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谷子RNA干扰相关酶类基(ji)因家族的鉴定与分析

张司雯 邓欣 王龙 罗皓天 王禹茜 王月 李清竹 王红艳

引用本文: 张司雯,邓欣,王龙,罗皓天,王禹茜,王月,李清竹,王红艳. 谷子RNA干扰相关酶类基因家族的鉴定与分析. 欧宝体育, 2021, 38(7): 1380-1392 doi: shu
Citation:  ZHANG S W, DENG X, WANG L, LUO H T, WANG Y Q, WANG Y, LI Q Z, WANG H Y. Identification and analysis of RNA interference-related enzyme gene families in . Pratacultural Science, 2021, 38(7): 1380-1392 doi: shu

谷子RNA干扰相关酶类基因家族的鉴定与分析

    作者简介: 张司雯(1995-),女,辽宁阜新人,在读硕士生,主要从事植物学研究。E-mail: 1429920789@qq.com; 邓欣(1989-),女,内蒙古呼伦贝尔人,讲师,博士,主要从事植物学研究。E-mail: dengxin@lnu.edu.cn
    通讯作者: 王红艳(1981-),女,辽宁沈阳人,副教授,博士,主要从事植物表观遗传学研究。E-mail: hongyan2003@126.com
  • 基金项目: 国家自然科学基金(31100172);辽宁省自然科学基金指导项目(20180550686);辽宁省教育厅科学研究经费项目(LJC201909)

摘要: Dicers酶类、Argonautes蛋白以及RNA依赖的RNA聚合酶(RNA-dependent RNA polymerases, RDRs)是RNA干扰(RNA interference, RNAi)机制中重要的核心蛋白,但在谷子(Setaria italica)中尚无系统报道。为了研究谷子中与RNA干扰相关酶类基因的特征,本研究对谷子的RNA干扰相关酶类基因家族进行了蛋白质理化性质、亚细胞定位预测、蛋白质保守基序、基因保守结构域、基因家族成员间系统发育关系以及组织特异性表达谱分析。研究共发现24个与谷子RNA干扰相关酶类基因,包括7个DCL (Dicers),13个AGO (Argonautes),4个RDRs。系统进化树分析表明,这些家族被分为3个进化支。同一家族基因成员具有共同的保守结构域。虽然大多数基因可同时在不同发育时期的叶、茎和穗中表达,但其在各时期的穗和茎中的表达量最高。本研究为详细探讨这些基因在谷子生殖和生长发育中的表观遗传修饰作用提供了理论依据。

English

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    图 1  谷子和水稻RNA干扰相关酶类基因的系统进化树

    Figure 1.  Phylogenetic tree for the RNA interference-related enzyme genes in Setaria italica and Oryza sativa

    进化树是(shi)(shi)用水稻和谷子的(de)蛋(dan)白(bai)(bai)质(zhi)序(xu)(xu)列绘制的(de),其中谷子的(de)蛋(dan)白(bai)(bai)质(zhi)序(xu)(xu)列用红色进化支(zhi)表示,水稻的(de)蛋(dan)白(bai)(bai)质(zhi)序(xu)(xu)列则用绿色进化支(zhi)表示。RDR家(jia)族(zu)是(shi)(shi)粉(fen)色背(bei)(bei)景(jing),DCL家(jia)族(zu)是(shi)(shi)黄色背(bei)(bei)景(jing),AGO家(jia)族(zu)是(shi)(shi)青色背(bei)(bei)景(jing)。

    The phylogenetic tree between Setaria italica and Oryza sativa genes using full length protein sequences. The protein sequences of S. italica are shown by the red branches, and the protein sequences of O. Sativa are shown by the green branches. The RDRs are shaded in pink, the DCLs are shaded in yellow, and the AGOs are shaded in turquoise.

    图 2  谷子和水稻RNA干扰相关酶类的氨基酸结构域分析

    Figure 2.  Analysis of the amino acid domains of enzymes related to RNA interference in Setaria italica and Oryza sativa

    图 3  谷子RNA干扰相关酶类基因蛋白质保守基序分析

    Figure 3.  Analysis of protein conservative motifs in Setaria italica RNA interference-related enzyme genes

    图 4  谷子RNA干扰相关酶类基因组织特异性表达分析

    Figure 4.  Transcriptome analysis of RNA interference-related enzyme genes in different Setaria italica tissues

    FPKM: 每千个碱基的转录每百万映射读取的fragments,图中所示数值是log2 (FPKM + 1)。

    FPKM: Fragments per kilobase million, the value shown in the figure is log2 (FPKM + 1).

