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作物学报 ›› 2022, Vol. 48 ›› Issue (6): 1357-1371.doi: 10.3724/SP.J.1006.2022.14091

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

甘蓝型油菜BnCNGC基因家族鉴定及其在核盘菌侵染和PEG处理下的表达特性分析

陈松余(), 丁一娟, 孙峻溟, 黄登文, 杨楠, 代雨涵, 万华方*(), 钱伟   

  1. 西南大学农学与生物科技学院 / 西南大学农业科学研究院, 重庆 400716
  • 收稿日期:2021-05-18 接受日期:2021-09-09 出版日期:2022-06-12 网络出版日期:2021-10-11
  • 通讯作者: 万华方
  • 作者简介:E-mail: chensongyu1123@163.com
  • 基金资助:
    重庆市自然科学基金项目(cstc2020jcyj-msxmX0957);国家重点研发计划项目(2018YFD0100500)

Genome-wide identification of BnCNGC and the gene expression analysis in Brassica napus challenged with Sclerotinia sclerotiorum and PEG-simulated drought

CHEN Song-Yu(), DING Yi-Juan, SUN Jun-Ming, HUANG Deng-Wen, YANG Nan, DAI Yu-Han, WAN Hua-Fang*(), QIAN Wei   

  1. College of Agronomy and Biotechnology, Southwest University / Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
  • Received:2021-05-18 Accepted:2021-09-09 Published:2022-06-12 Published online:2021-10-11
  • Contact: WAN Hua-Fang
  • Supported by:
    Natural Science Foundation of Chongqing, China(cstc2020jcyj-msxmX0957);National Key Research and Development Program of China(2018YFD0100500)

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摘要：

CNGC是植物中普遍存在的环核苷酸门控通道, 对植物的逆境响应有重要作用。系统分析甘蓝型油菜BnCNGC基因家族成员全基因组分布、结构、进化及其响应不同逆境胁迫的表达特性, 对于阐明其生物学功能具有重要意义。本研究利用拟南芥和甘蓝CNGC蛋白保守结构域及特异基序氨基酸序列在全基因组水平鉴定了甘蓝型油菜BnCNGC家族成员, 分析其基因结构、染色体定位、蛋白理化性质、蛋白保守结构域、系统进化及启动子顺式作用元件等。利用转录组数据, 筛选甘蓝型油菜逆境响应候选BnCNGC成员, 并采用实时荧光定量PCR分析其在核盘菌、PEG模拟干旱胁迫下的表达模式。结果显示, 共鉴定到49个甘蓝型油菜BnCNGC成员, 分布于除A08、C06的17对染色体上, 含有5~10个内含子, 其上游1500 bp包含大量逆境胁迫响应元件。BnCNGC家族成员编码的蛋白质含413~801个氨基酸, 相对分子量(MW)范围47.62~110.58 kD, 等电点(pI)范围6.10~9.88。系统进化分析表明, BnCNGC分为Group I、II、III和IV四类。转录组数据分析表明, BnCNGC9、BnCNGC27和BnCNGC48均参与逆境胁迫响应。实时荧光定量PCR分析表明, 甘蓝型油菜叶片中BnCNGC9、BnCNGC27和BnCNGC48均在核盘菌胁迫下表达下调, 下调量分别为48.2%~99.1%、79.4%~87.1%和39.7%~92.6%。PEG模拟干旱胁迫时, 甘蓝油菜叶片中BnCNGC9在处理24 h后上调3.34倍, BnCNGC48在处理48 h后上调6.27倍, BnCNGC27对干旱胁迫不敏感。

关键词: 甘蓝型油菜, CNGC基因家族, 核盘菌, PEG模拟干旱, 表达分析

Abstract:

CNGCs are common cyclic nucleotide-gated channel proteins in plants, which play important roles in plant stress response. In order to elucidate the biological function of the BnCNGC genes in Brassica napus, we identified the BnCNGC family members in the genome and analyzed the distribution, structure, evolution, and the expression of candidate members in B. napus exposed to Sclerotinia sclerotiorum or PEG-simulated drought. In this study, employing CNGC amino acid sequences of Arabidopsis thaliana and Brassica oleracea as references, the homologies were acquired using BLASTP software in Brassica napus Genome Browser, and the gene family members were identified according to the conserved domain and specific motif of BnCNGC in plants. The gene structure, chromosome distribution, protein physicochemical property, subcellular localization, phylogenetic evolution, and promoter cis-acting regulatory elements were analyzed. The relative expression profiles of the candidate BnCNGC genes, screened out based on the transcriptome data in B. napus challenged with S. sclerotiorum or PEG-simulated drought, were analyzed by qRT-PCR. As a result, a total of 49 BnCNGC genes were identified in B. napus genome. They were distributed at 17 pairs of chromosomes, except for A08 and C06, and generally had 5-10 introns. The 1500 bp region in the upstream sequence of BnCNGC contained lots of cis-acting regulatory elements involved in stress response. Most of the corresponding proteins were composed of 413-801 amino acids with molecular weight (MW) of 47.62-110.58 kD and isoelectric point (pI) of 6.10-9.88. All the identified family members had specific motif of CNGC in the CNBD region. Phylogenetic analysis showed that BnCNGC were divided into four categories, namely Group I, II, III, and IV. Transcriptome data analysis revealed that BnCNGC9, BnCNGC27, and BnCNGC48 were involved in stress response. The relative expression levels of the three genes were detected in B. napus leaves exposed to different stresses. All were down-regulated by 48.2%-99.1%, 79.4%-87.1%, and 39.7%-92.6% under inoculation with Sclerotinia sclerotiorum, respectively. The relative expression levels of BnCNGC9 and BnCNGC48 were increased 3.34 times and 6.27 times at 24 and 48 hours after simulated drought stress, respectively, thus BnCNGC27 was not sensitive to drought stress.

