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香蕉GDSL脂肪酶基因家族全基因组鉴定与表达分析

张城瑜 任纹慧 耿小慧 李丹 吴昊 倪珊珊 王梦鸽 罗彬彬 徐涵 赖钟雄

张城瑜,任纹慧,耿小慧,等. 香蕉GDSL脂肪酶基因家族全基因组鉴定与表达分析 [J]. 福建农业学报,2022,37(11):1415−1429 doi: 10.19303/j.issn.1008-0384.2022.011.007
引用本文: 张城瑜,任纹慧,耿小慧,等. 香蕉GDSL脂肪酶基因家族全基因组鉴定与表达分析 [J]. 福建农业学报,2022,37(11):1415−1429 doi: 10.19303/j.issn.1008-0384.2022.011.007
ZHANG C Y, REN W H, GENG X H, et al. Genome-wide Identification and Expressions of Banana GDSL Lipase Gene Family [J]. Fujian Journal of Agricultural Sciences,2022,37(11):1415−1429 doi: 10.19303/j.issn.1008-0384.2022.011.007
Citation: ZHANG C Y, REN W H, GENG X H, et al. Genome-wide Identification and Expressions of Banana GDSL Lipase Gene Family [J]. Fujian Journal of Agricultural Sciences,2022,37(11):1415−1429 doi: 10.19303/j.issn.1008-0384.2022.011.007

香蕉GDSL脂肪酶基因家族全基因组鉴定与表达分析

doi: 10.19303/j.issn.1008-0384.2022.011.007
基金项目: 国家重点研发计划项目(2019YFD1000901);国家现代农业产业技术体系(香蕉)建设专项(GARS-31-15);福建省高原学科建设项目(102/71201801101)
详细信息
    作者简介:

    张城瑜(1996−),男,硕士,研究方向:园艺植物生物技术(E-mail:738293225@qq.com

    通讯作者:

    赖钟雄(1966−),男,博士,研究员,研究方向:园艺植物生物技术与遗传资源(E-mail:laizx01@163.com

  • 中图分类号: S 668.1

Genome-wide Identification and Expressions of Banana GDSL Lipase Gene Family

  • 摘要:   目的  揭示香蕉GDSL脂肪酶基因家族(MaGDSL)序列特征及其在香蕉生长发育过程中的潜在功能。  方法  利用生物信息学方法对MaGDSL进行全基因组鉴定,分析其染色体、启动子顺式作用元件和转录因子结合位点(TFBS)的分布情况以及编码蛋白的理化性质、基因结构、保守基序和系统进化关系,并基于转录组数据库分析MaGDSLs在高温(45 ℃)/低温 (4 ℃)处理的叶片、枯萎病菌 FocTR4侵染的根系以及自然成熟/乙烯催熟的不同成熟阶段的果实中的表达模式,同时利用实时荧光定量PCR(qRT-PCR)分析部分MaGDSL成员在花粉中的表达情况。  结果  香蕉A基因组中有76个MaGDSL成员,分布于11个染色体上,可分为9个亚家族,各成员编码区长度为1014~ 2193 bp,其中有5个成员含有不同数量的转录本;多数MaGDSL成员包含5个外显子和4个内含子,编码蛋白具有信号肽且主要定位在内外膜上;启动子区存在多种植物激素和逆境胁迫相关响应元件以及22种TFBSs;MaGDSLs中有3个串联重复基因簇位于4、8号染色体,6个串联重复基因对分别位于1、6、7、8、9和10号染色体上,22对片段重复基因分布在除11号染色体外的所有染色体上。MaGDSLs在香蕉叶片和根部的表达水平差异较大,且个别成员受高、低温胁迫以及枯萎病菌调控,其中5个成员(MaGDSL4-5、8-1、8-12、9-4、9-5)受高、低温胁迫抑制表达,而MaGDSL2-1MaGDSL6-8受高、低温胁迫诱导表达,MaGDSL4-1MaGDSL11-1受低温和FocTR4调控,MaGDSL5~8仅响应低温胁迫,其中MaGDSL2-2MaGLP10-5对各种处理均有响应,而MaGDSL1-1在根系和花粉中均有高表达。  结论  MaGDSLs可能在香蕉生长发育过程中发挥重要作用,同时部分成员特异响应生物和非生物胁迫。
  • 图  1  MaGDSL家族成员的系统进化树

