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基于全长转录组序列、核基因与叶绿体基因分析琼岛杨在杨属的亲缘关系

徐家洪 曾晴 叶富余 胡杨阳 时寰宇 张璇 陈金辉

徐家洪, 曾晴, 叶富余, 胡杨阳, 时寰宇, 张璇, 陈金辉. 基于全长转录组序列、核基因与叶绿体基因分析琼岛杨在杨属的亲缘关系[J]. 北京林业大学学报, 2021, 43(10): 28-37. doi: 10.12171/j.1000-1522.20200286
引用本文: 徐家洪, 曾晴, 叶富余, 胡杨阳, 时寰宇, 张璇, 陈金辉. 基于全长转录组序列、核基因与叶绿体基因分析琼岛杨在杨属的亲缘关系[J]. 北京林业大学学报, 2021, 43(10): 28-37. doi: 10.12171/j.1000-1522.20200286
Xu Jiahong, Zeng Qing, Ye Fuyu, Hu Yangyang, Shi Huanyu, Zhang Xuan, Chen Jinhui. Genetic relationship of Populus qiongdaoensis in Populus based on full-length transcriptome sequences, nuclear genes and chloroplast genes[J]. Journal of Beijing Forestry University, 2021, 43(10): 28-37. doi: 10.12171/j.1000-1522.20200286
Citation: Xu Jiahong, Zeng Qing, Ye Fuyu, Hu Yangyang, Shi Huanyu, Zhang Xuan, Chen Jinhui. Genetic relationship of Populus qiongdaoensis in Populus based on full-length transcriptome sequences, nuclear genes and chloroplast genes[J]. Journal of Beijing Forestry University, 2021, 43(10): 28-37. doi: 10.12171/j.1000-1522.20200286

基于全长转录组序列、核基因与叶绿体基因分析琼岛杨在杨属的亲缘关系

doi: 10.12171/j.1000-1522.20200286
基金项目: 海南大学教育教学改革研究项目(hdjy2063),国家级大学生创新创业训练计划项目(202010589058),海南省研究生创新科研课题(Hys2020-111),海南大学科研启动经费项目(KYQD(ZR)1830)
详细信息
    作者简介:

    徐家洪。主要研究方向:林木分子育种学。Email:jiahongxuhn@sina.com 地址:570228海南省海口市美兰区人民大道58号海南大学林学院

    责任作者:

    陈金辉,副教授。主要研究方向:林木分子育种学。Email: jinhuichen@hainanu.edu.cn 地址:同上

  • 中图分类号: S722.3

Genetic relationship of Populus qiongdaoensis in Populus based on full-length transcriptome sequences, nuclear genes and chloroplast genes

  • 摘要:   目的  琼岛杨是我国热带地区发现的一种杨树,至今其分类和进化鲜有报道。本研究旨在通过三代全长转录组测序等方法了解琼岛杨在杨属中的分类与进化。  方法  基于Pacbio Sequel测序技术获取的热胁迫下琼岛杨、加杨和小叶杨完整全长转录本数据,通过直系同源基因计算非同义替换值(Ka)、同义替换值(Ks)及Ka/Ks值,比较直系同源基因在热胁迫下的表达模式,并结合毛果杨和簸箕柳的直系同源基因,构建了5个树种的进化树来分析杨树亲缘关系。通过克隆琼岛杨核基因(nrDNA:UDP-SQPOPTRDRAFT_575699)和叶绿体基因(cpDNA:atpⅠ和trnF),分析基因序列在琼岛杨种群中的多态性,计算琼岛杨种内遗传距离,及与19个树种(5个杨树组和1个类外群组)的种间遗传距离。基于最大似然法和最小进化法构建了琼岛杨与19个树种的进化树,以分析琼岛杨在杨属的亲缘关系。  结果  三代转录组测序共获得660组琼岛杨、小叶杨和加杨的直系同源基因,Ks平均值为0.150 5,峰值为0.02,Ka/Ks < 1,占比97.27%,这显示了3种杨树较近的亲缘关系。直系同源基因表达模式分析发现,3种杨树在热胁迫下具有相同的表达模式。利用遗传距离法计算琼岛杨与19个树种中atpⅠ、trnFUDP-SQPOPTRDRAFT_575699等4种基因遗传距离的平均值,发现琼岛杨与白杨组具有最近亲缘关系,平均值为0.011。  结论  基于三代全长转录组测序获得的直系同源基因分析显示出,琼岛杨与其他杨树具有较近亲缘关系。克隆cpDNA和nrDNA基因,计算遗传距离和构建的进化树均表明琼岛杨与白杨组具有最近亲缘关系。cpDNA的多态性以及进化分支置信度明显高于nrDNA,表明在琼岛杨中cpDNA比nrDNA基因更具备物种鉴别能力。

