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18个双孢蘑菇核心种质的重测序初步分析

施肖堃 蔡志欣 郭仲杰 卢园萍 陈美元 廖剑华

施肖堃,蔡志欣,郭仲杰,等. 18个双孢蘑菇核心种质的重测序初步分析 [J]. 福建农业学报,2019,34(10):1167−1172. doi: 10.19303/j.issn.1008-0384.2019.10.008
引用本文: 施肖堃,蔡志欣,郭仲杰,等. 18个双孢蘑菇核心种质的重测序初步分析 [J]. 福建农业学报,2019,34(10):1167−1172. doi: 10.19303/j.issn.1008-0384.2019.10.008
SHI X K, CAI Z X, GUO Z J, et al. A Preliminary Report on Resequencing 18 Representative Strains of Agaricus bisporus [J]. Fujian Journal of Agricultural Sciences,2019,34(10):1167−1172. doi: 10.19303/j.issn.1008-0384.2019.10.008
Citation: SHI X K, CAI Z X, GUO Z J, et al. A Preliminary Report on Resequencing 18 Representative Strains of Agaricus bisporus [J]. Fujian Journal of Agricultural Sciences,2019,34(10):1167−1172. doi: 10.19303/j.issn.1008-0384.2019.10.008

18个双孢蘑菇核心种质的重测序初步分析

doi: 10.19303/j.issn.1008-0384.2019.10.008
基金项目: 福建省科技计划公益类专项(2019R1035-1、2019R1035-2);现代农业产业技术体系建设专项(CARS20);福建省种业创新与产业化工程项目(fjzycxny2017009);福建省农业科学院科技创新团队建设项目(STIT2017-1-6)
详细信息
    作者简介:

    施肖堃(1984−),男,硕士,助理研究员,主要从事食用菌遗传育种研究(E-mail:39094061@qq.com

    通讯作者:

    陈美元(1972−),男,博士,教授级高级工程师,主要从事食用菌遗传育种研究(E-mail:cmy1972@gmail.com

  • 中图分类号: S 646.11

A Preliminary Report on Resequencing 18 Representative Strains of Agaricus bisporus

  • 摘要:   目的  通过对双孢蘑菇不同类型核心种质的基因组重测序分析,探讨双孢蘑菇不同类型菌株间基因组存在的差异及开发相关分子标记。  方法  对双孢蘑菇国内外杂交菌株、野生菌株、高产型或优质型传统菌株、棕色菌株、不育菌株等共18株核心种质进行基因组重测序,应用不同的生物信息学处理软件,对测序得到的原始reads序列与双孢蘑菇参考基因组H97序列进行比对,同时基于比对结果进行SNP、SV 检测,通过检测结果对多态性标记分布进行统计并实现DNA水平差异基因挖掘和差异基因功能注释等。  结果  样品测序共获得21.63 G数据量,Q30平均达到89.10%。样品的reads与参考基因组H97的比对效率平均为82.50%,基因组覆盖度为96.32%,平均深度分别在33X左右。基于测序数据与参考基因组的比对结果,共检测获得约813 768个SNP,53 840个InDel,平均每个个体获得924个SV变异。  结论  国内外菌株的亲缘关系表明As2796系列与U1系列是世界上并列的两大双孢蘑菇杂交品系。
  • 表  1  供试菌株及其来源