    表 1  谷子与水稻中RNA干扰相关酶类基因比较分析

    Table 1.  Comparative analysis of RNA interference-related enzyme genes in Setaria italica and Oryza sativa

    水稻 Oryza sativa 谷子 Setaria italica
    基因名
    Gene
    name
    序列长度
    Sequence
    length/aa
    NCBI基因编号
    NCBI
    gene ID
    基因名
    Gene
    name
    MDSi (xiaomi)Phytozome (Yugu1)
    基因编号
    Gene
    ID
    序列长度
    Sequence
    length/aa
    相似度
    Similarity/%
    基因编号
    Gene ID
    序列长度
    Sequence
    length/aa
    相似度
    Similarity/%
    OsDCL1a 1 925 XP_025879428.1 SiDCL1a Si9g54530.1 1 939 89 Seita.9G562200.1 1 933 89
    OsDCL1b 299 XP_015641965.1 SiDCL1b Si4g14070.1 313 76 Seita.4G153000.1 313 76
    OsDCL1c 371 XP_015637412.1 SiDCL1c Si3g28940.1 347 82 Seita.3G295600.1 375 82
    OsDCL2a 1 410 XP_015630302.1 SiDCL2 Si9g17530.1 1 404 71 Seita.9G179200.1 1 544 70
    OsDCL2b 1 377 XP_015611517.1 68 68
    OsDCL3a 1 651 XP_015621462.1 SiDCL3a Si5g42100.1 1 676 74 Seita.5G422300.1 1 645 72
    OsDCL3b 1 571 XP_015612988.1 SiDCL3b Si9g20960.1 1 338 81 Seita.9G215300.1 1 567 80
    OsSHO1 1 631 XP_015636293.1 SiSHO1 Si7g17550.1 1 632 76 Seita.7G162200.1 1 632 76
    OsAGO1a 1 082 XP_015626096.1 SiAGO1b Si7g21320.1 1 104 84 Seita.7G201100.1 1 104 84
    OsAGO1b 1 118 XP_015636291.1 88 88
    OsAGO1c 1 011 XP_015626468.1 SiAGO1c Si1g37860.1 1 050 87 Seita.1G378700.1 1 023 85
    OsAGO1d 1 038 XP_015642511.1 SiAGO1d Si4g27530.1 1 050 87 Seita.4G288700.1 1 041 86
    OsAGO2 1 034 XP_015636011.1 SiAGO2 Si7g24610.1 1 024 72 Seita.7G236800.1 1 024 72
    OsAGO4a 904 XP_015621073.1 SiAGO4a Si5g05140.1 902 83 Seita.5G043300.1 902 83
    OsAGO4b 911 XP_015636673.1 SiAGO4b Si3g11970.2 910 85 Seita.3G117800.1 910 85
    OsAGO11 1 021 XP_015629890.2 SiAGO12 Si9g13650.1 1 108 63 Seita.9G138800.1 1 148 62
    OsAGO12 914 XP_015629895.2 71 70
    OsAGO13 1 050 XP_015631376.2 SiMEL1 Si9g05810.1 1 060 84 Seita.9G052000.1 1 060 84
    OsMEL1 1 058 XP_015629235.1 83 83
    OsAGO14 1 052 XP_015645442.1 SiAGO14 Si2g07310.1 1 041 61 Seita.2G066500.1 1 041 61
    OsAGO16 893 XP_015647590.1 SiAGO16 Si2g15500.1 882 89 Seita.2G148000.1 882 89
    OsSHL4 1 048 XP_015629412.1 SiSHL4 Si9g35570.1 1 030 78 Seita.9G359200.1 1 030 78
    OsPNH1 979 XP_015643801.1 SiPNH1 Si4g21660.1 965 91 Seita.4G225900.3 965 91
    OsAGO18 1 088 XP_015644916.2 SiAGO18 Si2g31320.1 819 55 Seita.2G310800.1 954 50
    OsRDR1 1 106 XP_015627028.1 SiRDR1 Si1g29500.2 1 123 78 Seita.1G312200.1 1 123 78
    OsRDR2 1 136 XP_015636884.1 SiRDR2 Si7g14360.1 1 130 77 Seita.7G128700.1 1 130 77
    OsRDR3 994 XP_015628356.1 SiRDR3 Si7g02920.1 1 150 53 Seita.7G020600.1 1 150 53
    OsRDR4 1 183 XP_015624482.1 50 50
    OsSHL2 1 218 XP_015622237.1 SiSHL2 Si5g19380.1 1 211 78 Seita.5G184800.1 1 211 78
     xiaomi基因组数据库来自MDSi (http://foxtail-millet.biocloud.net/home),Yugu1基因组数据库来自Phytozome (Setaria italica v2.2) (http://phytozome.jgi.doe.gov/pz/portal.html)。
     The xiaomi genome database is from MDSi (http://foxtail-millet.biocloud.net/home) and the Yugu1 genome database is from Phytozome (Setaria italica v2.2) (http://phytozome.jgi.doe.gov/pz/portal.html).
    下载: 导出CSV

    表 2  谷子RNA干扰相关酶类基因的蛋白质理化性质分析

    Table 2.  Protein physical and chemical properties analysis of Setaria italica RNA interference-related enzyme genes

