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黄鳍东方鲀线粒体基因组结构及系统发育研究

朱春月 胡宗云 张健 张伯序 刘忠航 杨培民

朱春月,胡宗云,张健,等. 黄鳍东方鲀线粒体基因组结构及系统发育研究 [J]. 福建农业学报,2024,39(5):1−9
引用本文: 朱春月,胡宗云,张健,等. 黄鳍东方鲀线粒体基因组结构及系统发育研究 [J]. 福建农业学报,2024,39(5):1−9
ZHU C Y, HU Z Y, ZHANG J, et al. Mitochondrial Genome and Phylogeny of Takifugu xanthopterus [J]. Fujian Journal of Agricultural Sciences,2024,39(5):1−9
Citation: ZHU C Y, HU Z Y, ZHANG J, et al. Mitochondrial Genome and Phylogeny of Takifugu xanthopterus [J]. Fujian Journal of Agricultural Sciences,2024,39(5):1−9

黄鳍东方鲀线粒体基因组结构及系统发育研究

基金项目: 辽宁省农业科学院基本科研业务费项目(2020XKHBZ0706、2021HQ1918);辽宁省科技厅民生科技计划(2021JH2/10200031)
详细信息
    作者简介:

    朱春月(1995 —),女,硕士,助理工程师,主要从事鱼类分子生物学研究,E-mail:18747551907@163.com

    通讯作者:

    杨培民(1979 —),男,硕士,研究员,主要从事特色淡水鱼养殖技术研究,E-mail:pmyang313@163.com

  • 中图分类号: S917.4

Mitochondrial Genome and Phylogeny of Takifugu xanthopterus

  • 摘要:   目的  研究我国大洋河水域黄鳍东方鲀(Takifugu xanthopterus)的分子遗传学特性,为黄鳍东方鲀种质资源遗传多样性和系统发育分析提供基础数据。  方法  利用高通量测序技术,获得黄鳍东方鲀线粒体基因组全序列,分析线粒体基因组结构。  结果  黄鳍东方鲀线粒体基因组序列全长16444 bp(GenBank 登录号:MT560586),由13 个蛋白质编码基因、22 个 tRNAs 基因、2 个 rRNAs 基因、1个控制区和1个轻链复制起始区组成。13蛋白质编码基因中仅有cox1基因起始密码子为特殊的GTG,其余蛋白质编码基因均以ATG为起始密码子,cox2和nad4终止密码子以单独的T结尾。偏好密码子(RSCU>2)分别是Arg(CGA)和Ser(UCC)。22 个tRNAs基因除trnS1基因外,其余tRNAs二级结构均为典型的三叶草结构。以斑腰单孔鲀(Monotreta leiurus)为外类群,对16种东方鲀属线粒体基因组全序列进行进化关系分析。由贝叶斯法构建的系统发生树表明,黄鳍东方鲀与痣斑多纪鲀(T. chrysops)和豹纹多纪鲀(T. pardalis)的亲缘关系最近。  结论  黄鳍东方鲀的线粒体基因组结构和基因排列顺序符合鱼类基因组典型结构和排列特征。
  • 图  1  黄鳍东方鲀粒体基因组结构

    Figure  1.  Structure of T. xanthopterus mitochondrial genome

    图  2  黄鳍东方鲀线粒体基因组密码子使用频率分布

    Figure  2.  Frequency distribution of codon usage in T. xanthopterus mitochondrial genome

    图  3  黄鳍东方鲀22个 tRNAs的二级结构

    Figure  3.  Secondary structures of 22 tRNAs genes of T. xanthopterus

    图  4  基于最大似然法和贝叶斯法的黄鳍东方鲀系统进化树

    Figure  4.  Phylogenetic tree of T. xanthopterus based on maximum likelihood and Bayesian inference