    Table  1.   Strains and origins of A. bisporus studied

    序号 No.菌株 Strain来源 Origin菌株类型 Strain type
    1 As2796 1989年福建省农科院食用菌所杂交(02和8213)
    Crossbreeding of 02 and 8213 by IEF-FAAS in 1989
    国内杂交菌株
    Domestic hybrid
    2 W192 2008年福建省农科院食用菌所杂交(02和As2796)
    Crossbreeding of 02 and As2796 by IEF-FAAS in 2008
    国内杂交菌株
    Domestic hybrid
    3 192-38 2015年福建省农科院食用菌所单孢分离自W192
    Isolated from W192 by IEF-FAAS in 2015
    国内杂交菌株
    Domestic hybrid
    4 U1 1980年荷兰Horst蘑菇试验站杂交
    Crossbred by Horst Station of the Netherland in 1980
    国外杂交菌株
    Imported hybrid
    5 U3 1980年荷兰Horst蘑菇试验站杂交
    Crossbred by Horst Station of the Netherland in 1980
    国外杂交菌株
    Imported hybrid
    6 A15 1989年美国Sylvan公司选育,U1衍生品种
    Bred from U1 by Sylvan America in 1989
    国外杂交菌株
    Imported hybrid
    7 02 1980年轻工业部食品发酵所引自荷兰
    Introduced from the Netherland by Food Fermentation Institute of Light Industry Department
    高产传统菌株
    High-production traditional strain
    8 176 1979年中科院微生物所,张树庭教授引自法国
    From Microbiology Institute of CAS, introduced from France by Prof.S.T.Chang in 1979
    高产传统菌株
    High-production traditional strain
    9 8213 1982年分离自龙溪地区,013多孢子代
    Multi-spore offspring derived from 013 at Longxi in 1982
    优质传统菌株
    Good-quality traditional strain
    10 8211 1982年分离自浙江瑞安老法国品种
    Old French variety separated from Zhejiang Ruian in 1982
    优质传统菌株
    Good-quality traditional strain
    11 C1 1980年引自上海市农科院食用菌研究所
    Introduced from Edible Fungi Institute of SAAS in 1980
    优质传统菌株
    Good-quality traditional strain
    12 SA6 1987年上海市农科院食用菌研究所,引自波兰
    Introduced from Poland by Edible Fungi Institute of SAAS in 1987
    中间类型菌株
    Middle-type strain
    13 MC441 2005年引自美国滨州大学
    Introduced from The Pennsylvania State University in 2005
    棕色菌株 Brown strain
    14 Ag78331 2007年四川省农科院和福建省农科院采自西藏
    Collected from Tibet by SAAS and FAAS in 2007
    国内野生菌株
    Domestic wild strain
    15 AgLH830 2008年四川省农科院和福建省农科院采自四川
    Collected from Sichuan by SAAS and FAAS in 2008
    国内野生菌株
    Domestic wild strain
    16 ARP159 2002年引自美国Sylvan公司的四孢变种
    Tetraspore strain from Sylvan America in 2002
    国外野生菌株
    US wild strain
    17 02-S5 2014年福建省农科院分离自02的同核体
    Homokaryon isolated from 02 by FAAS in 2014
    不育菌株
    Sterile strain
    18 8213-S2 2014年福建省农科院食用菌所分离自8213的同核体
    Homokaryon isolated from 8213 by FAAS in 2014
    不育菌株
    Sterile strain
    注:福建省农科院食用菌所 (IEF-FAAs),中科院微生物所 (CAS),上海市农科院 (SAAS),四川省农科院 (SAAS),福建省农业科学院(FAAS) 。
    Note: The Institute of Edible Fungi, Fujian Academy of Agricultural Sciences (IEF-FAAS), Chinese Acadenmy of Sciences (CAS), Shanghai Academy of Agricultural Sciences (SAAS), Sichuan Academy of Agricultural Sciences (SAAS), Fujian Academy of Agricultural Sciences (FAAS).
    下载: 导出CSV

    表  2  18个双孢蘑菇菌株测序数据评估及与参考基因组H97比对结果

    Table  2.   Genetic sequences of 18 A. bisporus strains and their alignments with H97 reference genome