    Figure  1.  Phylogenetic tree of MaGDSLs in banana

    图  2  香蕉MaGDSL基因家族的蛋白保守基序及其基因结构分布图

    Figure  2.  Conserved motifs in encoded proteins and gene structure of MaGDSLs

    图  3  MaGDSL 的染色体定位和共线性分布

    绿色线表示 MaGDSL 的片段复制基因对, 标红的基因表示 MaGDSL 的串联复制基因。

    Figure  3.  Chromosome localization and collinear distribution of MaGDSLs

    Green line indicates segmental duplication gene pairs of MaGDSL; red color indicates tandem duplication genes of MaGDSL.

    图  4  MaGDSL 基因家族启动子顺式作用元件分析

    Figure  4.  Analysis of cis-acting elements of MaGDSL gene family promoter

    图  5  MaGDSL 基因家族启动子的转录因子结合位点分布

    Figure  5.  Distribution of transcription factor binding sites in MaGDSLs promoter

    图  6  MaGDSL 家族成员表达量热图

    Figure  6.  Heatmap for expression of MaGDSL gene family members

    图  7  MaGDSL家族部分成员在福州野生蕉最外层花粉的相对表达量

    Figure  7.  Relative expressions of MaGDSLs in outermost pollen layer of wild Fuzhou banana plants

    表  1  qPCR 分析引物

    Table  1.   Primers for qRT-PCR

    基因名称
    Gene ID
    引物名称
    Primer name
    引物序列
    Primer sequence
    内参UBQ F3′-GGCACCACAAACAACACAGG-5′
    R3′-AGACGAGCAAGGCTTCCATT-5′
    MaGDSL2-7F3′-GGAAGACGGGAGAGGGATAC-5′
    R3′-GCCTACGTTCATGGGGTAAGC-5′
    MaGDSL3-2F3′-ATCTTCGGAGACTCCCTCGT-5′
    R3′-GTGCTTGCCCTCTTGTGTTT-5′
    MaGDSL5-1F3′-TTGATGCAGCAACAGTGACA-5′
    R3′-AAACATAGCAGGCACCGACT-5′
    MaGDSL6-4F3′-GAGCTGAGAAGGACGATGCT-5′
    R3′-GTCAAGCCATTGGTGAACCT-5′
    MaGDSL6-7F3′-CCCAATGGCAACAAGTATCC-5′
    R3′-CCTGAGGGGCTACATACCAA-5′
    MaGDSL6-9F3′-TTGCCAGGCTCTTTCTTTGT-5′
    R3′-AGCACTTGTCAGCGATGATG-5′
    MaGDSL7-5F3′-TGAGGGCTCCATGGACATA-5′
    R3′-GCAAGTTCACGGGATAGCA-5′
    MaGDSL8-10F3′-CGGAACCACAGGACGATACT-5′
    R3′-TGTCCCAAAGGATTCCAGAG-5′
    MaGDSL9-2F3′-ATGAACTCAACGCCTTGGAC-5′
    R3′-GATGAGGACGATTGCAGCTT-5′
    MaGDSL11-6F3′-TGCTTCCCATGCTATCGAG-5′
    R3′-CCCAAATGGTCTGCAACAG-5′
    MaGDSL1-1F3′-CGTTGTGATTCTGTGCTGCT-5′
    R3′-GTTTCTCAGCGAGGAAGTCG-5′
    下载: 导出CSV

