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化州柚与柚的转录组比较及黄酮生物合成差异表达基因分析

颜仁梁 梁永枢 周国洪 夏黎 林励 周代营

颜仁梁, 梁永枢, 周国洪, 夏黎, 林励, 周代营. 化州柚与柚的转录组比较及黄酮生物合成差异表达基因分析[J]. 华南师范大学学报(自然科学版), 2020, 52(4): 71-78. doi: 10.6054/j.jscnun.2020063
引用本文: 颜仁梁, 梁永枢, 周国洪, 夏黎, 林励, 周代营. 化州柚与柚的转录组比较及黄酮生物合成差异表达基因分析[J]. 华南师范大学学报(自然科学版), 2020, 52(4): 71-78. doi: 10.6054/j.jscnun.2020063
YAN Renliang, LIANG Yongshu, ZHOU Guohong, XIA Li, LIN Li, ZHOU Daiying. Differentially Expressed Genes in Flavonoid Biosynthesis and Transcriptome of Citrus Grandis 'Tomentosa' and Citrus Grandis (L.) Osbeck[J]. Journal of South China normal University (Natural Science Edition), 2020, 52(4): 71-78. doi: 10.6054/j.jscnun.2020063
Citation: YAN Renliang, LIANG Yongshu, ZHOU Guohong, XIA Li, LIN Li, ZHOU Daiying. Differentially Expressed Genes in Flavonoid Biosynthesis and Transcriptome of Citrus Grandis 'Tomentosa' and Citrus Grandis (L.) Osbeck[J]. Journal of South China normal University (Natural Science Edition), 2020, 52(4): 71-78. doi: 10.6054/j.jscnun.2020063

化州柚与柚的转录组比较及黄酮生物合成差异表达基因分析

doi: 10.6054/j.jscnun.2020063
基金项目: 

国家自然科学基金项目 81803693

广东省教育厅科研平台特色创新项目 2018GKTSCX040

广东省中医药局科研项目 20191235

详细信息
    通讯作者:

    周代营,副教授,Email:56166792@qq.com

  • 中图分类号: R282.6

Differentially Expressed Genes in Flavonoid Biosynthesis and Transcriptome of Citrus Grandis 'Tomentosa' and Citrus Grandis (L.) Osbeck

  • 摘要: 为获得化州柚和柚的转录组数据及黄酮类成分生物合成相关的差异表达基因,采集化州柚和柚的嫩叶样本作为受试材料,采用高通量二代测序技术进行转录组测序,并运用Nr、Swiss-Prot、KOG、KEGG等网络数据库进行转录组中表达基因功能的生物信息学分析,共组装得到116 202个单基因(Unigene),注释了68 923个单基因(59.31%),柚转录组中表达基因有94 798个,化州柚中表达基因107 196个,化州柚与柚的转录组差异表达基因共6 419个.结果表明:化州柚相对于柚上调基因有3 799个,占差异表达基因的59.18%,下调基因2 620个,占40.82%.通过与KEGG数据库进行比对,共获得771个基因功能注释,涉及125条代谢通路,找到9个与类黄酮、黄酮和黄酮醇生物合成相关基因,为化州柚和柚的化学成分差异分子基础研究奠定了基因数据基础.
  • 图  1  化州柚和柚转录组Unigene基因的长度分布图

    Figure  1.  The Unigene length distribution in the transcriptome of CGT and CGO

    图  2  化州柚与柚转录组在4个数据库基因注释的维恩图

    Figure  2.  The Venn diagram of the transcriptome annotated in the four databases of CGT and CGO

    图  3  化州柚与柚转录组Unigene基因的KOG功能分类图

    Figure  3.  The functional classification of KOG in the transcriptome of CGT and CGO

    图  4  化州柚与柚转录组Unigene基因的GO功能分类图

    Figure  4.  The functional classification of GO in the transcriptome of CGT and CGO

    图  5  化州柚与柚转录组Unigene基因的KEGG通路注释

    Figure  5.  The KEGG pathway annotation in the transcriptome of CGT and CGO

    表  1  化州柚与柚转录组中与黄酮类成分生物合成相关的差异表达基因

    Table  1.   The differentially expressed genes related to flavonoids biosynthesis in the transcriptome of CGT and CGO

