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薄壳山核桃全基因组LBD基因家族的生物信息学分析

黄元城 郭文磊 王正加

黄元城, 郭文磊, 王正加. 薄壳山核桃全基因组LBD基因家族的生物信息学分析[J]. 浙江农林大学学报. doi: 10.11833/j.issn.2095-0756.20200454
引用本文: 黄元城, 郭文磊, 王正加. 薄壳山核桃全基因组LBD基因家族的生物信息学分析[J]. 浙江农林大学学报. doi: 10.11833/j.issn.2095-0756.20200454
HUANG Yuancheng, GUO Wenlei, WANG Zhengjia. Genome-wide identification and bioinformatics analysis of LBD family of transcription factors in Carya illinoensis[J]. Journal of Zhejiang A&F University. doi: 10.11833/j.issn.2095-0756.20200454
Citation: HUANG Yuancheng, GUO Wenlei, WANG Zhengjia. Genome-wide identification and bioinformatics analysis of LBD family of transcription factors in Carya illinoensis[J]. Journal of Zhejiang A&F University. doi: 10.11833/j.issn.2095-0756.20200454

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薄壳山核桃全基因组LBD基因家族的生物信息学分析

doi: 10.11833/j.issn.2095-0756.20200454
基金项目: 浙江省科技厅重大研发专项(2018C02004);浙江省农业新品种选育重大科技专项(2016C02052-13);“十三五”国家重点研发计划资助项目(2018YFD1000604)
详细信息
    作者简介: 黄元城(ORCID: 0000-0002-2388-6057),从事经济林培育研究,E-mail: 834194037@qq.com
    通信作者: 王正加(ORCID: 0000-0002-6511-6771),教授,博士,博士生导师,从事经济林遗传育种、植物发育生物学研究。E-mail: wzhj21@163.com
  • 中图分类号: S722.3;Q75

Genome-wide identification and bioinformatics analysis of LBD family of transcription factors in Carya illinoensis

  • 摘要:   目的  研究薄壳山核桃Carya illinoensis LBD基因家族结构特征、进化模式和在胚发育过程中的表达模式。  方法  运用生物信息学手段鉴定薄壳山核桃LBD基因,分析该基因结构特征、系统发生学关系、显花植物中的进化历史和在胚发育过程中3个关键阶段的表达模式。  结果  薄壳山核桃全基因组中一共鉴定到52个候选LBD基因。根据基因结构、系统发生学最大似然树和Motif分析可分为3类:GroupⅠ、GroupⅡ和GroupⅢ。多序列比对分析中,52个LBD基因LOB结构域中鉴定出3个重要的结构:CX2CX6CX3C锌指结构、高度保守的甘氨酸GAS结构和亮氨酸拉链zipper-like结构,并且在3类内都分别发生了特异性的的变异或者缺失。根据代表性显花植物LBD基因家族的系统发生学分析,从变异程度看GroupⅠ和GroupⅡ相对较为保守,而GroupⅢ内的所有LBD基因共享1支较长的分支,它们已发生了较大的变异,可能已经分化出新的功能。表达分析结果显示:LBD基因家族参与调控胚发育过程,通常控制子叶的发育和形态建成。薄壳山核桃LBD基因中又有在整个胚发育过程中都高表达的一簇基因,这些基因可能在胚发育过程中发挥了更加重要的作用。  结论  薄壳山核桃全基因组中共获得LBD基因52个,共可分为3个亚家族,不同的亚家族具有不同的基因结构、蛋白质结构、进化模式和表达模式,转录组表达分析显示:不同亚家族之间在胚发育不同阶段具有差异性表达,它们共同参与调控薄壳山核桃胚发育过程。图5表2参47
  • 图  1  薄壳山核桃LBD基因家族系统进化树

    Figure  1  Phylogenetic tree constructed based on the full-length sequences of pecan LBD genes using JTT+CAT algorithm with FastTree software

    图  2  薄壳山核桃LBD转录因子家族系统发育树和保守蛋白质基序结构

    Figure  2  Phylogenetic tree constructed based on the full-length sequences of pecan LBD genes using JTT+CAT algorithm with FastTree software

    图  3  薄壳山核桃LBD 转录因子家族LOB蛋白质结构域多序列比对

    Figure  3  Multiple sequence alignment of LOB domain in Carya illinoensis transcription factor family