     

  • 图  1  琼岛杨转录本在Nr数据库中的物种分布图

    Figure  1.  Species distribution diagram of P. qiongdaoensis in Nr database

    图  2  3种杨树基因功能分类

    横坐标为3种杨树富集基因最多的前20条KEGG通路。PPER. 内质网中的蛋白质加工;SP. 剪接体;PHST. 植物激素信号转导;RT. RNA转运;SSM. 淀粉和蔗糖代谢;EN. 胞吞;RI. 核糖体;PPI. 植物与病原体的相互作用;GL. 糖酵解/糖异生;MSP. mRNA监测途径;GDM. 乙醛酸和二羧酸酯代谢;OP. 氧化磷酸化;UMP. 泛素介导的蛋白水解;RD. RNA降解;CFPO. 光合生物中的碳固定;PM. 丙酮酸代谢;PE. 过氧化物;PH. 光合作用;PUM. 嘌呤代谢;ASNS. 氨基糖和核苷酸糖代谢。Abscissa is top 20 KEGG pathways with the most enriched genes in three Populus. PPER, protein processing in endoplasmic reticulum; SP, spliceosome; PHST, plant hormone signal transduction; RT, RNA transport; SSM, starch and sucrose metabolism; EN, endocytosis; RI, ribosome; PPI, plant-pathogen interaction; GL, glycolysis/gluconeogenesis; MSP, mRNA surveillance pathway; GDM, glyoxylate and dicarboxylate metabolism; OP, oxidative phosphorylation; UMP, ubiquitin mediated proteolysis; RD, RNA degradation; CFPO, carbon fixation in photosynthetic organisms; PM, pyruvate metabolism; PE, peroxisome; PH, photosynthesis; PUM, purine metabolism; ASNS, amino sugar and nucleotide sugar metabolism.

    Figure  2.  Function classification in three Populus genes

    图  3  杨树直系同源基因的Ka/Ks (A)及Ks (B)分布图

    Figure  3.  Distribution bar graph of Ka/Ks (A) and Ks (B) of Populus orthologous genes

    图  4  琼岛杨系统进化树

    A.琼岛杨、加杨和小叶杨直系同源基因进化树;B.琼岛杨、加杨、小叶杨毛果杨和簸箕柳直系同源基因进化树。A, phylogenetic tree of orthologous genes of P. qiongdaoensis, P. canadensis and P. simonii; B, phylogenetic tree of orthologous genes of P. qiongdaoensis, P. canadensis, P. simonii, P. trichocarpa and Salix suchowensis.

    Figure  4.  Phylogenetic tree of P. qiongdaoensis

    图  5  3种杨树直系同源基因表达热图

    pch、pqh和psh分别为加杨、琼岛杨和小叶杨热胁迫处理;pcq、pqq和psq分别为加杨、琼岛杨和小叶杨对照组。The heat stress of P. canadensis, P. qiongdaoensis and P. simonii is named as pch, pqh and psh; the control of P. canadensis, P. qiongdaoensis and P. simonii is named as pcq, pqq and psq.

    Figure  5.  Heat map of orthologus genes in three Populus species

    图  6  琼岛杨与19个树种的系统进化树

    A. cpDNA组合序列最大似然进化树;B. nrDNA组合序列最大似然进化树。A, cpDNA combination sequence maximum likelihood phylogenetic tree; B, maximum likelihood evolutionary tree of nrDNA combined sequence.