    基因编号 基因 CGO_rpkm CG_rpkm P 错误发现率(FDR)
    Unigene0018220 C12RT1 27.22±3.76 9.51±2.18 1.81E-08 9.79E-07
    Unigene0001546 RT 9.36±2.44 23.75±3.62 3.20E-06 1.21E-04
    Unigene0062842 3GGT 18.53±5.34 0.05±0.072 7.37E-51 5.51E-48
    Unigene0102621 CYP73A12 0.054±0.004 0 0.40±0.34 1.72E-03 3.11E-02
    Unigene0032665 TSM1 0.078 5±0.07 2.47±0.47 2.16E-22 3.98E-20
    Unigene0000397 CHS1 0.46±0.28 1.29±0.07 8.21E-04 1.68E-02
    Unigene0024628 FLS 15.06±4.48 4.97±0.48 1.50E-07 7.08E-06
    Unigene0011342 HCT 8.50±4.28 0.06±0.04 2.30E-34 8.25E-32
    Unigene0029908 HCT 0.32±0.13 2.65±0.53 1.32E-14 1.39E-12
    Unigene0037769 HCT 53.54±1.68 25.88±1.19 2.66E-07 1.21E-05
    Unigene0093083 HCT 0.77±0.24 0.09±0.06 8.08E-08 3.98E-06
    Unigene0115527 HCT 0.005 6±0.009 7 2.01±0.74 1.35E-27 3.41E-25
    Unigene0018220 C12RT1 27.22±3.76 9.51±2.18 1.81E-08 9.79E-07
    Unigene0015054 LAR 0.90±0.38 0.08±0.05 3.19E-08 1.67E-06
    下载: 导出CSV
  • [1] 李晓光, 林励, 陈志霞.化州柚与柚的性状及组织显微鉴别[J].中药材, 2002, 25(6):401-402. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=zyc200206010

    LI X G, LIN L, CHEN Z X. Descriptions and microscopy identification of Citrus grandis var. tomentosa hort. and Citrus grandis Osbeck[J]. Journal of Chinese Medicinal Materials, 2002, 25(6):401-402. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=zyc200206010
    [2] 邬龙怡, 胡珊, 杨志业, 等. SCoT分子标记对不同品种化橘红的亲缘关系分析[J].现代中药研究与实践, 2018, 32(6):12-16. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=jczyzz201806004

    WU L Y, HU S, YANG Z Y, et al. Study on the genetic relationship of exocarpium Citrus grandis by SCoT molecular markers[J]. Research and Practice on Chinese Medicines, 2018, 32(6):12-16. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=jczyzz201806004
    [3] 田静, 庞一波, 陈嘉景, 等.化州柚种质资源的SSR分析及其果实不同发育期柚皮苷含量变化[J].华中农业大学学报, 2019, 38(5):64-70. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=hznydx201905009

    TIAN J, PANG Y B, CHEN J J, et al. SSR analyses of germplasm resources and changes of naringin content at different developmental stages of Citrus grandis 'Tomentosa' fruit[J]. Journal of Huazhong Agricultural University, 2019, 38(5):64-70. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=hznydx201905009
    [4] 芦海生, 李婷, 姜丹, 等.基于DNA条形码、UPLC及色度学方法鉴定与评价化橘红[J].中国中药杂志, 2019, 44(20):4419-4425. http://www.cnki.com.cn/Article/CJFDTotal-ZGZY201920021.htm

    LU H S, LI T, JIANG D, et al. Identification and evaluation of Citrus grandis based on DNA barcode, UPLC and chromaticity method[J]. China Journal of Chinese Materia Medica, 2019, 44(20):4419-4425. http://www.cnki.com.cn/Article/CJFDTotal-ZGZY201920021.htm
    [5] YU E A, KIM G S, LEE J E, et al. Flavonoid profiles of immature and mature fruit tissues of Citrus grandis Osbeck (Dangyuja) and overall contribution to the antioxidant effect[J]. Biomedical Chromatography, 2015, 29(4):590-594. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=10.1002/bmc.3496
    [6] YU X, CAO J P, LUO F L, et al. Simultaneous purification of limonin, nomilin and isoobacunoic acid from pomelo fruit (Citrus grandis) segment membrane[J]. Journal of Food Science, 2014, 79(10):C1956-1963. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=10.1111/1750-3841.12581
    [7] LI P L, LIU M H, HU J H, et al. Systematic chemical profiling of Citrus grandis 'Tomentosa' by ultra-fast liquid chromatography/diode-array detector/quadrupole time-of-flight tandem mass spectrometry[J]. Journal of Pharmaceutical and Biomedical Analysis, 2014, 90:167-179. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=f4751754292e0dc23e9802119520aaed
    [8] WANG P X, BO F, ZHAO Q Y, et al. Flavonoid composition and antioxidant activities of Chinese local pummelo (Citrus grandis Osbeck.) varieties[J]. Food Chemistry, 2014, 161:230-238. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=5cef4e95686653b34bafe29b03176dd4
    [9] 陈昭, 张靖年, 陈伟韬, 等. UHPLC-MS-MS同时测定化橘红中3个影响PXR-CYP3A4调控血脂成分[J].辽宁中医药大学学报, 2020, 22(1):54-58. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=lnzyxyxb202001017