    菌株
    Strain
    总片段数目
    Total Reads
    ≥Q30的百分比
    Percentage of ≥Q30/%
    覆盖深度
    Depth
    匹配片段百分比
    Mapped Reads/%
    基因组覆盖率
    Coverage/%
    As2796 10 832 772 91.51 29 78.53 95.75
    02 9 969 928 91.60 26 84.91 99.82
    8213 11 279 190 91.68 27 76.44 95.98
    W192 11 529 394 91.54 30 78.52 95.80
    A15 10 590 252 91.39 31 90.34 99.90
    U1 11 492 098 91.56 33 89.20 99.92
    U3 10 838 354 83.40 26 73.97 99.42
    MC441 11 032 666 86.19 30 83.33 97.05
    SA6 11 180 630 85.31 28 73.92 96.20
    176 11 244 788 86.68 30 84.28 99.55
    Ag78331 10 903 678 86.12 31 80.44 92.85
    C1 11 037 982 85.44 30 81.65 96.02
    192-38 10 066 128 90.38 36 83.93 95.60
    8211 8 255 514 90.19 30 87.16 95.74
    ARP159 11 103 174 89.19 42 82.31 90.20
    AgLH830 9 167 040 90.30 32 77.27 93.43
    02-S5 9 930 026 90.42 37 90.32 97.33
    8213-S2 17 432 836 90.88 67 88.52 93.16
    下载: 导出CSV

    表  3  18个双孢蘑菇菌株与参考基因组H97比较的SNP和SV统计

    Table  3.   Statistics on SNP and SV of 18 A. bisporus strains as compared with H97 reference genome

    菌株 Strain多态性位点 SNP结构变异 SV插入类型 INS删除类型 DEL倒位类型 INV染色体内易位 ITX染色体间易位 CTX
    As2796 510 425 1 000 70 459 80 43 348
    W192 510 122 1 111 216 441 79 53 322
    192-38 553 782 932 18 398 91 62 363
    U1 258 738 755 214 290 44 29 178
    U3 286 594 596 73 281 51 28 163
    A15 256 674 704 145 300 39 28 192
    02 248 100 609 105 238 37 28 201
    176 266 232 701 189 242 41 25 204
    ARP159 326 622 828 31 343 74 66 314
    Ag78331 574 890 1 001 108 438 70 60 325
    AgLH830 396 488 880 26 366 77 66 345
    8213 386 625 1 798 995 418 68 43 274
    8211 426 241 1 283 521 324 73 56 309
    C1 404 756 956 99 417 71 55 314
    MC441 407 661 1 015 213 405 72 34 291
    SA6 417 898 845 46 398 74 55 272
    02-S5 102 187 419 141 110 28 21 119
    8213-S2 300 352 1 195 421 327 72 51 324
    下载: 导出CSV

    表  4  18个双孢蘑菇菌株与H97相比产生的3种差异基因的分类统计

    Table  4.   Differentially expressed genes of 18 A. bisporus strains as compared with H97 reference genome

    菌株
    Strain
    非同义突变的
    差异基因
    Genes with Non-
    synonymous SNP
    存在InDel的
    差异基因
    Genes with
    InDel
    存在SV的
    差异基因
    Genes with
    SV
    As279625 4805 578357
    W19225 4335 551461
    192-3825 4875 606330
    U116 7423 156325
    U317 4043 262241
    A1516 6213 148293
    0216 9023 089240
    17616 9253 064284
    ARP15921 1123 311299
    Ag7833122 6703 998383
    AgLH83022 6114 002304
    821322 2604 511832
    821122 3314 585624
    C122 2464 531348
    MC44120 9633 840427
    SA622 5544 564301
    02-S56 1371 269175
    8213-S217 0143 349557
    下载: 导出CSV

    表  5  2个菌株之间的SNP与InDel比较

    Table  5.   Comparison between SNP and InDel of 2 strains of A. bisporus

    菌株比较
    Strains comparison
    SNP数目
    SNP number
    InDel 数目
    InDel number
    As2796 与 19231 6302 568
    W192 与 192-3835 2322 806
    A15 与 U120 0711 594
    A15 与 U360 8224 711
    As2796 与 A15490 99835 292
    As2796 与 U1490 20135 176
    As2796 与 U3488 39134 978
    As2796 与 02524 35937 764
    As2796 与 8213405 42129 926
    ARP159 与 AgLH830295 92718 801
    02 与 02-S5268 30418 514
    8213 与 8213-S2265 15119 039
    下载: 导出CSV
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  • 收稿日期:  2019-05-07
  • 修回日期:  2019-06-29
  • 刊出日期:  2019-10-01

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