高级检索

留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

旱柳扩展蛋白基因家族与基因组分化

杨锐霞 尹鹏 刘晓 王艳 刘家福 徐吉臣

杨锐霞, 尹鹏, 刘晓, 王艳, 刘家福, 徐吉臣. 旱柳扩展蛋白基因家族与基因组分化[J]. 北京林业大学学报, 2021, 43(1): 37-48. doi: 10.12171/j.1000-1522.20200216
引用本文: 杨锐霞, 尹鹏, 刘晓, 王艳, 刘家福, 徐吉臣. 旱柳扩展蛋白基因家族与基因组分化[J]. 北京林业大学学报, 2021, 43(1): 37-48. doi: 10.12171/j.1000-1522.20200216
Yang Ruixia, Yin Peng, Liu Xiao, Wang Yan, Liu Jiafu, Xu Jichen. Expansin gene family in association with the genome differentiation of Salix matsudana[J]. Journal of Beijing Forestry University, 2021, 43(1): 37-48. doi: 10.12171/j.1000-1522.20200216
Citation: Yang Ruixia, Yin Peng, Liu Xiao, Wang Yan, Liu Jiafu, Xu Jichen. Expansin gene family in association with the genome differentiation of Salix matsudana[J]. Journal of Beijing Forestry University, 2021, 43(1): 37-48. doi: 10.12171/j.1000-1522.20200216

旱柳扩展蛋白基因家族与基因组分化

doi: 10.12171/j.1000-1522.20200216
基金项目: 国家自然科学基金面上项目(31870648)
详细信息
    作者简介:

    杨锐霞。主要研究方向:林木基因组与分子育种。Email:2413536685@qq.com 地址:100083北京市海淀区清华东路35号北京林业大学生物科学与技术学院

    责任作者:

    徐吉臣,博士,教授。主要研究方向:林木基因组与分子育种。Email:jcxu282@sina.com 地址:同上

  • 中图分类号: S718.46

Expansin gene family in association with the genome differentiation of Salix matsudana

  • 摘要:   目的  扩展蛋白是植物中重要的基因家族之一,在生长发育和逆境抗性过程中发挥重要的作用。本研究拟探讨旱柳中的扩展蛋白基因组成变化,为理解旱柳AA、BB基因组的分化提供理论依据,也为柳树分子设计育种提供参考。  方法  本研究基于毛果杨扩展蛋白基因氨基酸序列,鉴定旱柳中的扩展蛋白基因;通过生物信息学软件,分析旱柳AA、BB基因组扩展蛋白基因家族的特征和变化。  结果  在异源四倍体旱柳基因组中鉴定了65个扩展蛋白基因,其中AA基因组32个、BB基因组33个,共有的扩展蛋白基因28个,有3个基因产生了重复;AA、BB基因组中各有3个扩展蛋白基因缺失,并分别有2个和1个基因结构域发生了缺失。基因结构分析表明,部分AA、BB基因组的对应基因在内含子数量和内含子剪切位点等方面存在明显变化。在密码子使用选择上,AA、BB基因组间各含有5个高频密码子,分别含有5个和10个最优密码子,部分密码子如AGG和UAG等的使用频率有很大的差别。比较蛋白理化性质,AA、BB基因组的扩展蛋白在亲疏水性、结构稳定性方面存在不同程度的变化。进化分析显示,两套基因组中EXPA23基因经历了正选择,其他同源基因经历了纯化选择,但Ka/Ks值变化较大。  结论  旱柳AA、BB基因组扩展蛋白家族具有各自的组成、结构及表达特征,是基因组分化的基础,体现了扩展蛋白在物种分化和分类中的重要地位。

     

  • 图  1  旱柳扩展蛋白进化关系及基因结构分析

    Figure  1.  Phylogenetic relationship and gene structure of expansin genes in S. matsudana