    Figure  6.  Phylogenetic tree of the P. qiongdaoensis and 19 tree species

    表  1  琼岛杨扩增序列引物信息

    Table  1.   Amplified sequence primer information of P. qiongdaoensis

    基因名称
    Gene name
    引物名称
    Primer name
    引物序列
    Primer sequence
    UDP-SQ DSH3 F: TCTGCTTTCCACTTCTTGC
    DSH3 R: CATACTCTCCCATTGTCCC
    POPTRDRAFT_
    575699
    DSH6 F: GCCTCCTGATTATTATGC
    DSH6 R: TATTACAAGCCCTTCCAG
    trnF trnL-trnF F: CGAAATTGGTAGACGCTACG
    trnL-trnF R: ATTTGAACTGGTGACACGAG
    atp atpⅠ-atpH F: CCAACCCAGCAGCAATAAC
    atpⅠ-atpH R: TATTTACAAGTGGTATTCAAGCT
    下载: 导出CSV

    表  2  NCBI数据库获取的基因序列

    Table  2.   Gene sequences obtained from NCBI database

    物种名称
    Species name
    序列编号 GenBank
    atptrnFUDP-SQPOPTRDRAFT_575699
    琼岛杨 Populus qiongdaoensis MW389752 ~ MW389771 MW389731 ~ MW389750 MW389689 ~ MW389708 MW389710 ~ MW389729
    山杨 P. davidiana KF941071 KF940742 KF940382 KF940143
    毛白杨 P. tomentosa KF941073 KF940744 KF940384 KF940145
    响叶杨 P. adenopoda KF941089 KF940760 KF940400 KF940150
    大叶杨 P. lasiocarpa KF941086 KF940757 KF940397 KF940158
    异叶杨 P. heterophylla KX454634 KX454606 KX417462 KX417432
    椅杨 P. wilsonii KX454638 KX454610 KX417466 KX417436
    小叶杨 P. simonii KF941080 KF940751 KF940391 KF940152
    苦杨 P. laurifolia KF941083 KF940754 KF940394 KF940155
    毛果杨 P. trichocarpa KF941091 KF940762 KF940402 KF940163
    加杨 P. canadensis MW389772 MW389751 MW389709 MW389730
    黑杨 P. nigra KF941087 KF940758 KF940398 KF940159
    阿富汗杨 P. afghanica KF941088 KF940759 KF940399 KF940160
    美洲黑杨 P. deltoides KF941099 KF940770 KF940410 KF940171
    灰胡杨 P. pruinosa KF941092 KF940763 KF940403 KF940164
    胡杨 P. euphratica KF941096 KF940767 KF940407 KF940168
    冬青叶杨 P. ilicifolia KX454633 KX454605 KX417461 KX417431
    三蕊柳 Salix triandra KF941097 KF940768 KF940408 KF940169
    钻天柳 S. arbutifolia KF941094 KF940765 KF940405 KF940166
    大黄柳 S. raddeana KF941095 KF940766 KF940406 KF940167
    下载: 导出CSV

    表  3  转录组数据注释结果

    Table  3.   Annotation of transcriptome data

    注释数据库
    Annotation database
    加杨
    P. canadensis
    琼岛杨
    P. qiongdaoensis
    小叶杨
    P. simonii
    Nt 33 530 (50.30%) 38 920 (44.15%) 44 886 (44.10%)
    Nr 33 035 (49.56%) 38 338 (43.49%) 44 366 (43.59%)
    KEGG 32 611 (48.92%) 37 898 (42.99%) 43 820 (43.05%)
    Swiss-Prot 28 388 (42.59%) 32 860 (37.27%) 38 210 (37.54%)
    GO 22 121 (33.19%) 25 472 (28.89%) 30 206 (29.67%)
    Pfam 22 121 (33.19%) 25 472 (28.89%) 30 206 (29.67%)
    KOG 21 311 (31.97%) 24 422 (27.70%) 28 118 (27.62%)
    合计 Total 33 840 (44.42%) 39 343 (44.63%) 45 217 (50.77%)
    下载: 导出CSV

