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绿鲍(Haliotis fulgens)线粒体基因组全序列测定及分析

郭睿 张善霹 蔡雷鸣 杨小强 王伟 江小斌 林钦 林枫 林哲龙

郭睿,张善霹,蔡雷鸣,等. 绿鲍(Haliotis fulgens)线粒体基因组全序列测定及分析[J]. 海洋学报,2023,45(5):64–78 doi: 10.12284/hyxb2023050
引用本文: 郭睿,张善霹,蔡雷鸣,等. 绿鲍(Haliotis fulgens)线粒体基因组全序列测定及分析[J]. 海洋学报,2023,45(5):64–78 doi: 10.12284/hyxb2023050
Guo Rui,Zhang Shanpi,Cai Leiming, et al. Sequencing and analysis of the complete mitochondrial genome of green abalone (Haliotis fulgens)[J]. Haiyang Xuebao,2023, 45(5):64–78 doi: 10.12284/hyxb2023050
Citation: Guo Rui,Zhang Shanpi,Cai Leiming, et al. Sequencing and analysis of the complete mitochondrial genome of green abalone (Haliotis fulgens)[J]. Haiyang Xuebao,2023, 45(5):64–78 doi: 10.12284/hyxb2023050

绿鲍(Haliotis fulgens)线粒体基因组全序列测定及分析

doi: 10.12284/hyxb2023050
基金项目: 福州海洋研究院项目(2021F12);福建省科技厅项目(2021S0010)。
详细信息
    作者简介:

    郭睿(1986-),男,河北省石家庄市人,高级农艺师,从事水生动物遗传和疫病研究。E-mail:ariesgreen86@hotmail.com

    通讯作者:

    张善霹(1969-),男,高级工程师,主要从事水产养殖技术研究。E-mail:309468990@qq.com

  • 中图分类号: P735;Q959.212

Sequencing and analysis of the complete mitochondrial genome of green abalone (Haliotis fulgens)

  • 摘要: 为高效鉴别鲍属物种和更好地管理和保护鲍种质资源,本研究通过高通量测序获得了养殖绿鲍(Haliotis fulgens)稚贝的线粒体基因组全序列,并对其序列和结构特征进行分析。结果表明,绿鲍线粒体基因组全长17 041 bp,含有37个编码基因,其中蛋白质编码基因13个、tRNA基因22个、rRNA基因2个。13个蛋白质编码基因均以AUG为起始密码子,以UAG或UAA为终止密码子。除tRNA-Ser(AGN)外的21个tRNA基因可折叠成典型三叶草结构。分析发现tRNA-Glu和COX3间存在富含A+T的非编码区,其内含有2个带回文序列的发卡结构。基于已报道的10个鲍属线粒体基因组全序列构建系统发育树,发现绿鲍与皱纹盘鲍(Haliotis discus hannai)、红鲍(Haliotis rufescens)、黑鲍(Haliotis cracherodii)聚为一支。将绿鲍与皱纹盘鲍13个线粒体编码蛋白的结构域比较,发现二者ND2ND4的跨膜结构域数量存在差异,这是否与二者的高温耐受性差异有关,有待进一步研究。总之,绿鲍线粒体基因组全序列的首次获取和分析,丰富了鲍类细胞遗传信息,为分类、种质鉴定与种质资源保护提供了基础数据和参考。
  • 图  1  鲍属cytB基因NJ系统发育树

    Fig.  1  Phylogenetic tree based on the neighbor-joining (NJ) analysis of the cytB genes of Haliotis spp.

    图  2  绿鲍线粒体基因组结构

    Fig.  2  Mitochondrial genome structure of Haliotis fulgens

    图  3  绿鲍线粒体编码基因及非编码基因排列图

    Fig.  3  The mitochondrial coding and non-coding genes arrangement diagram of Haliotis fulgens

    图  4  绿鲍特殊tRNA基因二级结构

    Fig.  4  The unusual secondary structures of the tRNA genes in Haliotis fulgens

    图  5  绿鲍线粒体控制区序列及结构特征示意图

    下划线表示存在回文序列的两个发卡结构序列,下方为对应的发卡结构

    Fig.  5  Schematic map of the control region sequences and characteristics of Haliotis fulgens

    Underline shows the sequences of two hairpin structures containing palindromes and bottom is the corresponding hairpin structures

    图  6  鲍属线粒体基因组NJ系统发育树

    Fig.  6  Phylogenetic tree based on the neighbor-joining (NJ) analysis of Haliotis genus whole mitochondrial genomes

    图  7  绿鲍与皱纹盘鲍线粒体蛋白质氨基酸序列相似性及二级结构比较

    Fig.  7  Comparison of amino acid sequence identity and secondary structure of mitochondrial proteins between Haliotis fulgens and Haliotis discus hannai

    表  1  已报道鲍属贝类线粒体基因组

    Tab.  1  The complete mitochondrial genomes reported of Haliotis genus for analysis