    表  1  旱柳扩展蛋白基因信息

    Table  1.   Information of expansin genes in Salix matsudana

    基因名称
    Gene name
    染色体
    Chromosome
    信号肽
    长度
    Signal peptide length/bp
    外显子
    长度
    Length of exon/bp
    内含子
    长度
    Length of intron/bp
    外显子数
    Number of exon
    基因名称
    Gene name
    染色体
    Chromosome
    信号肽
    长度
    Signal peptide length /bp
    外显子
    长度
    Length of exon /bp
    内含子
    长度
    Length of intron /bp
    外显子数
    Number of exon
    SmA_EXPA1 1A 75 789 1 136 3 SmB_EXPA1 1B 75 789 1 087 3
    SmA_EXPA2 Contig01890 69 753 237 3 SmB_EXPA2 13B 69 753 562 3
    SmA_EXPA3 10A 60 750 712 3 SmB_EXPA3 10B 60 750 715 3
    SmA_EXPA4 8A 66 750 277 3 SmB_EXPA4 8B 片段缺失 Fragment deletion
    SmA_EXPA5 9A 78 792 733 3 SmB_EXPA5 9B 78 792 668 3
    SmA_EXPA6 17A 60 726 218 3 SmB_EXPA6 17B 片段缺失 Fragment deletion
    SmA_EXPA7 8A 63 777 796 3 SmB_EXPA7 Contig01117 63 777 821 3
    SmA_EXPA8 Contig02775 93 789 1 070 2 SmB_EXPA8 4B 93 819 1 045 2
    SmA_EXPA9 17A 60 726 205 3 SmB_EXPA9 17B 60 528 397 4
    SmA_EXPA10 16A 60 744 225 3 SmB_EXPA10 16B 60 816 936 4
    SmA_EXPA11 13A 60 729 469 3 SmB_EXPA11 13B 结构域缺失 Domain deletion
    SmA_EXPA12 19A 69 753 437 3 SmB_EXPA12 Contig02348 69 753 285 3
    SmA_EXPA13 4A 45 741 321 4 SmB_EXPA13 4B 72 756 286 3
    SmA_EXPA15 10A 63 777 497 3 SmB_EXPA15 10B 63 777 578 3
    SmA_EXPA16a 6A 69 783 751 3 SmB_EXPA16a 6B 69 783 730 3
    SmA_EXPA16b 19A 片段缺失 Fragment deletion SmB_EXPA16b 19B 69 750 758 4
    SmA_EXPA17a 2A 72 771 185 3 SmB_EXPA17a 2B 66 771 181 3
    SmA_EXPA17b 2A 片段缺失 Fragment deletion SmB_EXPA17b 2B 66 726 223 4
    SmA_EXPA18a 5A 72 771 181 3 SmB_EXPA18a 5B 72 771 191 3
    SmA_EXPA18b 18A 72 771 191 3 SmB_EXPA18b 18B 片段缺失 Fragment deletion
    SmA_EXPA19 2A 结构域缺失 Domain deletion SmB_EXPA19 2B 81 765 5 796 4
    SmA_EXPA20 1A 84 765 394 3 SmB_EXPA20 1B 84 765 386 3
    SmA_EXPA21 9A 片段缺失 Fragment deletion SmB_EXPA21 9B 63 753 228 3
    SmA_EXPA22 4A 63 753 208 3 SmB_EXPA22 4B 63 753 233 3
    SmA_EXPA23 17A 111 843 1 067 2 SmB_EXPA23 17B 102 834 1 072 2
    SmA_EXPA24 16A 87 807 366 3 SmB_EXPA24 16B 87 807 436 3
    SmA_EXPA25 Contig01569 72 783 458 4 SmB_EXPA25 Contig01569 72 861 427 3
    SmA_EXPA27 17A 66 774 146 2 SmB_EXPA27 17B 75 783 228 2
    SmA_EXPA28 3A 63 747 224 3 SmB_EXPA28 3B 63 747 220 3
    SmA_EXPB1 6A 78 828 540 4 SmB_EXPB1 14B 78 825 569 4
    SmA_EXPB2 19A 60 789 1 260 4 SmB_EXPB2 Contig01569 75 789 1 171 4
    SmA_EXPB3 13A 66 798 1 507 4 SmB_EXPB3 13B 60 789 1 107 4
    SmA_EXLA1 Contig00810 结构域缺失 Domain deletion SmB_EXLA1 4B 51 852 546 4
    SmA_EXLA2 9A 96 825 729 5 SmB_EXLA2 9B 51 780 925 5
    SmA_EXLB1 3A 72 750 533 4 SmB_EXLB1 3B 72 750 581 4
    SmA_EXLB3 Contig01873 69 774 981 5 SmB_EXLB3 16B 69 774 672 5
    SmA_EXLB4 3A 72 771 673 5 SmB_EXLB4 3B 72 741 803 6
    下载: 导出CSV

    表  2  旱柳扩展蛋白亚家族成员间氨基酸及核苷酸(括号)序列一致性比较

    Table  2.   Sequence identity of amino acid and nucleotides (in brackets) among the expansin genes in S. matsudana %