    表  2  MaGDSL家族成员基本信息和编码蛋白理化性质

    Table  2.   Information and physiochemical properties of MaGDSL encoded proteins

    基因 ID
    Gene ID
    染色体位置
    Chromosome
    location
    基因
    Gene
    长度
    Length/aa
    等电点
    pI
    不稳定指数
    Instability index
    亲水性
    GRAVY
    信号肽
    Signal
    peptide
    跨膜结构
    Transmembrane
    domain
    亚细胞定位
    Protein subcellular
    localization
    Prediction
    Ma01_g03770chr01:2506772..2513988(−)MaGDSL1-13625.9740.6−0.1180外膜 Outer membrane
    Ma01_g03780chr01:2514735..2517040(+)MaGDSL1-23635.5836.14−0.0640胞外 Extracellular
    Ma01_g04800chr01:3286719..3288349(−)MaGDSL1-33636.9039.640.0341外膜 Outer membrane
    Ma01_g17620chr01:12898520..12900562(+)MaGDSL1-43906.2542.89−0.0450外膜 Outer membrane
    Ma02_g12980chr02:21545341..21546931(+)MaGDSL2-13556.5232.180.0921周质 Periplasmic
    Ma02_g13020chr02:21592310..21594060(+)MaGDSL2-23556.2233.060.0841外膜 Outer membrane
    Ma02_g13050chr02:21608508..21610184(+)MaGDSL2-33536.9928.540.0411外膜 Outer membrane
    Ma02_g13620chr02:21929576..21940378(+)MaGDSL2-44308.0536.67−0.0261外膜 Outer membrane
    Ma02_g14360chr02:22465764..22467578(−)MaGDSL2-5a4015.2533.590.2100外膜 Outer membrane
    MaGDSL2-5b3965.2435.010.2110外膜 Outer membrane
    Ma02_g18570chr02:25021259..25022978(−)MaGDSL2-63586.2322.580.0000外膜 Outer membrane
    Ma02_g21270chr02:26951434..26952967(+)MaGDSL2-73769.2136.69−0.0900外膜 Outer membrane
    Ma03_g03330chr03:2232832..2235731(−)MaGDSL3-14197.1632.55−0.1130周质 Periplasmic
    Ma03_g16970chr03:22263933..22266432(+)MaGDSL3-23665.9735.88−0.1350外膜 Outer membrane
    Ma03_g25700chr03:29665153..29668011(+)MaGDSL3-3a3725.7945.250.0970外膜 Outer membrane
    MaGDSL3-3b3645.9047.020.0810周质 Periplasmic
    Ma03_g26380chr03:30141639..30143572(−)MaGDSL3-44106.3540.42−0.0790外膜 Outer membrane
    Ma04_g05070chr04:3833650..3836264(−)MaGDSL4-13568.5934.730.0440胞外 Extracellular
    Ma04_g18170chr04:19831827..19833593(−)MaGDSL4-23476.6427.420.0900外膜 Outer membrane
    Ma04_g19770chr04:22407980..22409457(+)MaGDSL4-33736.0937.180.0080外膜 Outer membrane
    Ma04_g32080chr04:32208763..32212100(+)MaGDSL4-43638.2522.570.2430外膜 Outer membrane
    Ma04_g32090chr04:32217091..32219380(+)MaGDSL4-53675.1332.770.0940外膜 Outer membrane
    Ma04_g32250chr04:32308311..32310571(+)MaGDSL4-63628.5422.380.1670外膜 Outer membrane
    Ma04_g32390chr04:32366386..32368477(−)MaGDSL4-73649.4737.07−0.0180外膜 Outer membrane
