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草莓Metacaspase基因家族全基因组鉴定及表达分析

郑益平 陈坚 朱炳耀

郑益平,陈坚,朱炳耀. 草莓Metacaspase基因家族全基因组鉴定及表达分析 [J]. 福建农业学报,2020,35(11):1188−1197 doi: 10.19303/j.issn.1008-0384.2020.11.003
引用本文: 郑益平,陈坚,朱炳耀. 草莓Metacaspase基因家族全基因组鉴定及表达分析 [J]. 福建农业学报,2020,35(11):1188−1197 doi: 10.19303/j.issn.1008-0384.2020.11.003
ZHENG Y P, CHEN J, ZHU B Y. Genome-wide Identification and Expression Analysis of Metacaspase Gene Family in strawberry [J]. Fujian Journal of Agricultural Sciences,2020,35(11):1188−1197 doi: 10.19303/j.issn.1008-0384.2020.11.003
Citation: ZHENG Y P, CHEN J, ZHU B Y. Genome-wide Identification and Expression Analysis of Metacaspase Gene Family in strawberry [J]. Fujian Journal of Agricultural Sciences,2020,35(11):1188−1197 doi: 10.19303/j.issn.1008-0384.2020.11.003

草莓Metacaspase基因家族全基因组鉴定及表达分析

doi: 10.19303/j.issn.1008-0384.2020.11.003
基金项目: 福建省科技计划公益类专项(2018R1019-10)
详细信息
    作者简介:

    郑益平(1988−),女,硕士,研究实习员,研究方向:花卉遗传育种(E-mail:360213443@qq.com

    通讯作者:

    朱炳耀(1962−),男,副研究员,研究方向:植物资源收集与利用(E-mail:251112023@qq.com

  • 中图分类号: S 668.4

Genome-wide Identification and Expression Analysis of Metacaspase Gene Family in strawberry

  • 摘要:   目的  精氨酸/赖氨酸特异性半胱氨酸酶(metacaspases,MCs)在植物生长发育的细胞程序性死亡(programmed cell death,PCD)中发挥重要的调控作用,为系统鉴定草莓FaMC基因家族,进行草莓FaMC基因家族全基因组鉴定及表达分析。  方法  通过草莓全基因组数据分析FaMC蛋白的理化性质、结构域、系统发育关系和保守基序,采用qRT-PCR技术对草莓6个组织器官和6个果实发育时期中的FaMC基因进行表达分析。  结果  蛋白序列分析表明,草莓基因组中21个FaMC成员分为3种类型:I型、I*型和II型。系统发育树和保守结构域分析表明:I型FaMC含N端前结构域且包含1个锌指结构;I*型FaMC含N端前结构域,但其中没有锌指结构;II型FaMC不含N端前结构域。基因表达分析发现,FaMC基因在不同组织中存在表达差异性,I型、I*型和II型FaMC基因分别在叶片、根和花中高表达。在果实发育过程中,多数I*型FaMC基因的表达水平呈现出高-低-高的动态变化趋势;部分I型、II型FaMC在果实发育过程中呈现相反的表达模式。  结论  FaMC基因可能在草莓生长过程中发挥重要作用。
  • 图  1  草莓FaMC家族氨基酸序列比对分析

    注:矩形:LSD1型锌指结构域;大粗实线:脯氨酸和谷氨酰胺的N端前结构域;中粗实线:p10亚基;细实线:p20亚基;虚线:连接区

    Figure  1.  Multiple sequence alignments of FaMC proteins in strawberry

    Note: Rectangle: LSD1-type zinc finger motif; thickest solid line: Pro/Gln-rich NTD; thicker solid line: p10 subunit; solid line: p20 subunit; dotted line: linker.

    图  2  草莓与拟南芥MC家族蛋白质系统进化分析

    注:拟南芥MC蛋白登录号:AtMC1(NP_171719.2);AtMC2(NP_001031711.1);AtMC3(NP_201229.1);AtMC4(NP_178052.1);AtMC5(NP_178051.1);AtMC6(NP_178050.1);AtMC7(NP_178049.2);AtMC8(NP_173092.1);AtMC9(NP_196040.1)

    Figure  2.  Phylogenetic tree of MC gene family in strawberry and Arabidopsis

    Note: Accessions of AtMC proteins: AtMC1 (NP_171719.2); AtMC2 (NP_001031711.1); AtMC3 (NP_201229.1); AtMC4 (NP_178052.1); AtMC5 (NP_178051.1); AtMC6 (NP_178050.1); AtMC7 (NP_178049.2); AtMC8 (NP_173092.1); AtMC9 (NP_196040.1).

    图  3  草莓FaMC基因进化树、蛋白结构域及保守基序分布

    注:A:基因进化树;B:蛋白结构域;C:保守基序

    Figure  3.  Distribution of phylogenetic trees, protein domains, and conserved motifs of FaMC genes in strawberry

    Note: a: Phylogenetic tree; b: conserved domain; c: conserved motif.