    基因
    Gene
    name
    氨基酸数
    Number of
    amino acids
    分子量
    Molecular
    weight/Da
    理论等电点
    Theoretical
    pI
    带负电荷的
    残基数目
    Total No. of
    negatively
    charged
    residues
    带正电荷的
    残基数目
    Total No. of
    positively
    charged
    residues
    分子式
    Formula
    原子总数
    Total number
    of atoms
    脂肪指数
    Aliphatic
    index
    亲水性的平均值
    Grand average of
    hydropathicity
    亚细胞定位
    Subcellular
    localization
    SiDCL1a 1 933 216 227.3 6.42 257 241 C9555H15091N2701O2860S83 30 290 82.52 −0.397 细胞核
    Nucleus
    SiDCL1b 313 35 044.76 5.01 52 36 C1559H2447N419O477S11 4 913 82.88 −0.396 细胞核
    Nucleus
    SiDCL1c 375 41 187.62 8.91 43 49 C1840H2960N518O529S12 5 859 92.35 −0.192 细胞核
    Nucleus
    SiDCL2 1544 172 946.17 8.02 172 178 C7682H12221N2125O2254S79 24 361 92.23 −0.172 细胞核
    Nucleus
    SiDCL3a 1 645 184 281.86 6.10 208 185 C8173H12985N2215O2475S75 25 923 91.05 −0.260 细胞核
    Nucleus
    SiDCL3b 1 567 177 008.27 6.00 194 167 C7897H12463N2123O2337S77 24 897 94.66 −0.149 细胞核
    Nucleus
    SiSHO1 1 632 184 717.28 6.21 211 191 C8239H12963N2215O2426S89 25 932 90.53 −0.227 细胞核
    Nucleus
    SiAGO1b 1 104 122 434.78 9.49 103 137 C5373H8484N1612O1591S41 17 101 73.10 −0.536 细胞核
    Nucleus
    SiAGO1c 1 023 113 730.47 9.53 101 135 C4998H7939N1509O1461S37 15 944 77.72 −0.492 细胞核
    Nucleus
    SiAGO1d 1 041 115 632.26 9.21 103 127 C5093H8007N1499O1503S42 16 144 75.05 −0.437 细胞核
    Nucleus
    SiAGO2 1 024 110 788.93 9.31 98 129 C4884H7721N1417O1455S38 15 515 75.68 −0.423 细胞核
    Nucleus
    SiAGO4a 902 101 015.61 9.16 99 121 C4472H7100N1268O1321S39 14 200 78.65 −0.430 细胞核
    Nucleus
    SiAGO4b 910 101 605.23 9.02 100 118 C4514H7131N1273O1324S37 14 279 79.13 −0.405 细胞核
    Nucleus
    SiAGO12 1 148 125 449.97 9.55 99 142 C5535H8874N1626O1613S45 17 693 83.22 −0.288 细胞核
    Nucleus
    SiMEL 1 060 117 168.76 9.33 106 136 C5189H8197N1507O1512S40 16 445 76.56 −0.403 细胞核
    Nucleus
    SiAGO14 1 041 112 646.37 9.51 83 121 C4977H7830N1462O1447S42 15 758 73.67 −0.347 细胞核
    Nucleus
    SiAGO16 882 98 605.68 9.29 91 118 C4348H7004N1240O1282S45 13 919 87.26 −0.292 细胞核
    Nucleus
    SiSHL4 1 030 115 462.02 9.46 99 140 C5142H8151N1471O1463S46 16 273 82.16 −0.391 细胞核
    Nucleus
    SiPNH1 965 107 674.01 9.34 94 127 C4783H7614N1370O1374S43 15 184 83.07 −0.356 细胞核
    Nucleus
    SiAGO18 954 105 726.39 8.89 114 131 C4668H7442N1342O1400S30 14 882 83.19 −0.441 细胞核
    Nucleus
    SiRDR1 1 123 128 311.11 7.88 131 134 C5783H8976N1544O1665S48 18 016 87.00 −0.246 细胞核
    Nucleus
    SiRDR2 1 130 126 334.56 6.90 146 143 C5633H8838N1554O1650S50 17 725 85.42 −0.223 叶绿体类囊体膜
    Chloroplast
    thylakoid
    membrane
    SiRDR3 1 150 131 081.65 6.18 158 144 C5805H9120N1588O1744S63 18 320 80.81 −0.431 叶绿体
    Chloroplast
    SiSHL2 1 211 136 712.90 6.48 156 149 C6078H9499N1699O1786S55 19 117 79.41 −0.333 细胞核
    Nucleus
    下载: 导出CSV
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                        • 通讯作者:  王红艳, hongyan2003@126.com
                        • 收稿日期:  2021-01-14
                        • 接受日期:  2021-04-02
                        • 网络出版日期:  2021-05-07
                        • 刊出日期:  2021-07-15
                        通讯作者: 陈斌, bchen63@163.com
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