    Ma04_g35750chr04:34368316..34369739(−)MaGDSL4-83655.2743.480.0750细胞质 Cytoplasmic
    Ma04_g37620chr04:35437527..35439771(+)MaGDSL4-9a3588.7537.230.0190外膜 Outer membrane
    MaGDSL4-9b3588.7537.230.0190外膜 Outer membrane
    Ma05_g01340chr05:780195..783192(−)MaGDSL5-14135.2820.21−0.0150胞外 Extracellular
    Ma05_g10980chr05:7975525..7978280(+)MaGDSL5-23556.0340.10−0.0820外膜 Outer membrane
    Ma05_g14230chr05:10339954..10341215(+)MaGDSL5-33615.3537.32−0.0550细胞 Cytoplasmic
    Ma05_g15830chr05:12426846..12430706(+)MaGDSL5-43759.0539.01−0.1301胞外 Extracellular
    Ma05_g17280chr05:19801910..19803428(−)MaGDSL5-53666.1238.93−0.0151外膜 Outer membrane
    Ma05_g17650chr05:21042672..21044837(+)MaGDSL5-63868.7136.61−0.0850周质 Periplasmic
    Ma05_g23460chr05:35527091..35528767(−)MaGDSL5-73746.7535.27−0.1461外膜 Outer membrane
    Ma05_g23660chr05:35833232..35837552(+)MaGDSL5-83775.4943.04−0.0160外膜 Outer membrane
    Ma06_g04310chr06:3104879..3106481(−)MaGDSL6-1a3725.4031.37−0.1020外膜 Outer membrane
    MaGDSL6-1b3385.5230.790.0330外膜 Outer membrane
    Ma06_g24960chr06:25117515..25118735(−)MaGDSL6-23556.7934.760.0921内膜 Inner membrane
    Ma06_g25030chr06:25237635..25243333(−)MaGDSL6-33808.2337.330.0080周质 Periplasmic
    Ma06_g27800chr06:29688900..29691154(−)MaGDSL6-43655.2042.08−0.1210外膜 Outer membrane
    Ma06_g29860chr06:31225349..31227058(−)MaGDSL6-54117.5634.71−0.0130周质 Periplasmic
    Ma06_g30580chr06:31830895..31832818(+)MaGDSL6-6a3758.9743.590.0220周质 Periplasmic
    MaGDSL6-6b3748.8643.710.0320周质 Periplasmic
    Ma06_g30640chr06:31860762..31862418(−)MaGDSL6-74479.2131.85−0.1490外膜 Outer membrane
    Ma06_g37580chr06:36585560..36587436(−)MaGDSL6-83985.9441.69−0.0551胞外 Extracellular
    Ma06_g38100chr06:36975407..36978177(+)MaGDSL6-93656.5042.060.0610内膜 Inner membrane
    Ma07_g08760chr07:6557127..6558543(+)MaGDSL7-13597.5924.74−0.0010外膜 Outer membrane
    Ma07_g12320chr07:9208788..9210632(+)MaGDSL7-23896.0630.740.0001外膜 Outer membrane
    Ma07_g13910chr07:10418714..10420475(+)MaGDSL7-33608.0831.580.0160内膜 Inner membrane
    Ma07_g13920chr07:10420620..10422694(+)MaGDSL7-43659.5342.01−0.0770外膜 Outer membrane
    Ma07_g14440chr07:10888114..10890751(+)MaGDSL7-53635.1249.96−0.0090外膜 Outer membrane
    Ma08_g06100chr08:4121189..4123492(−)MaGDSL8-13718.5537.99−0.0070周质 Periplasmic
    Ma08_g09750chr08:7078632..7081137(+)MaGDSL8-23666.6031.020.0540外膜 Outer membrane
    Ma08_g10150chr08:7392254..7396118(−)MaGDSL8-33816.6533.87−0.0010外膜 Outer membrane