    CHEN Z, ZHANG J N, CHEN W T, et al. Simultaneous determination of three active compounds with PXR-CYP3A4 mediated lipid regulatory effect in Citrus grandis tomentosa[J]. Journal of Liaoning University of Traditional Chinese Medicine, 2020, 22(1):54-58. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=lnzyxyxb202001017
    [10] ZHANG M, NAN H, WANG Y, et al. Comparison of flavonoid compounds in the flavedo and juice of two pummelo cultivars (Citrus grandis L. Osbeck) from different cultivation regions in China[J]. Molecules, 2014, 19(11):17314-17328. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=molecules-19-17314
    [11] 林励, 李向明, 万建义, 等.化橘红药材质量评价、监测与应用研究[J].中国现代中药, 2010, 12(8):21-26;36. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=zyyjyxx201008006

    LIN L, LI X M, WAN J Y, et al. Quality evaluation, monitoring and application study of the medicinal material Citrus grandis 'Tomentosa'[J]. Modern Chinese Medicine, 2010, 12(8):21-26;36. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=zyyjyxx201008006
    [12] 文海涛, 赵红英, 林励, 等.化橘红黄酮类生物合成中功能基因的克隆与序列分析[J].中药材, 2010, 33(11):1686-1689. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=zyc201011005

    WEN H T, ZHAO H Y, LI L, et al. Cloning and sequence analysis on functional genes of flavonoid biosynthesis in Citrus grandis 'Tomentosa'[J]. Journal of Chinese Medicinal Materials, 2010, 33(11):1686-1689. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=zyc201011005
    [13] LI J, MA L, ZHANG S, et al. Transcriptome analysis of 1- and 3-year-old Panax notoginseng roots and functional characterization of saponin biosynthetic genes DS and CYP716A47-like[J]. Planta, 2019, 249(4):1229-1237. https://pubmed.ncbi.nlm.nih.gov/30607503/
    [14] FABIO P, ALESSANDRO V, VITULO N, et al. The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants[J]. Scientific Reports, 2018, 8:10459/1-12. https://www.nature.com/articles/s41598-018-28775-2
    [15] DENG Y, ZHENG H, YAN Z, et al. Full-length transcriptome survey and expression analysis of Cassia obtusifolia to discover putative genes related to aurantio-obtusin biosynthesis, seed formation and development, and stress response[J]. International Journal of Molecular Sciences, 2018, 19:2476/1-30.
    [16] AN H Q, ZHU Q K, PEI W, et al. Whole-transcriptome selection and evaluation of internal reference genes for expression analysis in protocorm development of Dendrobium officinale Kimura et Migo[J]. Plos One, 2016, 11(11):e0163478/1-19. https://pubmed.ncbi.nlm.nih.gov/27814359/
    [17] WANG X, CHEN D, WANG Y, et al. De Novo transcriptome assembly and the putative biosynthetic pathway of steroidal sapogenins of Dioscorea composita[J]. PLoS One, 2015, 10(4):e0124560/1-18. https://pubmed.ncbi.nlm.nih.gov/25860891/
    [18] LIN W J, HUANG W, NING S J, et al. De Novo characterization of the Baphicacanthus cusia (Nees) Bremek transcriptome and analysis of candidate genes involved in indican biosynthesis and metabolism[J]. PLoS One, 2018, 13(7):e0199788/1-15. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6033399/
    [19] YU G, ZHOU Y, YU J, et al. Transcriptome and digital gene expression analysis unravels the novel mechanism of early flowering in Angelica sinensis[J]. Scientific Reports, 2019, 9:10035/1-11. https://www.nature.com/articles/s41598-019-46414-2
    [20] LIN W J, SUN F L, ZHANG Y M, et al. Comparative transcriptome and metabolite profiling of four tissues from Alisma orientale (Sam.) Juzep reveals its inflorescence developmental and medicinal characteristics[J]. Scientific Reports, 2019, 9:12310/1-12. https://www.researchgate.net/publication/335352950_Comparative_transcriptome_and_metabolite_profiling_of_four_tissues_from_Alisma_orientale_Sam_Juzep_reveals_its_inflorescence_developmental_and_medicinal_characteristics