    AABB
    EXPAEXPBEXLAEXLBEXPAEXPBEXLAEXLB
    AA EXPA 41.1 ~ 99.4
    (48.3 ~ 97.5)
    EXPB 28.0 ~ 38.7 51.2 ~ 91.7
    (38.5 ~ 45.3) (49.2 ~ 86.3)
    EXLA 21.4 ~ 32.1 33.9 ~ 35.1
    (33.6 ~ 42.6) (40.5 ~ 44.2)
    EXLB 20.8 ~ 32.7 31.0 ~ 39.3 41.7 ~ 46.4 49.4 ~ 81.5
    (36.1 ~ 42.3) (39.8 ~ 44.0) (43.0 ~ 45.3) (45.5 ~ 85.1)
    BB EXPA 43.6 ~ 100.0 29.3 ~ 41.4 21.4 ~ 32.9 23.6 ~ 35.0 42.5 ~ 99.3
    (52.0 ~ 99.7) (37.5 ~ 47.1) (36.0 ~ 40.8) (34.3 ~ 42.3) (51.5 ~ 97.0)
    EXPB 32.9 ~ 42.9 54.3 ~ 97.1 35.7 ~ 38.6 35.7 ~ 44.3 30.1 ~ 41.2 54.9 ~ 90.2
    (38.0 ~ 46.9) (55.2 ~ 97.5) (41.6 ~ 46.3) (40.1 ~ 44.3) (39.2 ~ 47.5) (55.9 ~ 88.7)
    EXLA 21.4 ~ 32.9 32.1 ~ 35.0 89.3 ~ 95.7 41.4 ~ 49.3 22.2 ~ 32.7 32.7 ~ 36.6 87.6
    (35.3 ~ 41.8) (40.8 ~ 46.1) (87.9 ~ 96.7) (52.4 ~ 55.2) (36.2 ~ 42.1) (43.1 ~ 46.3) (86.2)
    EXLB 24.3 ~ 35.0 35.7 ~ 44.3 43.6 ~ 49.3 51.4 ~ 96.8 23.5 ~ 34.0 35.9 ~ 44.4 41.2 ~ 48.4 52.9 ~ 86.9
    (34.8 ~ 41.6) (39.0 ~ 44.8) (51.6 ~ 54.4) (54.4 ~ 97.5) (34.2 ~ 42.9) (41.4 ~ 45.6) (51.0 ~ 53.4) (48.0 ~ 89.4)
    下载: 导出CSV

    表  3  旱柳扩展蛋白密码子碱基组成

    Table  3.   Codon base composition of expansin genes in S. matsudana

    参数 ParameterAABB
    T3 0.38 0.38
    C3 0.31 0.30
    A3 0.29 0.30
    G3 0.23 0.23
    ENC 53.92 54.12
    CAI 0.21 0.21
    GC3 0.44 0.43
    GC 0.49 0.48
    CT/AG 1.33 1.29
    AT/GC 1.25 1.28
    下载: 导出CSV

    表  4  旱柳扩展蛋白密码子中第二和第三位碱基组成的比例

    Table  4.   Second and third base combination proportions of expansin gene codons in S. matsudana %

    密码子组成 Codon combinationAABB
    *TT 7.81 7.87
    *TC 7.52 7.36
    *TA 2.73 3.06
    *TG 6.86 6.99
    *CT 9.59 9.38
    *CC 5.68 5.35
    *CA 7.15 7.21
    *CG 1.88 2.08
    *AT 8.69 8.82
    *AC 6.77 6.51
    *AA 4.71 5.20
    *AG 4.84 4.83
    *GT 6.47 6.44
    *GC 6.59 6.45
    *GA 6.14 5.90
    *GG 6.58 6.55
    下载: 导出CSV

    表  5  旱柳扩展蛋白基因密码子的相对使用频率

    Table  5.   RFSC values of expansin genes in S. matsudana %

    氨基酸 Amino acid密码子 CodonRFSC (AA)RFSC (BB) 氨基酸 Amino acid密码子 CodonRFSC (AA)RFSC (BB)
    Phe UUU 42.99 43.25 Tyr UAU 50.16 52.99
    UUC 57.01 56.75 UAC 49.84 47.01
    Leu UUA 9.96 11.21 TER UAA 34.38 42.42
    UUG 21.22 22.24 UAG 46.88 36.36
    CUU 18.45 18.79 His CAU 54.97 53.74
    CUC 21.77 21.03 CAC 45.03 46.26
    CUA 9.23 8.45 Gln CAA 51.78 52.51
    CUG 19.37 18.28 CAG 48.22 47.49
    Ile AUU 49.18 48.88 Asn AAU 54.76 56.34
    AUC 34.70 34.41 AAC 45.24 43.66
    AUA 16.12 16.71 Lys AAA 45.79 49.52
    Met AUG 100.00 100.00 AAG 54.21 50.48
    Val GUU 33.14 32.46 Asp GAU 65.77 66.23
    GUC 23.43 21.83 GAC 34.23 33.77
    GUA 11.81 14.74 Glu GAA 51.33 54.60
    GUG 31.62 30.97 GAG 48.67 45.40
    Ser UCU 23.20 21.45 Cys UGU 47.14 46.64
    UCC 15.84 15.48 UGC 52.86 53.36
    UCA 18.10 19.46 TER UGA 18.75 21.21
    UCG 5.37 5.40 Trp UGG 100.00 100.00
    Pro CCU 42.93 44.53 Arg CGU 11.56 9.92
    CCC 18.48 17.07 CGC 9.41 10.70
    CCA 29.89 29.60 CGA 7.26 7.31
    CCG 8.70 8.80 CGG 5.11 5.22
    Thr ACU 34.79 36.38 Ser AGU 14.85 15.77
    ACC 28.83 26.07 AGC 22.63 22.44
    ACA 29.22 27.24 Arg AGA 37.37 51.59
    ACG 7.16 10.31 AGG 29.30 38.87
    Ala GCU 42.53 40.78 Gly GGU 26.11 27.09
    GCC 20.75 20.53 GGC 20.64 19.87
    GCA 29.61 31.28 GGA 34.47 33.47
    GCG 7.11 7.40 GGG 18.78 19.56
    注:粗体字的密码子为高频密码子。Note: codons in bold mean high frequency codons.
    下载: 导出CSV