    表  1  黄鳍东方鲀线粒体基因组结构组成

    Table  1.   Composition of T. xanthopterus mitochondrial genome

    名称
    Name
    起始位点
    Start site/bp
    终止位点
    Stop site/bp
    编码链
    Strand
    长度
    Length/bp
    基因间隔
    Intergenic length/bp
    起始/终止密码子
    Start/stop Codons
    trnF(gaa) 1 68 H 68 0  
    12S rRNA 69 1015 H 947 0  
    trnV(tac) 1016 1088 H 73 38  
    16S rRNA 1127 2756 H 1630 0  
    trnL2(taa) 2757 2829 H 73 0  
    nad1 2830 3804 H 975 2 ATG/TAA
    trnI(gat) 3807 3876 H 70 −1  
    trnQ(ttg) 3876 3946 L 71 −1  
    trnM(cat) 3946 4014 H 69 0  
    nad2 4015 5061 H 1047 −1 ATG/TAA
    trnW(tca) 5061 5131 H 71 1  
    trnA(tgc) 5133 5201 L 69 2  
    trnN(gtt) 5204 5277 L 74 3  
    OL 5281 5312 H 32 −1  
    trnC(gca) 5312 5375 L 64 −1  
    trnY(gta) 5375 5444 L 70 1  
    cox1 5446 7005 H 1560 −9 GTG/AGG
    trnS2(tga) 6997 7067 L 71 3  
    trnD(gtc) 7071 7142 H 72 6  
    cox2 7149 7839 H 691 0 ATG/T(AA)
    trnK(ttt) 7840 7912 H 73 1  
    atp8 7914 8081 H 168 −10 ATG/TAA
    atp6 8072 8755 H 684 −1 ATG/TAA
    cox3 8755 9540 H 786 −1 ATG/TAA
    trnG(tcc) 9540 9610 H 71 0  
    nad3 9611 9961 H 351 −2 ATG/TAG
    trnR(tcg) 9960 10028 H 69 1  
    nad4l 10030 10326 H 297 −7 ATG/TAA
    nad4 10320 11700 H 1381 0 ATG/T(AA)
    trnH(gtg) 11701 11769 H 69 0  
    trnS1(gct) 11770 11837 H 68 5  
    trnL1(tag) 11843 11915 H 73 0  
    nad5 11916 13754 H 1839 −5 ATG/TAA
    nad6 13750 14271 L 522 0 ATG/AGG
    trnE(ttc) 14272 14340 L 69 4  
    cob 14345 15481 H 1137 3 ATG/TAA
    trnT(tgt) 15485 15556 H 72 −1  
    trnP(tgg) 15556 15625 L 70 0  
    D-loop 15626 16444 H 423 0
    下载: 导出CSV

    表  2  黄鳍东方鲀偏好密码子RSCU值

    Table  2.   RSCUs for preference codons in T. xanthopterus

    密码子
    Codon
    数量
    Number
    相对密码子
    使用频率
    RSCU
    密码子
    Codon
    数量
    Number
    相对密码子
    使用频率
    RSCU
    密码子
    Codon
    数量
    Number
    相对密码子
    使用频率
    RSCU
    密码子
    Codon
    数量
    Number
    相对密码子
    使用频率
    RSCU
    UUU(F)670.73UCU(S)891.42UAU(Y)540.82UGU(C)90.53
    UUC(F)1161.27UCC(S)1402.23UAC(Y)771.18UGC(C)251.47
    UUA(L)1231.29UCA(S)721.15UAA(*)671.00UGA(*)671.00
    UUG(L)620.65UCG(S)380.60UAG(*)671.00UGG(W)311.00
    CUU(L)880.92CCU(P)921.15CAU(H)440.78CGU(R)70.66
    CUC(L)1101.16CCC(P)1091.36CAC(H)691.22CGC(R)80.75
    CUA(L)1401.47CCA(P)811.01CAA(Q)941.26CGA(R)292.72
    CUG(L)480.50CCG(P)380.48CAG(Q)550.74CGG(R)80.75
    AUU(I)911.02ACU(T)750.90AAU(N)470.67AGU(S)90.14
    AUC(I)1031.15ACC(T)1241.49AAC(N)931.33AGC(S)290.46
    AUA(I)740.83ACA(T)1061.27AAA(K)771.33AGA(R)70.66
    AUG(M)531.00ACG(T)290.35AAG(K)390.67AGG(R)50.47
    GUU(V)360.95GCU(A)610.98GAU(D)390.99GGU(G)220.63
    GUC(V)481.26GCC(A)1091.76GAC(D)401.01GGC(G)491.41
    GUA(V)491.29GCA(A)671.08GAA(E)611.13GGA(G)491.41
    GUG(V)190.50GCG(A)110.18GAG(E)470.87GGG(G)190.55
    下载: 导出CSV

    表  3  黄鳍东方鲀线粒体基因组核苷酸组成

    Table  3.   Nucleotide composition of T. xanthopterus mitochondrial genome

    项目
    Item
    T含量
    T content/%
    C含量
    C content/%
    A含量
    A content/%
    G含量
    G content/%
    AT含量
    AT content/%
    GC 偏好性
    GC-skew
    AT 偏好性
    AT-skew
    tRNA 24.4 25.18 31.96 18.46 56.36 −0.1539 0.1341
    rRNA 21.11 24.78 34.46 19.66 55.56 −0.1152 0.2402
    蛋白质编码基因 PCGs 26.58 31.47 28.13 13.82 54.71 −0.3897 0.0283
    控制区 Control region 32.23 18.93 36.39 12.45 68.62 −0.2065 0.0606
    下载: 导出CSV
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出版历程
  • 收稿日期:  2023-10-30
  • 修回日期:  2024-02-01
  • 网络出版日期:  2024-06-26

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