYB gene regulates anthocyanin biosynthesis in red apples. Plant Physiology, 2006, 142(3): 1216-1232.

[16] 向珣, 曹家树, 叶纨芝, 崔辉梅, 俞建浓. 白菜OguCMS相关MYB家族新基因BcMYBogu的克隆与特征分析. 遗传, 2007, 29(5): 621-628.

XIANG X, CAO J S, YE W Z, CUI H M, YU J N. Molecular cloning and characterization of BcMYBogu, a novel member of the MYB family involved in OguCMS in Brassiac campestris. Chinensis, Yichuan (Heredites), 2007, 29(5): 621-628. (in Chinese)

[17] 朱婷婷, 梁东, 夏惠. R2R3-MYB调控果实花色苷合成的研究进展. 基因组学与应用生物学, 2016, 35(4): 985-991.

ZHU T T, LIANG D, XIA H. Progress in the study of the regulation of anthocyanin synthesis by R2R3-MYB in fruits. Genomics and Applied Biology, 2016, 35(4): 985-991. (in Chinese)

[18] MEHRTENS F, KRANZ H, BEDNA P, WEISSHAAR B. The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis. Plant Physiology, 2005, 138(2): 1083-1096.

[19] LOTKOWSKA M E. Functional analysis of MYB112 transcription factor in the model plant Arabidopsis thaliana. Text.thesis.doctoral, 2014.

[20] FENG S Q, SUN S S, CHEN X L, WU S J, WANG D Y, CHEN X S. PyMYB10 and PyMYB10.1 interact with bHLH to enhance anthocyanin accumulation in pears. PLoS ONE, 2015, 10(11): e0142112.

[21] 李莹. 金鱼草中R2R3-MYB基因AmMYB308L的克隆及其功能研究[D]. 北京: 中国科学院大学, 2015.

LI Y. Cloning and functional analysis of the R2R3-MYB transcription factors AmMYB308L in Snapdragon [D]. Beijing: Chinese Academy of Sciences University, 2015. (in Chinese)

[22] 叶广继, 张波, 陈文杰, 刘宝龙, 张华刚. 紫粒小麦高原115中R2R3-MYB转录因子TaMYB3-4A的克隆及功能分析. 分子植物育种, 2016, 8(8): 1940-1947.

YE G J, ZHANG B, CHEN W J, LIU B L, ZHANG H G. Cloning and functional analysis of the R2R3-MYB transcription factors TaMYB3-4A in the purple wheat variety Gaoyuan 115. Molecular Plant Breeding, 2016, 8(8): 1940-1947. (in Chinese)

[23] ZHANG L, ZHAO G, XIA C, JIA J, LIU X, KONG X. A wheat R2R3-MYB gene, TaMYB30-B, improves drought stress tolerance in transgenic Arabidopsis. Journal of Experimental Botany, 2012, 63(63): 5873-5885.

[24] ZHU N, CHENG S, LIU X, DU H, DAI M, ZHOU D X, YANG W, ZHAO Y. The R2R3-type MYB gene OsMYB91 has a function in coordinating plant growth and salt stress tolerance in rice. Plant Science, 2015, 10(236): 146-156.

[25] YANG A, DAI X, ZHANG W H. A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. Journal of Experimental Botany, 2012, 63(7): 2541-2556.

[26] CHENG Y J, KIM M D, DENG X P, KWAK S S, CHEN W. Enhanced salt stress tolerance in transgenic potato plants expressing IbMYB1, a sweet potato transcription factor. Journal of Microbiology & Biotechnology, 2013, 23(12): 1737-1746.

[27] HIGGINSON T, LI S F, PARISH R W. AtMYB103 regulates tapetum and trichome development in Arabidopsis thaliana. Plant Journal for Cell & Molecular Biology, 2003, 35(2): 177-192.

[28] CAMPOS J F, CARA B, MARTIN F, PINEDA B, EGEA I, FLORES F B, FERNANDEZ G N, CAPEL J, MORENO V, ANGOSTO T, LOZANO R, BOLARIN M C. The tomato mutant ars1 (altered response to salt stress 1) identifies an R1-type MYB transcription factor involved in stomatal closure under salt acclimation. Plant Biotechnology Journal, 2016, 14(6): 1345-1356.

[29] BALDONI E, GENGA A, COMINELLI E. Plant MYB transcription factors: Their role in drought response mechanisms. International Journal of Molecular Sciences, 2015, 16(7): 15811-15851.