    表  6  旱柳扩展蛋白最优密码子

    Table  6.   Optimal codons of expansin genes in S. matsudana

    基因组
    Genome
    最优密码子
    Optimal codon
    AACUG ACC GCC GCA UGC CGU AGG
    BBUUC UUA CUG CCA ACC GCC UAG UGC CGU CGC
    下载: 导出CSV

    表  7  旱柳扩展蛋白基因编码蛋白氨基酸组分

    Table  7.   Amino acid composition of expansinproteins in S. matsudana %

    氨基酸 Amino acidAABB变幅 Variation
    Gly 11.80 11.30 4.46
    Ser 8.61 8.32 3.50
    Ala 8.39 8.46 −0.83
    Leu 6.60 6.86 −3.69
    Val 6.40 6.34 0.94
    Asn 6.14 6.06 1.25
    Thr 6.13 6.08 0.85
    Phe 5.38 5.17 4.24
    Arg 4.53 4.53 0.10
    Pro 4.48 4.43 1.13
    Ile 4.46 4.74 −5.94
    Gln 4.12 4.01 2.75
    Tyr 3.91 3.95 −0.95
    Asp 3.63 3.64 −0.29
    Cys 3.41 3.52 −3.17
    Lys 3.33 3.70 −10.11
    Trp 2.83 2.83 0.04
    Met 2.18 2.28 −4.42
    His 1.84 1.74 5.86
    Glu 1.83 2.06 −11.16
    注:变幅 = AA基因组氨基酸含量/BB基因组氨基酸含量 − 1。Note: variation = AA genome amino acid content/BB genome amino acid content − 1.
    下载: 导出CSV