    Ma08_g10160chr08:7397273..7398935(−)MaGDSL8-44046.5437.62−0.1010周质 Periplasmic
    Ma08_g10170chr08:7404987..7406648(−)MaGDSL8-53676.2639.19−0.0810外膜 Outer membrane
    Ma08_g10480chr08:7659127..7660505(+)MaGDSL8-63765.3623.810.1061外膜 Outer membrane
    Ma08_g21060chr08:35064951..35067710(+)MaGDSL8-73596.8831.43−0.0680内膜 Inner membrane
    Ma08_g21070chr08:35068690..35077978(+)MaGDSL8-87318.6138.450.1130外膜 Outer membrane
    Ma08_g28640chr08:40487336..40489392(−)MaGDSL8-93845.0245.15−0.0501胞外 Extracellular
    Ma08_g30430chr08:41700756..41702316(+)MaGDSL8-103976.7039.810.1150内膜 Inner membrane
    Ma08_g30470chr08:41727515..41729409(+)MaGDSL8-113565.1631.840.1420细胞外 Extracellular
    Ma08_g30480chr08:41730080..41733085(+)MaGDSL8-123834.5439.030.1161外膜 Outer membrane
    Ma09_g01870chr09:1401507..1405717(+)MaGDSL9-13817.1135.50−0.1110周质 Periplasmic
    Ma09_g05540chr09:3558484..3560119(−)MaGDSL9-23696.8933.29−0.0490外膜 Outer membrane
    Ma09_g19240chr09:21599052..21600910(−)MaGDSL9-33654.9442.590.0501内膜 Inner membrane
    Ma09_g24520chr09:36179911..36182176(+)MaGDSL9-43607.6135.810.0741胞外 Extracellular
    Ma09_g24530chr09:36193365..36196041(+)MaGDSL9-53608.7335.210.0770胞外 Extracellular
    Ma10_g12640chr10:25677743..25681254(+)MaGDSL10-13816.1638.280.1081周质 Periplasmic
    Ma10_g14470chr10:26912910..26916293(+)MaGDSL10-23606.5928.16−1.0190外膜 Outer membrane
    Ma10_g14480chr10:26917998..26919683(−)MaGDSL10-33707.9842.030.0250周质 Periplasmic
    Ma10_g14730chr10:27073351..27075394(+)MaGDSL10-43937.6339.370.0400周质 Periplasmic
    Ma10_g21620chr10:31338004..31344227(+)MaGDSL10-53597.2333.110.0230内膜 Inner membrane
    Ma11_g05100chr11:3940477..3942390(+)MaGDSL11-13745.3634.010.0590外膜 Outer membrane
    Ma11_g09200chr11:7355875..7357479(−)MaGDSL11-23745.2834.440.0750周质 Periplasmic
    Ma11_g10620chr11:10119577..10121852(−)MaGDSL11-33668.8734.88−0.0420胞外 Extracellular
    Ma11_g14690chr11:20398154..20399698(+)MaGDSL11-43687.5037.23−0.1330外膜 Outer membrane
    Ma11_g15240chr11:20938047..20940295(−)MaGDSL11-53606.0137.080.0700外膜 Outer membrane
    Ma11_g16030chr11:21634731..21637078(−)MaGDSL11-63615.4932.42−0.0330胞外 Extracellular
    Ma11_g18800chr11:23822530..23824109(+)MaGDSL11-73675.3428.72−0.0151外膜 Outer membrane
    Ma11_g25050chr11:27802837..27804653(+)MaGDSL11-83866.4931.58−0.0061周质 Periplasmic
    跨膜结构中,0代表不存在跨膜结构,1代表存在跨膜结构。
    In the table, 0 means no transmembrane domain existed, 1 transmembrane domain existed.
    下载: 导出CSV