    物种长度/bpGC含量/%GenBank登录号
    皱纹盘鲍(Haliotis discus hannai16 88639.6KF724723.1
    黑足鲍(Haliotis iris17 13140.2KU310895.1
    黑唇鲍(Haliotis rubra16 90740.9AY588938.1
    绿唇鲍(Haliotis laevigata16 54542.2KJ472483.1
    欧洲疣鲍(Haliotis tuberculata15 93839.5FJ605488.1
    杂色鲍(Haliotis diversicolor16 54340.1MZ465525.1
    羊鲍(Haliotis ovina16 53140.7NC056350.1
    红鲍(Haliotis rufescens16 64639.7NC036928.1
    黑鲍(Haliotis cracherodii18 39137.7CM039063.1
    下载: 导出CSV

    表  2  绿鲍线粒体基因组注释结果

    Tab.  2  The results of the complete mitochondrial genome annotation for Haliotis fulgens

    基因长度/bp定位间隔区/bp反密码子密码子编码链
    起始位点终止位点起始密码子终止密码子
    COX378017800AUGUAAH
    trnD7381288431GUCH
    trnK72884955−1UUUH
    trnA699511 019−5UGCH
    trnR661 0211 0861UCGH
    trnI701 0991 16812GAUH
    ND33541 1711 5242AUGUAAH
    trnN711 5371 60712GUUH
    trnS671 6111 6773GCUH
    ND21 0951 6812 7753 AUGUAAH
    COX11 5422 7954 33619 AUGUAAH
    COX26964 3755 07038 AUGUAGH
    ATP81655 1555 31984AUGUAAH
    ATP66965 3746 06954 AUGUAAH
    trnF686 1136 18043GAAL
    ND51 7406 1957 93414AUGUAAL
    trnH687 9358 0020GUGL
    ND41 2338 0509 28247 AUGUAAL
    ND4L3009 4389 737155 AUGUAGL
    trnT709 7629 83124UGUH
    trnS679 8589 92426UGAL
    CYTB1 1409 93711 07612 AUGUAGL
    ND650711 11411 62037AUGUAGL
    trnP6711 62111 6870UGGL
    ND194511 71012 65422 AUGUAGL
    trnL6812 65612 7231UAAL
    trnL6812 81412 88190UAGL
    16S1 40012 89814 29716 L
    trnV6614 39014 45592AACL
    12S1 03314 46915 50113 L
    trnM7015 51615 58514CAUL
    trnY6815 58815 6552GUAL
    trnC7015 66415 7338GCAL
    trnW7315 73715 8093UCAL
    trnQ7015 82015 88910UUGL
    trnG6815 89215 9592UCCL
    trnE6815 96416 0314UUCL
    注:trn表示rRNA,后面的大写字母表示该tRNA转运的氨基酸;16S12S为rRNA基因;−代表无密码子。
    下载: 导出CSV

    表  3  鲍属线粒体基因组碱基组成

    Tab.  3  Composition and skewness in the mitochondrial genomes of Haliotis genus species

    物种碱基组成/%AT偏移GC偏移
    ATCGA+T
    线粒体全基因组
    绿鲍 Haliotis fulgens36.224.426.512.960.60.195−0.345
    皱纹盘鲍 Haliotis discus hannai35.425.026.113.560.40.172−0.318
    黑足鲍 Haliotis iris35.923.926.813.459.80.201−0.333
    黑唇鲍 Haliotis rubra34.624.526.714.259.10.171−0.306
    绿唇鲍 Haliotis laevigata23.933.914.927.357.8−0.1730.294
    欧洲疣鲍 Haliotis tuberculata34.825.725.813.660.50.150−0.310
    杂色鲍 Haliotis diversicolor35.224.726.413.759.90.175−0.317
    羊鲍 Haliotis ovina34.824.527.413.459.30.174−0.343
    红鲍 Haliotis rufescens35.424.925.913.760.30.174−0.308
    黑鲍 Haliotis cracherodii26.635.713.524.262.3−0.1460.284
    蛋白质编码基因
    绿鲍 Haliotis fulgens23.436.319.121.259.7−0.2160.052
    皱纹盘鲍 Haliotis discus hannai23.436.319.221.159.7−0.2160.047
    黑足鲍 Haliotis iris22.536.019.621.958.5−0.2310.055
    黑唇鲍 Haliotis rubra22.335.119.922.657.4−0.2230.064
    绿唇鲍 Haliotis laevigata22.234.520.422.856.7−0.2170.056
    欧洲疣鲍 Haliotis tuberculata23.736.118.921.359.8−0.2070.060
    杂色鲍 Haliotis diversicolor23.235.919.121.859.1−0.2150.066
    羊鲍 Haliotis ovina22.635.819.322.258.4−0.2260.070
    红鲍 Haliotis rufescens23.536.019.321.259.5−0.2100.047
    黑鲍 Haliotis cracherodii23.235.919.421.659.1−0.2150.054
    tRNA基因
    绿鲍 Haliotis fulgens28.131.016.924.059.1−0.0500.174
    皱纹盘鲍 Haliotis discus hannai28.230.517.324.058.7−0.0390.162
    黑足鲍 Haliotis iris27.630.617.524.358.2−0.0520.163
    黑唇鲍 Haliotis rubra27.530.417.424.857.9−0.0500.175
    绿唇鲍 Haliotis laevigata27.330.717.124.958.0−0.0590.186
    欧洲疣鲍 Haliotis tuberculata28.731.017.023.359.7−0.0390.156
    杂色鲍 Haliotis diversicolor27.230.817.224.958.0−0.0620.183
    羊鲍 Haliotis ovina27.531.217.024.458.7−0.0630.179
    红鲍 Haliotis rufescens28.330.517.423.858.8−0.0370.155
    黑鲍 Haliotis cracherodii28.030.817.124.158.8−0.0480.170
    rRNA基因
    绿鲍 Haliotis fulgens26.135.113.425.461.2−0.1470.309
    皱纹盘鲍 Haliotis discus hannai27.235.213.124.562.4−0.1280.303
    黑足鲍 Haliotis iris25.835.712.925.661.5−0.1610.330
    黑唇鲍 Haliotis rubra26.234.913.625.361.1−0.1420.301
    绿唇鲍 Haliotis laevigata26.333.914.325.660.2−0.1260.283
    欧洲疣鲍 Haliotis tuberculata28.034.413.224.462.4−0.1030.298
    杂色鲍 Haliotis diversicolor27.135.113.224.562.2−0.1290.300
    羊鲍 Haliotis ovina25.834.613.526.160.4−0.1460.318
    红鲍 Haliotis rufescens27.334.913.324.562.2−0.1220.296
    黑鲍 Haliotis cracherodii27.135.013.324.662.1−0.1270.298
    假定控制区
    绿鲍 Haliotis fulgens37.629.424.68.467.00.122−0.491
    下载: 导出CSV