    图  4  利用从裸子植物银杏到高等植物551个LBD基因全长蛋白质序列构建系统发育树

    Figure  4  Phylogenetic tree constructed based on the full-length sequences of 551 LBD genes from gymnosperm ginkgo to higher angiosperms

    图  5  薄壳山核桃LBD 转录因子家族胚发育表达模式

    Figure  5  Transcriptome expression profile of LBD gene family in embryo development

    表  1  多物种LBD基因鉴定结果

    Table  1.   Identify result of LBD genes in multi-species

    鉴定程序基因数量/个
    银杏无油樟蓝星睡莲水稻拟南芥葡萄大豆核桃山核桃薄壳山核桃
    BLASTX904551619198153878980
    HMMER502635295857116725652
    下载: 导出CSV

    表  2  薄壳山核桃LBD转录因子家族蛋白质理化性质

    Table  2.   Physicochemical properties of LBD transcription factor family protein in Carya illinoensis

    蛋白质氨基酸残基数/个分子量/kD理论等电点酸性氨基酸/个碱性氨基酸/个不稳定系数脂肪系数总平均亲水性
    pecanLBD1 21023 309.198.24171947.6573.52−0.485
    pecanLBD2 20822 353.777.55202158.3288.650
    pecanLBD3 28831 617.018.99293561.9276.88−0.326
    pecanLBD4 22324 069.377.69171873.8977.89−0.171
    pecanLBD5 18820 808.567.63171867.2469.15−0.490
    pecanLBD6 26028 451.228.23313452.5569.38−0.501
    pecanLBD7 15617 540.209.03121855.8778.91−0.235
    pecanLBD8 17218 611.248.59141761.2470.35−0.238
    pecanLBD9 27630 985.118.55283230.8476.96−0.522
    pecanLBD1032636 029.866.91232264.4577.58−0.472
    pecanLBD1120422 376.577.53181960.7877.99−0.233
    pecanLBD1223225 857.685.90211450.5265.22−0.425
    pecanLBD1317018 808.036.42181765.0457.47−0.607
    pecanLBD1420221 823.688.59141757.4180.20−0.175
    pecanLBD1520323 706.088.15272952.0077.39−0.556
    pecanLBD1619120 998.776.08191770.0572.04−0.423
    pecanLBD1723025 054.589.22172378.9470.04−0.284
    pecanLBD1817218 626.238.82141867.6473.14−0.296
    pecanLBD1930633 113.727.95333546.0381.54−0.280
    pecanLBD2016218 029.726.70141451.7688.52−0.133
    pecanLBD2112714 182.024.4814736.1892.20−0.246
    pecanLBD2217619 971.985.17251844.8880.34−0.186
    pecanLBD2313015 042.749.84102545.4377.23−0.541
    pecanLBD2416218 285.758.23131557.6578.40−0.337
    pecanLBD2521423 771.708.25171949.4274.44−0.472
    pecanLBD2631033 384.038.22343747.4480.87−0.302
    pecanLBD2716818 892.286.28171372.8663.87−0.476
    pecanLBD2821523 539.685.33181475.4770.88−0.272
    pecanLBD2916718 504.186.94151559.0081.80−0.217
    pecanLBD3017619 230.736.50181769.1573.75−0.242
    pecanLBD3116918 881.586.49171651.2879.59−0.219
    pecanLBD3223626 157.915.74221346.7365.76−0.405
    pecanLBD3321323 405.507.06191965.2367.37−0.380
    pecanLBD3432637 266.205.47543549.0574.29−0.813
    pecanLBD3525127 236.496.44242259.5580.08−0.322
    pecanLBD3622824 949.426.29171683.4071.05−0.271
    pecanLBD3722824 709.228.06222459.2076.14−0.244
    pecanLBD3821623 449.536.03171364.1175.05−0.227
    pecanLBD3915817 663.156.27151353.4480.25−0.243
    pecanLBD4022124 171.044.97211258.4578.60−0.143
    pecanLBD4126530 244.096.42332946.8677.66−0.594
    pecanLBD4223724 801.388.20131569.0779.87−0.065
    pecanLBD4321323 452.556.74191856.4580.61−0.203
    pecanLBD4422424 373.778.93172269.4173.62−0.276
    pecanLBD4520221 927.158.56192354.6683.47−0.159
    pecanLBD4622124 114.379.01182373.1866.29−0.421
    pecanLBD4728932 466.215.27292167.1965.92−0.600
    pecanLBD4817619 971.985.17251844.8880.34−0.186
    pecanLBD4917018 770.956.19191760.44 55.18−0.615
    pecanLBD50 9210 319.086.26111039.17115.65 0.018
    pecanLBD5131334 650.037.29202064.34 73.07−0.490
    pecanLBD5232035 091.256.83232166.59 67.53−0.593
    下载: 导出CSV
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  • 收稿日期:  2020-07-14
  • 修回日期:  2020-12-24