    表  8  旱柳扩展蛋白的理化特征

    Table  8.   Physicochemic properties of expansin proteins in S. matsudana

    扩展蛋白
    Expansin
    分子量
    Molecular weight/ kDa
    理论等电点
    Isoelectric point (pI)
    脂溶指数
    Aliphatic index (AI)
    总平均疏水性
    Grand
    average of hydropathicity (GRAVY)
    蛋白不稳定指数
    Instability index (II)
    扩展蛋白
    Expansin
    分子量
    Molecular weight /kDa
    理论等电点
    Isoelectric point (pI)
    脂溶指数
    Aliphatic index (AI)
    总平均疏水性
    Grand
    average of hydropathicity (GRAVY)
    蛋白不稳定指数
    Instability index (II)
    SmA_EXPA1 28.40 9.63 67.44 −0.053 48.87 SmB_EXPA1 28.44 9.82 66.72 −0.068 43.99
    SmA_EXPA2 26.59 7.53 64.84 −0.086 37.79 SmB_EXPA2 26.63 8.04 63.28 −0.123 36.91
    SmA_EXPA3 26.53 9.36 67.75 −0.108 36.02 SmB_EXPA3 26.53 9.36 66.59 −0.096 35.55
    SmA_EXPA4 26.55 9.50 70.08 −0.100 40.95
    SmA_EXPA5 28.60 9.62 67.57 −0.041 41.92 SmB_EXPA5 28.64 9.53 66.08 −0.031 41.81
    SmA_EXPA6 26.03 8.94 66.76 −0.066 36.98
    SmA_EXPA7 27.62 9.45 69.57 −0.033 30.24 SmB_EXPA7 27.74 9.63 72.64 −0.065 31.84
    SmA_EXPA8 28.23 7.57 73.74 −0.042 30.49 SmB_EXPA8 29.54 8.60 74.60 −0.066 31.97
    SmA_EXPA9 26.11 9.06 67.97 −0.077 36.63 SmB_EXPA9 22.79 8.63 69.15 0.036 35.82
    SmA_EXPA10 26.36 9.34 67.53 −0.170 26.51 SmB_EXPA10 29.08 9.16 77.38 −0.040 26.68
    SmA_EXPA11 25.71 9.35 68.97 0.013 37.83
    SmA_EXPA12 26.57 6.86 63.28 −0.124 29.47 SmB_EXPA12 26.53 8.06 61.72 −0.144 31.33
    SmA_EXPA13 27.02 9.06 69.76 −0.125 26.92 SmB_EXPA13 27.00 8.94 72.05 −0.092 31.23
    SmA_EXPA15 28.15 9.33 69.88 −0.049 35.32 SmB_EXPA15 28.07 9.30 70.66 −0.080 36.13
    SmA_EXPA16a 28.09 9.50 71.27 −0.047 31.41 SmB_EXPA16a 28.22 9.45 71.27 −0.040 31.28
    SmB_EXPA16b 27.18 9.34 73.25 0.002 30.90
    SmA_EXPA17a 27.85 9.19 64.14 −0.055 30.07 SmB_EXPA17a 27.75 9.07 63.36 −0.048 29.57
    SmB_EXPA17b 26.10 8.96 64.07 −0.031 28.55
    SmA_EXPA18a 27.65 9.17 63.71 −0.060 33.09 SmB_EXPA18a 27.68 9.17 64.10 −0.059 33.09
    SmA_EXPA18b 27.68 9.17 64.10 −0.059 33.09
    SmB_EXPA19 27.56 9.24 78.78 −0.019 32.75
    SmA_EXPA20 28.16 10.13 67.20 −0.120 42.97 SmB_EXPA20 28.05 10.13 69.88 −0.114 44.59
    SmB_EXPA21 27.92 8.08 76.84 −0.124 39.07
    SmA_EXPA22 27.57 8.37 75.68 −0.133 32.68 SmB_EXPA22 27.68 7.57 74.92 −0.152 31.42
    SmA_EXPA23 30.46 9.01 80.46 −0.068 37.22 SmB_EXPA23 30.18 8.90 79.57 −0.095 38.82
    SmA_EXPA24 28.97 9.30 60.49 −0.015 35.5 SmB_EXPA24 29.23 9.78 64.81 0.028 31.03
    SmA_EXPA25 28.54 9.25 68.69 −0.354 35.64 SmB_EXPA25 31.75 9.33 70.66 −0.390 35.47
    SmA_EXPA27 28.24 8.35 71.79 −0.114 27.69 SmB_EXPA27 28.44 8.54 75.08 −0.087 25.98
    SmA_EXPA28 26.65 8.88 69.64 −0.103 21.72 SmB_EXPA28 26.64 9.00 68.47 −0.120 23.03
    SmA_EXPB1 29.04 5.29 71.64 −0.067 42.36 SmB_EXPB1 28.44 5.53 72.96 −0.044 42.72
    SmA_EXPB2 28.59 8.55 79.27 −0.139 30.37 SmB_EXPB2 28.70 8.79 80.34 −0.105 28.82
    SmA_EXPB3 29.08 8.60 74.34 −0.235 32.10 SmB_EXPB3 28.70 8.35 76.30 −0.225 27.88
    SmB_EXLA1 30.80 8.86 83.07 0.083 34.02
    SmA_EXLA2 29.85 8.88 74.42 −0.051 33.37 SmB_EXLA2 28.24 8.73 71.97 −0.099 30.84
    SmA_EXLB1 27.49 6.42 74.10 −0.157 31.04 SmB_EXLB1 27.45 6.30 76.83 −0.127 25.80
    SmA_EXLB3 27.84 5.00 79.69 −0.168 30.42 SmB_EXLB3 28.01 4.72 78.17 −0.214 38.08
    SmA_EXLB4 28.14 4.70 74.30 −0.172 38.18 SmB_EXLB4 26.99 5.37 78.54 −0.093 36.23
    均值
    Average value
    27.94 8.40 70.36 −0.106 33.78 均值
    Average value
    27.96 8.49 71.36 −0.098 33.49
    下载: 导出CSV

    表  9  旱柳中旁系同源扩展蛋白基因对Ka/Ks比值

    Table  9.   Ka/Ks ratios between the paralogous expansin gene pairs in S. matsudana

