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紫菜薹线粒体基因组SSR分布特征的比较分析

肖婉钰 周贤玉 任海龙 黄红弟 郑岩松 张晶 许东林

肖婉钰,周贤玉,任海龙,等. 紫菜薹线粒体基因组SSR分布特征的比较分析 [J]. 福建农业学报,2024,39(1):49−56 doi: 10.19303/j.issn.1008-0384.2024.01.007
引用本文: 肖婉钰,周贤玉,任海龙,等. 紫菜薹线粒体基因组SSR分布特征的比较分析 [J]. 福建农业学报,2024,39(1):49−56 doi: 10.19303/j.issn.1008-0384.2024.01.007
XIAO W Y, ZHOU X Y, REN H L, et al. Characteristics of SSRs in Zicaitai Mitochondrial Genome [J]. Fujian Journal of Agricultural Sciences,2024,39(1):49−56 doi: 10.19303/j.issn.1008-0384.2024.01.007
Citation: XIAO W Y, ZHOU X Y, REN H L, et al. Characteristics of SSRs in Zicaitai Mitochondrial Genome [J]. Fujian Journal of Agricultural Sciences,2024,39(1):49−56 doi: 10.19303/j.issn.1008-0384.2024.01.007

紫菜薹线粒体基因组SSR分布特征的比较分析

doi: 10.19303/j.issn.1008-0384.2024.01.007
基金项目: 2022年省级乡村振兴战略专项资金种业振兴项目(2022-NPY-03-001);广东省农业科技创新及推广项目(2023KJ133)
详细信息
    作者简介:

    肖婉钰(1991 —),女,硕士,农艺师,主要从事蔬菜遗传育种研究,E-mail:yuwanxiao22@126.com

    通讯作者:

    任海龙(1985 —),男,博士,副研究员,主要从事作物遗传育种研究,E-mail:renhailong_2006@163.com

  • 中图分类号: S634.6

Characteristics of SSRs in Zicaitai Mitochondrial Genome

  • 摘要:   目的  分析紫菜薹(Brassica rapa var. purpuraria)线粒体基因组SSR序列的分布特征,并与芸薹属主要物种进行比较,为紫菜薹SSR分子标记的开发及遗传进化研究提供参考。  方法  利用MISA软件对紫菜薹及芸薹属6个基本种(包括白菜3个变种)的线粒体基因组进行搜索,并对搜索到的SSR序列分布特征进行比较分析。  结果  在紫菜薹及芸薹属6个基本种(包括白菜3个变种)的线粒体基因组中,分别筛选到168、170、167、168、180、280、185、165、179个完整的SSR序列,相对密度分别为764 、774 、760 、764 、775 、777、721 、744 、771 个·Mb−1,SSR序列的总长度分别为1562、1577、1547、1562、1664、2564、1722、1524、1646 bp,占各自线粒体基因组序列总长度的比例分别为0.71%、0.72%、0.70%、0.71%、0.72%、0.71%、0.67%、0.69%和0.71%。在1~6个不同核苷酸重复单元中,紫菜薹及芸薹属6个基本种的SSR序列均是单核苷酸重复单元最多,然后依次是二核苷酸、四核苷酸、三核苷酸、五核苷酸,均未发现六核苷酸重复单元。其中,A/T、AG/CT、AT/AT和C/G是芸薹属线粒体基因组共有的常见重复单元类型。  结论  紫菜薹线粒体基因组大小为219 779 bp,共筛选出168个SSR分子标记,相对密度为764 个·Mb−1,平均长度为9 bp,以单核苷酸重复单元的数量最多,其次为二、四核苷酸重复单元类型,具有较大的多态性标记开发潜力。
  • 图  1  紫菜薹及芸薹属线粒体基因组不同片段长度SSR数量

    Figure  1.  Number in SSR fragment lengths of mitochondrial genomes of zicaitai and other Brassica species

    表  1  紫菜薹及芸薹属线粒体基因组信息

    Table  1.   Mitochondrial genome sequences of zicaitai and other Brassica species

    物种
    Species
    染色体数
    Number of chromosomes
    GenBank
    登录号
    GenBank accession
    线粒体
    基因组大小
    Genome size/bp
    紫菜薹
    Brassica rapa var. purpuraria
    AA, 2n = 2x = 20OP729396.1219779
    芜菁
    Brassica rapa ssp. rapa
    AA, 2n = 2x = 20NC_049892.1219736
    芸薹
    Brassica rapa subsp. Campestris
    AA, 2n = 2x = 20NC_016125.1219747
    大白菜
    Brassica rapa L. ssp. pekinensis
    AA, 2n = 2x = 20MN910310219778
    黑芥
    Brassica nigra
    BB, 2n = 2x = 16NC_029182.1232407
    甘蓝
    Brassica oleracea
    CC, 2n = 2x = 18NC_016118.1360271
    芥菜
    Brassica juncea
    AABB, 2n = 4x = 36MG872829.1256592
    甘蓝型油菜
    Brassica napus
    AACC, 2n = 4x = 38NC_008285.1221853
    埃塞俄比亚芥
    Brassica carinata
    BBCC, 2n = 4x = 34NC_016120.1232241
    下载: 导出CSV

    表  2  紫菜薹及芸薹属线粒体基因组中SSR的分布概况

    Table  2.   Distribution of SSRs in mitochondrial genomes of zicaitai and other Brassica species