    [21] LIU Y Y, CHEN X R, WANG J P, et al. Transcriptomic analysis reveals flavonoid biosynthesis of Syringa oblata Lindl. in response to different light intensity[J]. BMC Plant Biology, 2019, 19:487/1-16. https://www.researchgate.net/publication/337179865_Transcriptomic_analysis_reveals_flavonoid_biosynthesis_of_Syringa_oblata_Lindl_in_response_to_different_light_intensity
    [22] PENG X, WU H, CHEN H, et al. Transcriptome profiling reveals candidate flavonol-related genes of Tetrastigma hemsleyanum under cold stress[J]. BMC Genomics, 2019, 20:687/1-15.
    [23] CHEN K, HU Z M, SONG W, et al. Diversity of O-Glycosyltransferases contributes to the biosynthesis of flavonoid and triterpenoid glycosides in Glycyrrhiza uralensis[J]. ACS Synthetic Biology, 2019, 8(8):1858-1866. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=e22b797fa590af26a4de2357f42f9723
    [24] YUE J Y, ZHU C X, ZHOU Y, et al. Transcriptome analysis of differentially expressed unigenes involved in flavonoid biosynthesis during flower development of Chrysanthemum morifolium 'Chuju'[J]. Scientific Reports, 2018, 8(1):715-766. https://pubmed.ncbi.nlm.nih.gov/30194355/
    [25] CHEN Z X, LIU G H, TANG N, et al. Transcriptome analysis reveals molecular signatures of luteoloside accumulation in senescing leaves of Lonicera macranthoides[J]. International Journal of Molecular Sciences, 2018, 19:1012/1-19. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=ijms-19-01012
    [26] GUO D D, LIU F, TU Y H, et al. Expression patterns of three UGT genes in different chemotype safflower lines and under MeJA stimulus revealed their potential role in flavonoid biosynthesis[J]. PLoS One, 2016, 11(7):e0158159/1-14. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=Doaj000004675386
    [27] SAVITA B, VASUNDHARA T, JAGDEEP K, et al. Elucidating genes involved in sesquiterpenoid and flavonoid biosynthetic pathways in Saussurea lappa by de novo leaf transcriptome analysis[J]. Genomics, 2019, 111(6):1474-1482. https://www.onacademic.com/detail/journal_1000040866870210_3fe7.html
    [28] YUN Z, JIN S, DING Y D, et al. Comparative transcriptomics and proteomics analysis of citrus fruit, to improve understanding of the effect of low temperature on maintaining fruit quality during lengthy post-harvest storage[J]. Journal of Experimental Botany, 2012, 63(8):2873-2893. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=8b4013a64aa0c30396df8964a4928b21
    [29] LIANG M, YANG X, LI H, et al. De Novo transcriptome assembly of pummelo and molecular marker development[J]. PLoS One, 2015, 10(3):e0120615/1-20. https://pubmed.ncbi.nlm.nih.gov/25799271/
    [30] GUO F, YU H W, XU Q, et al. Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis)[J]. BMC Plant Biology, 2015, 15:44/1-12. doi: 10.1186/s12870-015-0435-3
    [31] LIN W J, HUANG W, NING S J, et al. Comparative transcriptome analyses revealed differential strategies of roots and leaves from methyl jasmonate treatment Baphicacanthus cusia (Nees) Bremekand differentially expressed genes involved in tryptophan biosynthesis[J]. PLoS One, 2019, 14(3):e0212863/1-17.
    [32] LIU S Q, LI W S, WU Y M, et al. De Novo transcriptome assembly in chili pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of capsaicinoids[J]. PLoS One, 2013, 8(1):e48156/1-8. https://europepmc.org/articles/PMC3551913
    [33] CHEN J F, DONG X, LI Q, et al. Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling[J]. BMC Genomics, 2013, 14:857/1-13. doi: 10.1186/1471-2164-14-857
    [34] GAO M P, ZHANG S W, LUO C, et al. Transcriptome analysis of starch and sucrose metabolism across bulb development in Sagittaria sagittifolia[J]. Gene, 2018, 649:99-112. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=446959ab3cb62cc3e45fc3a2df159fc8
    [35] YU R G, XU L, ZHANG W, et al. De Novo taproot transcriptome sequencing and analysis of major genes involved in sucrose metabolism in radish (Raphanus sativus L.)[J]. Frontiers in Plant Science, 2016, 7:585/1-12. https://core.ac.uk/reader/82834243
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