    同源基因 Homologous gene Ka KsKa/Ks选择压 Selective pressure
    SmA_EXPA1 & SmB_EXPA1 0.010 5 0.081 4 0.128 5 纯化选择 Purify selection
    SmA_EXPA2 & SmB_EXPA2 0.005 6 0.190 8 0.029 5 纯化选择 Purify selection
    SmA_EXPA3 & SmB_EXPA3 0.013 3 0.099 8 0.133 0 纯化选择 Purify selection
    SmA_EXPA5 & SmB_EXPA5 0.010 7 0.127 0 0.084 6 纯化选择 Purify selection
    SmA_EXPA7 & SmB_EXPA7 0.016 2 0.118 6 0.137 0 纯化选择 Purify selection
    SmA_EXPA8 & SmB_EXPA8 0.019 7 0.090 9 0.216 9 纯化选择 Purify selection
    SmA_EXPA9 & SmB_EXPA9 0.965 1 1.098 5 0.878 6 纯化选择 Purify selection
    SmA_EXPA10 & SmB_EXPA10 0.018 3 0.116 4 0.157 5 纯化选择 Purify selection
    SmA_EXPA12 & SmB_EXPA12 0.010 6 0.195 6 0.054 2 纯化选择 Purify selection
    SmA_EXPA13 & SmB_EXPA13 0.023 2 0.129 1 0.180 1 纯化选择 Purify selection
    SmA_EXPA15 & SmB_EXPA15 0.013 0 0.084 1 0.154 2 纯化选择 Purify selection
    SmA_EXPA16a & SmB_EXPA16a 0.012 5 0.111 0 0.112 3 纯化选择 Purify selection
    SmA_EXPA17a & SmB_EXPA17a 0.017 9 0.087 9 0.203 7 纯化选择 Purify selection
    SmA_EXPA18a & SmB_EXPA18a 0.003 8 0.083 1 0.046 2 纯化选择 Purify selection
    SmA_EXPA20 & SmB_EXPA20 0.012 3 0.077 1 0.160 0 纯化选择 Purify selection
    SmA_EXPA22 & SmB_EXPA22 0.012 9 0.120 2 0.107 2 纯化选择 Purify selection
    SmA_EXPA23 & SmB_EXPA23 0.084 3 0.073 8 1.142 0 正选择 Purify selection
    SmA_EXPA24 & SmB_EXPA24 0.051 3 0.156 5 0.327 8 纯化选择 Purify selection
    SmA_EXPA25 & SmB_EXPA25 0.151 8 0.183 9 0.825 5 纯化选择 Purify selection
    SmA_EXPA27 & SmB_EXPA27 0.012 3 0.028 7 0.427 9 纯化选择 Purify selection
    SmA_EXPA28 & SmB_EXPA28 0.020 6 0.039 2 0.523 7 纯化选择 Purify selection
    SmA_EXPB1 & SmB_EXPB1 0.015 3 0.157 3 0.097 3 纯化选择 Purify selection
    SmA_EXPB2 & SmB_EXPB2 0.027 7 0.065 9 0.420 5 纯化选择 Purify selection
    SmA_EXPB3 & SmB_EXPB3 0.025 6 0.070 3 0.363 6 纯化选择 Purify selection
    SmA_EXLA2 & SmB_EXLA2 0.017 4 0.106 4 0.163 4 纯化选择 Purify selection
    SmA_EXLB1 & SmB_EXLB1 0.018 0 0.065 4 0.275 4 纯化选择 Purify selection
    SmA_EXLB3 & SmB_EXLB3 0.028 0 0.089 9 0.312 0 纯化选择 Purify selection
    SmA_EXLB4 & SmB_EXLB4 0.023 1 0.089 7 0.257 4 纯化选择 Purify selection
    注: Ka/Ks > 1、= 1和 < 1分别表示基因受正选择、中性选择和纯化选择压力。Notes: Ka/Ks > 1, = 1 and < 1 indicate that the genes are subject to positive selection, neutral selection and purify selection pressure, respectively.
    下载: 导出CSV
  • [1] Ma N, Wang Y, Qiu S, et al. Overexpression of OsEXPA8, a root-specific gene, improves rice growth and root system architecture by facilitating cell extension[J/OL]. PLoS One, 2013, 8(10): e75997 (2013−10−04) [2019−03−13]. https://doi.org/10.1371/journal.pone.0075997.eCollection 2013.
    [2] Kuluev B, Safiullina M, Knyazev A, et al. Effect of ectopic expression of NtEXPA5 gene on cell size and growth of organs of transgenic tobacco plants[J]. Russian Journal of Developmental Biology, 2013, 44: 28−34. doi: 10.1134/S1062360413010049.
    [3] Yan A, Wu M, Yan L, et al. AtEXP2 is involved in seed germination and abiotic stress response in Arabidopsis[J/OL]. PLoS One, 2014, 9(1): e85208 (2014−01−03) [2019−04−07]. https://doi.org/10.1371/journal.pone.0085208.
    [4] Ouyang K X, Liu M Q, Pian R Q, et al. Methodology Isolation and analysis of α-expansin genes in the tree Anthocephalus chinensis (Rubiaceae)[J]. Genetics and Molecular Research, 2013, 12(2): 1061−1073. doi: 10.4238/2013.April.10.2.
    [5] Zenoni S, Fasoli M, Tornielli G B, et al. Overexpression of PhEXPA1 increases cell size, modifies cell wall polymer composition and affects the timing of axillary meristem development in Petunia hybrida[J]. New Phytologist, 2011, 191(3): 662−677. doi: 10.1111/j.1469-8137.2011.03726.x.
    [6] Perini M A, Sin I N, Villarreal N M, et al. Overexpression of the carbohydrate binding module from, Solanum lycopersicum, expansin 1 (Sl-EXP1) modifies tomato fruit firmness and Botrytis cinereal susceptibility[J]. Plant Physiology and Biochemistry, 2017, 113: 122−132. doi: 10.1016/j.plaphy.2017.01.029.
    [7] Castillo F M, Canales J, Claude A, et al. Expansin genes expression in growing ovaries and grains of sunflower are tissue-specific and associate with final grain weight[J/OL]. BMC Plant Biology, 2018, 18(1): 327 (2018−12−10) [2019−01−14]. https://doi.org/10.1186/s12870-018-1535-7.
    [8] Feng X, Xu Y, Peng L, et al. TaEXPB7-B, a β-expansin gene involved in low-temperature stress and abscisic acid responses, promotes growth and cold resistance in Arabidopsis thaliana [J/OL]. Journal of Plant Physiology, 2019, 240: 153004 (2019−06−25) [2019−09−07]. https://doi.org/10.1016/j.jplph.2019.153004.
    [9] Ren Y Q, Chen Y H, An J, et al. Wheat expansin gene, TaEXPA2, is involved in conferring plant tolerance to Cd toxicity[J]. Plant Science, 2018, 270: 245−256. doi: 10.1016/j.plantsci.2018.02.022.
    [10] Chen L J, Zou W S, Wu G, et al. Tobacco alpha-expansin EXPA4 plays a role in Nicotiana benthamiana defence against tobacco mosaic virus[J]. Planta, 2018, 247(2): 355−368. doi: 10.1007/s00425-017-2785-6
    [11] Ding A, Marowa P, Kong Y. Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum)[J]. Molecular Genetics & Genomics, 2016, 291(5): 1891−1907.
    [12] Han Z S, Liu Y L, Deng X, et al. Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)[J/OL]. BMC Genomics, 2019, 20(1): 101 (2019−02−01) [2019−11−25]. https://doi.org/10.1186/s12864-019-5455-1.
    [13] 李昊阳, 施杨, 丁亚娜. 杨树扩展蛋白基因家族的生物信息学分析[J]. 北京林业大学学报, 2014, 36(2):59−67.