[30] ZHANG Z J, CHEN J M, SU Y Y, LIU H M, CHEN Y G, LUO P G, DU X G, WANG D, ZHANG H Y. TaLHY, a 1R-MYB transcription factor, plays an important role in disease resistance against stripe rust fungus and ear heading in wheat. PLoS ONE, 2015, 10(5): e0127723.

[31] YE H, YIN Y. MYBL2 is a substrate of GSK3-like kinase BIN2 and acts as a corepressor of BES1 in brassinosteroid signaling pathway in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(49): 20142-20147.

[32] CROOKS G E, HON G, CHANDONIA J M, BRENNER S E. Web Logo: a sequence logo generator. Genome Research, 2004, 14(6): 1188-1190.

[33] FENG C, CHEN M, XU C J, BAI L, YIN X R, LI X, ALLAN A C, FERGUSON L B, CHEN K S. Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq. BMC Genomics, 2012, 13(1): 13-19.

[34] LIVAK K J, SCHMITTGEN T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2^-ΔΔCT-method. Methods, 2001, 25(4): 402-408.

[35] 杜海. 植物MYB转录因子家族的分子进化机制及调控类黄酮生物合成MYB基因的鉴定[D]. 四川: 四川农业大学, 2013.

DU H. Molecular evolution of MYB transcription factor gene family in plants and characterization of the MYB genes involved in flavonoid biosynthesis. Sichuan: Sichuan Agricultural University, 2013. (in Chinese)

[36] 成舒飞, 端木慧子, 陈超, 刘艾林, 肖佳雷, 朱延明. 大豆MYB转录因子的全基因组鉴定及生物信息学分析. 大豆科学, 2016, 35(1): 52-57.

CHENG S F, DUAN MU H Z, CHEN C, LIU A L, XIAO J L, ZHU Y M. Whole genome identification of soybean MYB transcription factors and bioinformatics analysis. Soybean Science, 2016, 35(1): 52-57. (in Chinese)

[37] MATUS J T, AQUEA F, JOHNSON P. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes. BMC Plant Biology, 2008, 8(1): 83.

[38] GULATI S, PADGETT W J. Arabidopsis thaliana MYB75/PAP1 transcription factor induces anthocyanin production in transgenic tomato plants. Functional Plant Biology, 2008, 35(7): 606-618.

[39] VIMOLMANGKANG S, HAN Y P, WEI G C, KORBAN S. An apple MYB transcription factor, MdMYB3, is involved in regulation of anthocyanin biosynthesis and flower development. BMC Plant Biology, 2013, 13(1): 176.

[40] FRERIGMANN H, GLAWISCHNIG E, GIGOLASHVILI T. The role of MYB34, MYB51 and MYB122 in the regulation of camalexin biosynthesis in Arabidopsis thaliana. Photochemical & Photobiological Sciences Official Journal of the European Photochemistry Association & the European Society for Photobiology, 2004, 3(6): 587-591.

[41] Li S F, MILLIKEN O N, PHAM H, SEYIT R, NAPOLI. The Arabidopsis MYB5 transcription factor regulates mucilage synthesis, seed coat development, and trichome morphogenesis. Plant Cell, 2009, 21(1): 72-89.

[42] ZULUAGA D, GONZALI S, LORETI E, PUCCIARIELLO C, DEGLINNOCENTI E, GUIDI L, ALPI A, PERATA P. Arabidopsis thaliana MYB75/PAP1 transcription factor induces anthocyanin production in transgenic tomato plants. Functional Plant Biology, 2008, 35(7): 606-618.

[43] VELTEN J, CAKIR C, CAZZONELLI C I. A spontaneous dominant-negative mutation within a 35S:AtMYB90 transgene inhibits flower pigment production in tobacco. PLoS ONE, 2010, 5(3): e9917.

[44] HEPPEL S C, JAFFE F W, TAKOS A M, SCHELLMANN S, RAUSCH T, AMANDA W. Identification of key amino acids for the evolution of promoter target specificity of anthocyanin and proanthocyanidin regulating MYB factors. Plant Molecular Biology, 2013, 82(5): 457-471.

[45] YANG X Y, LI J G, PEI M, L G J, P M, GU H, CHEN Z L, QU L G. Over-expression of a flower-specific transcription factor gene AtMYB24 causes aberrant anther development. Plant Cell Reports, 2007, 26(2): 219-228.

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