薄壳山核桃全基因组LBD基因家族的生物信息学分析

doi: 10.11833/j.issn.2095-0756.20200454
    基金项目:  浙江省科技厅重大研发专项(2018C02004);浙江省农业新品种选育重大科技专项(2016C02052-13);“十三五”国家重点研发计划资助项目(2018YFD1000604)
    作者简介:

    黄元城(ORCID: 0000-0002-2388-6057),从事经济林培育研究,E-mail: 834194037@qq.com

    通信作者: 王正加(ORCID: 0000-0002-6511-6771),教授,博士,博士生导师,从事经济林遗传育种、植物发育生物学研究。E-mail: wzhj21@163.com
  • 中图分类号: S722.3;Q75

摘要:   目的  研究薄壳山核桃Carya illinoensis LBD基因家族结构特征、进化模式和在胚发育过程中的表达模式。  方法  运用生物信息学手段鉴定薄壳山核桃LBD基因,分析该基因结构特征、系统发生学关系、显花植物中的进化历史和在胚发育过程中3个关键阶段的表达模式。  结果  薄壳山核桃全基因组中一共鉴定到52个候选LBD基因。根据基因结构、系统发生学最大似然树和Motif分析可分为3类:GroupⅠ、GroupⅡ和GroupⅢ。多序列比对分析中,52个LBD基因LOB结构域中鉴定出3个重要的结构:CX2CX6CX3C锌指结构、高度保守的甘氨酸GAS结构和亮氨酸拉链zipper-like结构,并且在3类内都分别发生了特异性的的变异或者缺失。根据代表性显花植物LBD基因家族的系统发生学分析,从变异程度看GroupⅠ和GroupⅡ相对较为保守,而GroupⅢ内的所有LBD基因共享1支较长的分支,它们已发生了较大的变异,可能已经分化出新的功能。表达分析结果显示:LBD基因家族参与调控胚发育过程,通常控制子叶的发育和形态建成。薄壳山核桃LBD基因中又有在整个胚发育过程中都高表达的一簇基因,这些基因可能在胚发育过程中发挥了更加重要的作用。  结论  薄壳山核桃全基因组中共获得LBD基因52个,共可分为3个亚家族,不同的亚家族具有不同的基因结构、蛋白质结构、进化模式和表达模式,转录组表达分析显示:不同亚家族之间在胚发育不同阶段具有差异性表达,它们共同参与调控薄壳山核桃胚发育过程。图5表2参47

English Abstract

黄元城, 郭文磊, 王正加. 薄壳山核桃全基因组LBD基因家族的生物信息学分析[J]. 浙江农林大学学报. doi: 10.11833/j.issn.2095-0756.20200454
引用本文: 黄元城, 郭文磊, 王正加. 薄壳山核桃全基因组LBD基因家族的生物信息学分析[J]. 浙江农林大学学报. doi: 10.11833/j.issn.2095-0756.20200454
HUANG Yuancheng, GUO Wenlei, WANG Zhengjia. Genome-wide identification and bioinformatics analysis of LBD family of transcription factors in Carya illinoensis[J]. Journal of Zhejiang A&F University. doi: 10.11833/j.issn.2095-0756.20200454
Citation: HUANG Yuancheng, GUO Wenlei, WANG Zhengjia. Genome-wide identification and bioinformatics analysis of LBD family of transcription factors in Carya illinoensis[J]. Journal of Zhejiang A&F University. doi: 10.11833/j.issn.2095-0756.20200454

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