    表  4  3种杨树差异表达直系同源基因

    Table  4.   Differentially expression of orthologous genes in three Populus

    直系同源基因编号
    Gene No. of orthologous gene
    琼岛杨 P. qiongdaoensis 加杨 P. canadensis 小叶杨 P. simonii
    热处理
    Heat stress
    对照
    Control
    log2FC热处理
    Heat stress
    对照
    Control
    log2FC热处理
    Heat stress
    对照
    Control
    log2FC
    OG07438 354.35 35.80 4.56 88.68 7.28 5.05 52.66 4.20 4.56
    OG07244 188.23 4.62 6.66 1 329.18 31.22 6.85 103.81 1.39 7.16
    OG09422 23.28 0.37 7.43 22.24 0.24 7.97 3.46 0.38 4.18
    OG05822 3 381.21 2.03 12.19 318.20 0.48 10.80 370.24 0.11 12.65
    OG07321 7.95 118.86 −2.97 6.49 115.96 −2.74
    OG07470 75.24 13.14 3.82 17.13 3.28 3.84
    OG07300 16.63 0.70 6.06 557.70 1.35 10.04
    OG07384 279.51 11.27 6.08 583.29 20.48 6.31
    OG09172 1 918.37 35.74 7.28 188.21 21.07 4.62
    OG07291 113.69 13.64 4.39 242.96 4.12 6.94
    OG07327 366.43 0.47 11.10 254.73 0.59 9.79
    注:FC. 差异倍数。Note: FC, fold change.
    下载: 导出CSV

    表  5  琼岛杨克隆基因序列长度及变异位点信息

    Table  5.   Length and variant site information of amplified sequences of P. qiongdaoensis

    基因名称
    Gene name
    长度
    Length /bp
    插入/缺失个数
    Number of the insertion
    or deletion
    单倍型数
    Number of
    haplotype
    单倍型多样性
    Haplotype
    diversity
    多态位点
    Polymorphic
    site
    突变总数
    Number of
    mutation
    简约型位点
    Parsimony
    informative site
    单一位点
    Single
    site
    atp 1 025 27 19 0.995 16 18 11 5
    trnF 902 18 18 0.989 53 56 37 16
    UDP-SQ 608 4 4 0.521 16 17 2 14
    POPTRDRAFT_575699 485 2 2 0.100 1 1 0 1
    下载: 导出CSV

    表  6  琼岛杨与其他树种遗传距离

    Table  6.   Genetic distance between P. qiongdaoensis and other Populus species

    物种名称
    Species name
    分组
    Group
    nrDNA组合
    nrDNA
    combination
    cpDNA组合
    cpDNA
    combination
    UDP-SQPOPTRDRAFT_575699atptrnF平均值
    Average
    各组平均值
    Average of
    each group
    P. davidiana 白杨组
    Leuce
    0.009 0.014 0.007 0.004 0.014 0.025 0.012 0.011
    P. tomentosa 0.006 0.014 0.007 0.000 0.014 0.023 0.011
    P. adenopoda 0.006 0.012 0.007 0.000 0.013 0.023 0.010
    P. lasiocarpa 大叶杨组
    Leucoides
    0.013 0.013 0.007 0.007 0.014 0.025 0.013 0.388
    P. heterophylla 1.073 0.016 0.013 1.158 0.017 1.169 0.575
    P. wilsonii 1.064 0.016 0.009 1.160 0.017 1.193 0.577
    P. simonii 青杨组
    Tacamahaca
    0.015 0.013 0.009 0.007 0.014 0.026 0.014 0.015
    P. laurifolia 0.015 0.017 0.009 0.007 0.018 0.032 0.016
    P. trichocarpa 0.009 0.017 0.009 0.002 0.017 0.029 0.014
    P. nigra 黑杨组
    Aigeiros
    0.020 0.011 0.011 0.011 0.012 0.023 0.015 0.016
    P. afghanica 0.018 0.014 0.011 0.009 0.014 0.026 0.015
    P. canadensis 0.018 0.016 0.010 0.008 0.022 0.026 0.017
    P. deltoides 0.018 0.016 0.011 0.009 0.017 0.029 0.017
    P. pruinosa 胡杨组
    Turanga
    0.013 0.018 0.013 0.002 0.020 0.027 0.016 0.205
    P. euphratica 0.016 0.018 0.015 0.004 0.020 0.027 0.017
    P. ilicifolia 1.088 0.018 0.017 1.159 0.020 1.195 0.583
    S. triandra 外类群
    Outgroup
    0.083 0.053 0.049 0.040 0.053 0.062 0.057 0.056
    S. arbutifolia 0.083 0.052 0.053 0.036 0.051 0.062 0.056
    S. raddeana 0.081 0.053 0.047 0.038 0.052 0.062 0.056
    下载: 导出CSV
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出版历程
  • 收稿日期:  2020-09-17
  • 修回日期:  2020-12-16
  • 网络出版日期:  2021-09-22
  • 刊出日期:  2021-10-30

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