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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(X):1−8
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(X):1−8
XIAO W - Y, ZHOU X - Y, REN H - L, et al. Characteristics and analysis of simple sequence Repeats(SSR)in zicaitai mitochondrial Genome [J]. Fujian Journal of Agricultural Sciences,2024,39(X):1−8
Citation: XIAO W - Y, ZHOU X - Y, REN H - L, et al. Characteristics and analysis of simple sequence Repeats(SSR)in zicaitai mitochondrial Genome [J]. Fujian Journal of Agricultural Sciences,2024,39(X):1−8

紫菜薹线粒体基因组SSR分布特征的比较分析

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

Characteristics and analysis of simple sequence Repeats(SSR)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个、170个、167个、168个、180个、280个、185个、165个和179个完整的SSR序列,相对密度分别为764 个/Mb、774 个/Mb、760 个/Mb、764 个/Mb、775 个/Mb、777 个/Mb、721 个/Mb、744 个/Mb和771 个/Mb,SSR序列的总长度分别为1562 bp、1577 bp、1547 bp、1562 bp、1664 bp、2564 bp、1722 bp、1524 bp和1646 bp,占各自线粒体基因组序列总长度分别为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,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“优选洪山”

    Figure  1.  Photograph of Brassica rapa var. purpuraria (L.H.Bailey) Kitam.

    图  2  紫菜薹及芸薹属线粒体基因组SSR不同片段长度的数量

    Figure  2.  The number of different fragment length SSR of mitochondrial genome in zicaitai and Brassica species

    表  1  紫菜薹及芸薹属线粒体基因组信息

    Table  1.   Mitochondrial genome sequencing information of zicaitai and 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 = 20 OP729396.1 219,779
    芜菁
    Brassica rapa ssp. rapa
    AA, 2n = 2x = 20 NC_049892.1 219,736
    芸薹
    Brassica rapa subsp. Campestris
    AA, 2n = 2x = 20 NC_016125.1 219,747
    大白菜
    Brassica rapa L. ssp. pekinensis
    AA, 2n = 2x = 20 MN910310 219,778
    黑芥
    Brassica nigra
    BB, 2n = 2x = 16 NC_029182.1 232,407
    甘蓝
    Brassica oleracea
    CC, 2n = 2x = 18 NC_016118.1 360,271
    芥菜
    Brassica juncea
    AABB, 2n = 4x = 36 MG872829.1 256,592
    甘蓝型油菜
    Brassica napus
    AACC, 2n = 4x = 38 NC_008285.1 221,853
    埃塞俄比亚芥
    Brassica carinata
    BBCC, 2n = 4x = 34 NC_016120.1 232,241
    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 SSR in mitochondrial genome of zicaitai and Brassica species

    物种
    Species
    SSR总长度
    Total lengh of SS/bp
    SSR数量
    Number of SSR
    SSR分布密度
    Density of SSR/Mb−1
    SSR平均长度
    Average lengh of SSR/bp
    SSR长度占比
    Length ratio of SSR/%
    紫菜薹
    Brassica rapa var. purpuraria
    1562 168 764 9 0.71
    芜菁
    Brassica rapa ssp. rapa
    1577 170 774 9 0.72
    芸薹
    Brassica rapa subsp. Campestris
    1547 167 760 9 0.70
    大白菜
    Brassica rapa L. ssp. pekinensis
    1562 168 764 9 0.71
    黑芥
    Brassica nigra
    1664 180 775 9 0.72
    甘蓝
    Brassica oleracea
    2564 280 777 9 0.71
    芥菜
    Brassica juncea
    1722 185 721 9 0.67
    甘蓝型油菜
    Brassica napus
    1524 165 744 9 0.69
    埃塞俄比亚芥
    Brassica carinata
    1646 179 771 9 0.71
    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 different SSR repeat types in mitochondrial genome of zicaitai and Brassica species

    物种
    Species
    重复单元 Repeat type
    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.   The number of different SSR in of zicaitai and Brassica species of Brassica mitochondrial genome

    重复基元类型
    Motif types
    物种 Species
    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

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