    Li H Y, Shi Y, Ding Y N. Bioinformatics analysis of expansin gene family in poplar genome[J]. Journal of Beijing Forestry University, 2014, 36(2): 59−67.
    [14] Hou L, Zhang Z Y, Dou S H, et al. Genome-wide identification, characterization, and expression analysis of the expansin gene family in Chinese jujube (Ziziphus jujuba Mill.)[J]. Planta, 2019, 249(3): 815−829.
    [15] Santiago T R, Pereira V M, de Souza W R, et al. Genome-wide identification, characterization and expression profile analysis of expansins gene family in sugarcane (Saccharum spp.)[J/OL]. PLoS One, 2018, 13(4): e0196140 (2018−04−17)[2019−05−17]. https://doi.org/10.1371/journal.pone.0196140.eCollection2018.
    [16] Li N, Pu Y, Gong Y, et al. Genomic location and expression analysis of expansin gene family reveals the evolutionary and functional significance in Triticum aestivum[J]. Genes & Genomics, 2016, 38(5): 1021−1030.
    [17] Zhang H, Li J, Wang R X, et al. Comparative analysis of expansin gene codon usage patterns among eight plant species[J]. Journal of Biomolecular Structure and Dynamics, 2019, 37(4): 910−917. doi: 10.1080/07391102.2018.1442746.
    [18] Quiñones Martorello A S, Fernández M E, Monterubbianesi M G, et al. Effect of combined stress (salinity + hypoxia) and auxin rooting hormone addition on morphology and growth traits in six Salix spp. clones[J]. New Forests, 2020, 51: 61−80. doi: 10.1007/s11056-019-09719-8.
    [19] 耿云红. 干旱胁迫对绿化木本植物抗逆性研究[J]. 山东农业大学学报(自然科学版), 2019, 50(1):12−18.

    Geng Y H. Study on resistance of woody plants under drought stress[J]. Journal of Shandong Agricultural University (Natural Science), 2019, 50(1): 12−18.
    [20] 刘春风. 淹水对15个树种苗木生长和形态特征的影响[D]. 南京: 南京林业大学, 2009.