    物种
    Species
    SSR总长度
    Total length of SSR/bp
    SSR数量
    SSR number
    SSR分布密度
    SSR density/(个·Mb−1
    SSR平均长度
    Average length of SSR/bp
    SSR长度占比
    Length ratio of SSR/%
    紫菜薹
    Brassica rapa var. purpuraria
    156216876490.71
    芜菁
    Brassica rapa ssp. rapa
    157717077490.72
    芸薹
    Brassica rapa subsp. Campestris
    154716776090.70
    大白菜
    Brassica rapa L. ssp. pekinensis
    156216876490.71
    黑芥
    Brassica nigra
    166418077590.72
    甘蓝
    Brassica oleracea
    256428077790.71
    芥菜
    Brassica juncea
    172218572190.67
    甘蓝型油菜
    Brassica napus
    152416574490.69
    埃塞俄比亚芥
    Brassica carinata
    164617977190.71
    下载: 导出CSV

    表  3  紫菜薹及芸薹属线粒体基因组SSR重复单元的数目和占比

    Table  3.   Number and proportion of SSR repeat types in mitochondrial genomes of zicaitai and other Brassica species

    物种
    Species
    单核苷酸
    Mononucleotide
    二核苷酸
    Dinucleotide
    三核苷酸
    Trinucleotide
    四核苷酸
    Tetranucleotide
    五核苷酸
    Pentanucleotide
    紫菜薹
    Brassica rapa var. purpuraria
    83
    (49.40%)
    61
    (36.31%)
    5
    (2.98%)
    18
    (10.71%)
    1
    (0.60%)
    芜菁
    Brassica rapa ssp. rapa
    84
    (49.41%)
    61
    (35.88%)
    5
    (2.94%)
    19
    (11.18%)
    1
    (0.59%)
    芸薹
    Brassica rapa subsp. Campestris
    82
    (49.10%)
    61
    (36.53%)
    5
    (2.99%)
    18
    (10.78%)
    1
    (0.60%)
    大白菜
    Brassica rapa L. ssp. pekinensis
    82
    (48.81%)
    62
    (36.90%)
    5
    (2.98%)
    18
    (10.71%)
    1
    (0.60%)
    黑芥
    Brassica nigra
    85
    (47.22%)
    69
    (38.33%)
    6
    (3.33%)
    19
    (10.56%)
    1
    (0.56%)
    甘蓝
    Brassica oleracea
    137
    (48.93%)
    106
    (37.86%)
    6
    (2.14%)
    29
    (10.36%)
    2
    (0.71%)
    芥菜
    Brassica juncea
    78
    (42.16%)
    71
    (38.38%)
    7
    (3.78%)
    28
    (15.14%)
    1
    (0.54%)
    甘蓝型油菜
    Brassica napus
    84
    (50.91%)
    58
    (35.15%)
    4
    (2.42%)
    18
    (10.91%)
    1
    (0.61%)
    埃塞俄比亚芥
    Brassica carinata
    85
    (47.49%)
    68
    (37.99%)
    6
    (3.35%)
    19
    (10.61%)
    1
    (0.56%)
    下载: 导出CSV

    表  4  紫菜薹及芸薹属线粒体基因组SSR的重复基元类型及数量

    Table  4.   Number of SSRs of mitochondrial genomes in zicaitai and other Brassica species

    重复基元类型
    Motif types
    紫菜薹
    Brassica rapa var.
    purpuraria
    芜菁
    Brassica rapa ssp.
    rapa
    芸薹
    Brassica rapa subsp.
    Campestris
    大白菜
    Brassica rapa L. ssp.
    pekinensis
    黑芥
    Brassica
    nigra
    甘蓝
    Brassica
    oleracea
    芥菜
    Brassica
    juncea
    甘蓝型油菜
    Brassica
    napus
    埃塞俄比亚芥
    Brassica
    carinata
    A/T 67 68 66 67 71 112 65 68 70
    AG/CT 36 36 36 37 41 62 45 34 41
    AT/AT 19 19 19 19 19 34 19 18 18
    C/G 16 16 16 15 14 25 13 16 15
    AATG/ATTC 5 5 5 5 5 8 5 5 5
    AC/GT 4 4 4 4 7 7 5 4 7
    AAG/CTT 4 4 4 4 4 5 5 3 4
    AAAG/CTTT 4 4 4 4 3 6 10 5 3
    AAAC/GTTT 3 4 3 3 4 5 4 3 4
    AAAT/ATTT 3 3 3 3 3 4 3 3 3
    CG/CG 2 2 2 2 2 3 2 2 2
    AAC/GTT 1 1 1 1 1 1 1 1 1
    AACG/CGTT 1 1 1 1 2 2 2 1 2
    ACTC/AGTG 1 1 1 1 1 2 2 1
    CCGG/CCGG 1 1 1 1 1 2 1 1 1
    ACTAG/AGTCT 1 1 1 1 1 2 1 1 1
    AGC/CTG 1 1 1
    ACTG/AGTC 1
    下载: 导出CSV
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出版历程
  • 收稿日期:  2023-05-10
  • 录用日期:  2024-01-08
  • 修回日期:  2024-01-04
  • 网络出版日期:  2024-01-25
  • 刊出日期:  2024-01-28

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