    表  4  绿鲍13个蛋白质编码基因密码子平均使用频率

    Tab.  4  Total codon average usage in the thirteen protein coding genes for Haliotis fulgens

    密码子数量使用率密码子数量使用率密码子数量使用率密码子数量使用率
    UCU(S)952.11GUU(V)1271.60ACU(T)671.48CAA(Q)441.19
    UCC(S)581.29GUA(V)750.94ACA(T)661.46CAG(Q)300.81
    UCA(S)521.15GUG(V)740.93ACC(T)360.80CAU(H)461.15
    AGU(S)501.11GUC(V)420.53ACG(T)120.27CAC(H)340.85
    AGG(S)380.84UUA(L)1511.56UUU(T)2161.38AAA(K)461.12
    AGA(S)340.75UUG(L)1481.53UUC(T)980.62AAG(K)360.88
    AGC(S)180.40CUA(L)1151.19UAU(Y)861.33UGA(W)601.10
    UCG(S)160.35CUU(L)740.77UAC(Y)430.67UGG(W)490.90
    CGA(R)291.81CUC(L)590.61GGA(G)921.31GAA(E)501.10
    CGU(R)191.19CUG(L)330.34GGG(G)921.31GAG(E)410.90
    CGG(R)90.56GCU(A)941.55GGU(G)690.99GAC(D)401.08
    CGC(R)70.44GCC(A)631.04GGC(G)270.39GAU(D)340.92
    CCA(P)611.64GCA(A)580.96AAU(N)771.29AUG(M)881.05
    CCU(P)521.40GCG(A)270.45AAC(N)420.71AUA(M)800.95
    CCG(P)200.54UGU(C)451.50AUU(I)1451.19UAA81.23
    CCC(P)160.43UGC(C)150.50AUC(I)980.81UAG50.77
    注:黑体表示偏好密码子。
    下载: 导出CSV

    表  5  基于线粒体全序列的10种鲍种间核酸相似性

    Tab.  5  Nucleotide sequence identity among 10 species of abalone based on whole mitochondrial genome

    物种核酸相似性/%
    绿鲍 Haliotis fulgens100
    皱纹盘鲍 Haliotis discus hannai89.15100
    黑足鲍 Haliotis iris82.8683.41100
    黑唇鲍 Haliotis rubra80.9480.9780.73100
    绿唇鲍 Haliotis laevigata80.8080.6680.2391.89100
    欧洲疣鲍 Haliotis tuberculata81.5181.3981.3283.8483.37100
    杂色鲍 Haliotis diversicolor81.0380.7780.1683.0982.8082.59100
    羊鲍 Haliotis ovina80.1079.9579.0682.1481.9281.3681.54100
    红鲍 Haliotis rufescens88.1690.9483.4181.5181.1281.6181.5980.75100
    黑鲍 Haliotis cracherodii87.9090.0383.4681.2580.9881.1980.6480.5591.62100
    下载: 导出CSV
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  • 收稿日期:  2022-07-19
  • 修回日期:  2022-10-21
  • 网络出版日期:  2022-11-02
  • 刊出日期:  2023-05-01

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