    Liu C F. Effects of artificial flooding on the growth and morphological characteristics of 15 trees species seedlings[D]. Nanjing: Nanjing Forestry University, 2009.
    [21] Shu Y, Li K L, Song J F, et al. Single and competitive adsorption of Cd (Ⅱ) and Pb (Ⅱ) from aqueous solution by activated carbon prepared with Salix matsudana Kiodz[J]. Water Science and Technology, 2016, 74 (12): 2751−2761. doi: 10.2166/wst.2016.428.
    [22] Gullberg U. Towards making willows pilot species for coppicing production[J]. The Forestry Chronicle, 1993, 69(6): 721−726. doi: 10.5558/tfc69721-6.
    [23] Argus G W. Infrageneric classification of Salix (Salicaceae) in the new world[J]. Systematic Botany Monographs, 1997, 52: 1−121. doi: 10.2307/25096638.
    [24] Zhang J, Yuan H, Li M, et al. A high-density genetic map of tetraploid Salix matsudana using specific length amplified fragment sequencing (SLAF-seq)[J/OL]. PLoS ONE, 2016, 11(6): e0157777 (2016−06−21) [2019−02−12]. https://doi.org/10.1371/journal.pone.0157777.eCollection2016.
    [25] Zhang J, Yuan H, Yang Q, et al. The genetic architecture of growth traits in Salix matsudana under salt stress[J/OL]. Horticulture Research, 2017, 4: 17024 (2017−06−14) [2019−01−21]. https://doi.org/10.1038/hortres.2017.24. eCollection2017.
    [26] Prabha R, Singh D P, Sinha S, et al. Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes[J]. Marine Genomics, 2017, 32: 31−39. doi: 10.1016/j.margen.2016.10.001.
    [27] Duret L, Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhab-ditis, Drosophila, and Arabidopsis[J]. Proceedings of the National Academy of Sciences, 1999, 96: 4482−4487. doi: 10.1073/pnas.96.8.4482.
    [28] 王兰伟. 异源多倍体物种的形成和演化:来自菊科蓍草属的证据[D]. 开封: 河南大学, 2011.

    Wang L W. Allotetraploid speciation and evolution: evidence from the eastern asia Achillea species[D]. Kaifeng: Henan University, 2011.
    [29] Tayale A, Parisod C. Natural pathways to polyploidy in plants and consequences for genome reorganization[J]. Cytogenetic & Genome Research, 2013, 140: 2−4.
    [30] Liu B, Wendel J F. Non-Mendelian phenomena in allopolyploid genome evolution[J]. Current Genomics, 2002, 3(6): 489−505. doi: 10.2174/1389202023350255.
    [31] Wei S, Yang Y, Yin T. The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution [J/OL]. Horticulture Research, 2020, 7: 45 (2020−04−01) [2020−04−25]. https://www.nature.com/articles.
    [32] Grantham R, Gautier C, Gouy M, et al. Codon catalog usage and the genome hypothesis[J]. Nucleic Acids Research, 1980, 8(1): 49−62.
    [33] Grantham R, Gautier C, Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type[J]. Nucleic Acids Research, 1980, 8(9): 1893−1912.
    [34] Lloyd A T, Sharp P M. Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae[J]. Nucleic Acids Research, 1992, 20(20): 5289−5295. doi: 10.1093/nar/20.20.5289.
    [35] Grocock R J, Sharp P M. Synonymous codon usage in Cryptosporidium parvum: identification of two distinct trends among genes[J]. International Journal for Parasitology, 2001, 31(4): 402−412. doi: 10.1016/S0020-7519(01)00129-1.
    [36] Povolotskaya I S, Kondrashov F A, Ledda A, et al. Stop codons in bacteria are not selectively equivalent[J/OL]. Biology Direct, 2012, 7: 30 (2012−09−13)[2019−06−19]. https://link.springer.com/article/10.1186/1745-6150-7-30.
    [37] Korkmaz G, Holm M, Wiens T, et al. Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance[J]. Journal of Biological Chemistry, 2014, 289(44): 30334−30342. doi: 10.1074/jbc.M114.606632.
    [38] Krisko A, Copic T, Gabaldón T, et al. Inferring gene function from evolutionary change in signatures of translation efficiency [J/OL]. Genome Biology, 2014, 15: 44 (2014−03−03) [2019−06−08]. https://link.springer.com/article/10.1186/gb-2014-15-3-r44.
    [39] Presnyak V, Alhusaini N, Chen Y H, et al. Codon optimality is a major determinant of mRNA stability[J]. Cell, 2015, 160(6): 1111−1124. doi: 10.1016/j.cell.2015.02.029.
    [40] Navarro A, Barton N H. Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes[J]. Science, 2003, 300: 321−324. doi: 10.1126/science.1080600.
  • 加载中
图(1) / 表(9)
计量
  • 文章访问数:  890
  • HTML全文浏览量:  266
  • PDF下载量:  39
  • 被引次数: 0
出版历程
  • 收稿日期:  2020-07-13
  • 修回日期:  2020-08-28
  • 网络出版日期:  2021-01-20
  • 刊出日期:  2021-02-05

目录

    /

    返回文章
    返回