    图  4  草莓FaMC基因的表达谱

    注:A:FaMC基因在不同组织部位的表达谱;P1:叶片;P2:花;P3:根;P4:茎;P5:匍匐茎;P6:幼果。B:FaMC基因在果实不同发育时期的表达谱;S1:小绿期;S2:大绿期;S3:白果期;S4:始红期;S5:片红期;S6:全红期。红色代表高表达,绿色代表低表达。

    Figure  4.  Expression patterns of FaMC genes in strawberry

    Note: a: Expression patterns of FaMC in different tissues; P1: leaf; P2: flower; P3: root; P4: stem; P5: stolon; P6: young fruit. b: expression patterns of FaMC in different fruit developmental stages; S1: small and green; S2: large and green; S3: white; S4: turning red; S5: partial red; S6: fully red. Red color represents high expression, green low expression.

    表  1  引物序列

    Table  1.   Primer sequences

    基因
    Gene
    上游引物(5′→3′)
    Forward primer
    下游引物(5′→3′)
    Reverse primer
    FaActin TGGGTTTGCTGGAGATGAT CAGTTAGGAGAACTGGGTGC
    FaMC1 ATGTTGGAGCACCTCACCTC GCTTGACACCCACTCAGAAG
    FaMC2 CAAAAACATCCGAAGGGCTA CGGCAACCTTTCTTTAGCTG
    FaMC3 CTCTCATCTTCCTCCTACAACG GCATCGAGCTCCATATTCTTCC
    FaMC4 TCTGGCAGTGCTGTTACGTC CGCAGGCAGTTAATTGAGGC
    FaMC5 CTTCCGTTCTCATGCTCACA CAAAATCCGAGGGACACAGT
    FaMC6 CGGTGTCAAGCTGCATTCTA CCACCTTTTGTTCCTTTCCA
    FaMC7 TCCCACTGACATGAACCTCA GCTAGACTCACGCTGGTTCC
    FaMC8 CGAGAAAGAGCAGATTGGACC GCAAGTTGAGATCGAGTAGAGG
    FaMC9 TGACCAGTATGTAAAGCCCG ATCTCCTGAAGGTGTGGCAT
    FaMC10 AATACGGAGCTCGATGGCTG CGTTATGTTTGTCTTGGTAGGG
    FaMC11 GAAATCCCTGAAATGGCTTG GTGGGTGAACGATGGTTGA
    FaMC12 ATTATCGTGGGGATGAAGTCG CCATACATATTTTCCACCCCTG
    FaMC13 GCCGCAATTGTTATGCCCAT CACCCCTGTCCATTCTGCAA
    FaMC14 CTTCACGATCTGCAACTCCA GGCAGTTGGAGCAGTCTACC
    FaMC15 CGAGTGGTCAGACAGCATCA ACCAGCCGGAACTTTCTCGT
    FaMC16 GCCCTTTCAATGCAGACCT ACACCAACGAATCTCCAGCTT
    FaMC17 ACAAACTCCAGAGCCACCAG TGACAGCCACTGATGAGAATG
    FaMC18 CGAGTTGTTGAAGCCGGA TCTATTGCTTAGCGGAGCC
    FaMC19 TACGGGAACATGATGACTGC AGCTTTCCAAGACTCCCTCC
    FaMC20 GCAGCAATTGTTAGTCCCAT CACTTGTTCCTTTCCATACGC
    FaMC21 GAAATACGGGTTCTGGTGGA CTCGCAGGCAGTTAATTGGG
    下载: 导出CSV

    表  2  草莓FaMC蛋白理化性质

    Table  2.   Physiochemical properties and subcellular localization of FaMC proteins in strawberry