    表  3  MaGDSLs同源基因 Ka/Ks 分析

    Table  3.   Ka/Ks analysis of MaGDSLs homologous genes

    复制类型
    Duplication type
    基因名称
    Gene name
    基因ID
    Gene ID
    基因名称
    Gene name
    基因ID
    Gene ID
    KaKsKa/Ks
    串联重复
    Tandem duplication
    MaGDSL1-1Ma01_g03770MaGDSL1-2Ma01_g037800.05670.15920.3562
    MaGDSL4-4Ma04_g32080MaGDSL4-5Ma04_g320900.36671.53480.2389
    MaGDSL4-6Ma04_g32250MaGDSL4-7Ma04_g323900.75902.11430.3590
    MaGDSL6-6Ma06_g30580MaGDSL6-7Ma06_g306400.97921.65650.5911
    MaGDSL7-3Ma07_g13910MaGDSL7-4Ma07_g139200.36501.22920.2969
    MaGDSL8-3Ma08_g10150MaGDSL8-4Ma08_g101600.46871.41350.3316
    MaGDSL8-4Ma08_g10160MaGDSL8-5Ma08_g101700.03550.02301.5416
    MaGDSL8-7Ma08_g21060MaGDSL8-8Ma08_g210700.28791.10930.2596
    MaGDSL8-10Ma08_g30430MaGDSL8-11Ma08_g304700.8306————
    MaGDSL8-11Ma08_g30470MaGDSL8-12Ma08_g304800.45361.44820.3132
    MaGDSL9-4Ma09_g24520MaGDSL9-5Ma09_g245300.02250.03030.7449
    MaGDSL10-2Ma10_g14470MaGDSL10-3Ma10_g144800.45061.35640.3322
    片段复制
    Segmental duplication
    MaGDSL1-3Ma01_g04800MaGDSL5-5Ma05_g172800.09630.76460.1259
    MaGDSL2-4Ma02_g13620MaGDSL4-8Ma04_g357500.19040.71110.2678
    MaGDSL2-6Ma02_g18570MaGDSL7-1Ma07_g087600.10220.59380.1721
    MaGDSL3-3Ma03_g25700MaGDSL8-1Ma08_g061000.11400.50420.2262
    MaGDSL3-2Ma03_g16970MaGDSL9-2Ma09_g055400.14360.71920.1997
    MaGDSL3-1Ma03_g03330MaGDSL10-2Ma10_g144700.10480.59440.1764
    MaGDSL4-4Ma04_g32080MaGDSL5-2Ma05_g109800.36942.36060.1565
    MaGDSL4-1Ma04_g05070MaGDSL9-4Ma09_g245200.19540.68810.2840
    MaGDSL5-8Ma05_g23660MaGDSL8-3Ma08_g101500.12510.49430.2531
    MaGDSL5-6Ma05_g17650MaGDSL9-1Ma09_g018700.11040.66480.1661
    MaGDSL5-8Ma05_g23660MaGDSL11-1Ma11_g051000.45391.88440.2409
    MaGDSL6-4Ma06_g27800MaGDSL9-2Ma09_g055400.09620.50620.1901
    MaGDSL7-3Ma07_g13910MaGDSL8-7Ma08_g210600.11330.42960.2638
    MaGDSL7-4Ma07_g13920MaGDSL8-8Ma08_g210700.22261.31690.1691
    MaGDSL7-3Ma07_g13910MaGDSL10-5Ma10_g216200.09390.42760.2196
    MaGDSL7-3Ma07_g13910MaGDSL10-2Ma10_g144700.25731.14300.2251
    MaGDSL7-4Ma07_g13920MaGDSL10-3Ma10_g144800.40681.38640.2934
    MaGDSL8-7Ma08_g21060MaGDSL10-5Ma10_g216200.09230.50030.1846
    MaGDSL8-2Ma08_g09750MaGDSL11-7Ma11_g188000.10810.72470.1491
    MaGDSL8-4Ma08_g10160MaGDSL11-1Ma11_g051000.36111.06900.3378
    MaGDSL8-11Ma08_g30470MaGDSL11-3Ma11_g106200.22120.54090.4090
    MaGDSL10-2Ma10_g14470MaGDSL10-5Ma10_g216200.23610.98990.2385
    下载: 导出CSV
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出版历程
  • 收稿日期:  2022-03-24
  • 修回日期:  2022-06-14
  • 网络出版日期:  2022-12-28
  • 刊出日期:  2022-11-28

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