    基因
    Gene
    基因组编号
    Genome ID
    氨基酸数
    Amino
    acid
    分子量
    Molecular
    weight
    等电点
    pI
    不稳定指数
    Instability
    index
    亲水性
    Hydropathicity
    亚细胞定位
    Subcellular
    localization
    FaMC1 augustus_masked-Fvb3-1-processed-gene-103.9 324 35555.30 5.43 37.04 −0.219 叶绿体 Chloroplast
    FaMC2 maker-Fvb3-1-snap-gene-242.61 402 44269.43 5.06 42.48 −0.582 细胞质 Cytoplasmic
    FaMC3 augustus_masked-Fvb3-1-processed-gene-281.5 326 36519.19 7.58 45.73 −0.110 叶绿体 Chloroplast
    FaMC4 maker-Fvb7-2-augustus-gene-79.38 381 40904.39 6.42 41.60 −0.302 叶绿体 Chloroplast
    FaMC5 maker-Fvb7-2-augustus-gene-253.66 358 38720.78 6.85 50.79 −0.327 细胞核 Nuclear
    FaMC6 snap_masked-Fvb3-3-processed-gene-22.24 347 38805.38 8.14 47.98 −0.354 叶绿体 Chloroplast
    FaMC7 maker-Fvb3-3-augustus-gene-63.33 413 45221.46 5.12 40.94 −0.616 细胞质 Cytoplasmic
    FaMC8 maker-Fvb3-4-augustus-gene-109.35 323 35386.06 5.19 37.43 −0.207 叶绿体 Chloroplast
    FaMC9 maker-Fvb3-4-augustus-gene-226.44 413 45224.44 5.06 40.97 −0.579 细胞质 Cytoplasmic
    FaMC10 augustus_masked-Fvb3-4-processed-gene-255.9 290 31963.38 6.09 39.67 −0.362 叶绿体 Chloroplast
    FaMC11 maker-Fvb5-1-augustus-gene-207.38 406 45451.82 8.95 52.83 −0.491 线粒体 Mitochondrial
    FaMC12 maker-Fvb7-1-augustus-gene-86.37 381 40803.28 6.37 44.55 −0.282 叶绿体 Chloroplast
    FaMC13 maker-Fvb7-1-augustus-gene-129.25 381 40807.37 6.48 45.56 −0.272 叶绿体 Chloroplast
    FaMC14 maker-Fvb7-1-snap-gene-270.81 338 37729.50 9.10 62.14 −0.194 叶绿体 Chloroplast
    FaMC15 maker-Fvb5-4-snap-gene-163.56 413 46277.63 8.88 54.06 −0.532 线粒体 Mitochondrial
    FaMC16 snap_masked-Fvb3-2-processed-gene-39.23 350 39121.78 7.47 49.27 −0.334 叶绿体 Chloroplast
    FaMC17 maker-Fvb3-2-augustus-gene-75.24 413 45214.42 5.06 41.30 −0.596 细胞质 Cytoplasmic
    FaMC18 augustus_masked-Fvb3-2-processed-gene-201.8 323 35426.17 5.27 36.96 −0.203 线粒体 Mitochondrial
    FaMC19 maker-Fvb7-3-augustus-gene-48.64 350 38180.67 7.59 39.34 −0.154 叶绿体 Chloroplast
    FaMC20 maker-Fvb7-3-augustus-gene-157.36 371 39964.41 6.93 39.93 −0.267 线粒体 Mitochondrial
    FaMC21 maker-Fvb7-4-augustus-gene-151.37 371 39772.15 6.34 40.74 −0.256 叶绿体 Chloroplast
    下载: 导出CSV

    表  3  草莓FaMC蛋白氨基酸保守序列

    Table  3.   Conserved motifs of FaMC proteins in strawberry

    Motif长度/aa
    Length
    氨基酸保守序列
    Amino acid conserved sequence
    motif1 50 PTKKNIRMALHWLVQGCQAGDSLVFHYSGHGTRQPNYTGDEVDGYDETLC
    motif2 34 ELKGCINDAKCMKYLlinkerFKFPESSIRMLTEEE
    motif3 50 PLDFETQGMIVDDEINAAIVRPJPAGVKLHAIVDACHSGTVLDLPFLCRM
    motif4 29 PRSGVWKGTSGGEVISISGCDDBQTSADT
    motif5 41 ITSTGAMTFAFIQAIERGHAATYGNJLNAMRSTIRNTGSGA
    motif6 29 NHAPPPPPPNVHGRKRAVICGISYKYSRH
    motif7 21 GLRQEPQLTASEEFDVYTKPF
    motif8 50 AIQTILAETDGEITNQELVLRARKILKEQGYTQRPGLYCSDHHTDAPFVC
    motif9 11 MLVGCSNCRTP
    motif10 50 PTDMNLITDDDFRZFVDQLKKGCRLTIVSDSCHSGGLIDESVEQIGESHK
    motif11 50 KTDIDVGKLRPTLFDVFGDDASPKVKKFMKVILNKLQSHEGEGSGGLMGK
    motif12 50 IKNFLKQSAGDALKSRGIHVPSAFRRHGGDEEESEDREIDMGDGERGYMK
    motif13 20 QLPPGAZSIRCALCQAVTLI
    motif14 29 SAVASLLGGSSGAVTSLVGMLLTGGSVGG
    motif15 11 RGGRYVWEDHR
    motif16 50 DTLSGSCNKTKAIPFESILEHLTSLTGISTSDIATHFLELFAADASLKFR
    motif17 21 GDPRALHSAPSSHEPPPPAPY
    motif18 15 TPPGPPSYAYGALSY
    motif19 11 GHPPPPPPRPY
    motif20 15 NRELPLLALIFLLEQ
    下载: 导出CSV
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出版历程
  • 收稿日期:  2020-08-16
  • 修回日期:  2020-10-08
  • 网络出版日期:  2020-11-24
  • 刊出日期:  2020-11-30

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