Key words: Brassica napus, CNGC gene family, Sclerotinia sclerotiorum, PEG-simulated drought, relative expression analysis

表1

实时荧光定量PCR引物"

基因名称
Gene name		 基因号
Gene ID		 正向引物序列
Forward sequence (5′-3′)		 反向引物序列
Reverse sequence (5′-3′)
BnCNGC9 BnaA03g34680D AGTTACCCTCTTTCCTCTACTCGT GTGCGGCTTTGAGCAGCTT
BnCNGC27 BnaA10g18740D ATAAATTCGCAAACGAGCGC GAACCGCCTACACCACCAC
BnCNGC48 BnaC09g42720D GAGCAGCAGCAGCAGCAGC CGGGCTCGAACCGGGTC
BnActin7 BnaA01g27090D CTGGAATTGCTGACCGTATGAG ATCTGTTGGAAAGTGCTGAGGG

图1

甘蓝型油菜BnCNGC家族成员的染色体分布"

图2

甘蓝型油菜BnCNGC家族成员的cNMP-binding/CNBD 特异基序 特异基序中特定氨基酸位置用方括号标识。X代表任何氨基酸, 圆括号内的数字表示氨基酸的数量。深蓝色、粉色和浅蓝色标识的氨基酸分别表示49个BnCNGC之间单个氨基酸100%、>75%和>50%的相似性。"

表2

甘蓝型油菜BnCNGC蛋白特征参数及亚细胞定位预测"

CNGC蛋白
CNGC
protein		 基因号
Gene ID		 染色体
Chr.		 起始位置
Initial
position		 终止位置
End
position		 氨基酸数
Amino acid amounts		 等电点
pI		 分子量
MW (kD)		 总平均
亲水性
GRAVY		 亚细胞定位
Subcellular localization
BnCNGC1 BnaA01g06670D A01 3095672 3099840 694 8.35 80.77 -0.205 质膜Plasma membrane
BnCNGC2 BnaA01g22170D A01 14545425 14551189 801 9.21 90.74 0.028 质膜Plasma membrane
BnCNGC3 BnaA01g27850D A01 19425000 19428539 760 9.57 86.26 -0.064 质膜Plasma membrane
BnCNGC4 BnaA01g27860D A01 19430256 19433767 743 9.64 85.28 -0.138 质膜Plasma membrane
BnCNGC5 BnaA02g07990D A02 3784851 3788310 721 9.13 82.42 -0.123 质膜Plasma membrane
BnCNGC6 BnaA02g09790D A02 4902667 4907022 621 9.38 71.77 -0.008 质膜Plasma membrane
BnCNGC7 BnaA02g10440D A02 5360323 5362868 711 9.38 82.56 -0.178 质膜Plasma membrane
BnCNGC8 BnaA03g26780D A03 13180480 13184496 705 9.26 81.49 -0.212 质膜Plasma membrane
BnCNGC9 BnaA03g34680D A03 16863304 16866599 680 8.91 77.60 -0.147 质膜Plasma membrane
BnCNGC10 BnaA03g34700D A03 16872203 16875542 654 8.92 74.72 -0.053 质膜Plasma membrane
BnCNGC11 BnaA03g50250D A03 26087831 26090699 741 9.29 84.40 -0.157 质膜Plasma membrane
BnCNGC12 BnaA04g14030D A04 11848036 11851336 736 9.44 84.50 -0.199 质膜Plasma membrane
BnCNGC13 BnaA04g14530D A04 12210464 12213711 703 9.33 81.07 -0.077 质膜Plasma membrane
BnCNGC14 BnaA04g15220D A04 12665265 12668409 647 9.50 74.80 -0.028 质膜Plasma membrane
BnCNGC15 BnaA05g01380D A05 808631 812078 702 9.14 81.03 -0.154 质膜Plasma membrane
BnCNGC16 BnaA05g22550D A05 17157632 17161030 753 9.55 85.87 -0.081 质膜Plasma membrane
BnCNGC17 BnaA05g22560D A05 17162980 17166118 751 9.19 86.39 -0.186 质膜Plasma membrane
BnCNGC18 BnaA05g22570D A05 17167881 17171529 790 9.71 90.63 -0.185 质膜Plasma membrane
BnCNGC19 BnaA06g10680D A06 5629756 5632689 722 9.50 82.80 -0.204 质膜Plasma membrane
BnCNGC20 BnaA06g16940D A06 9550763 9553801 706 8.46 81.62 -0.247 质膜Plasma membrane
BnCNGC21 BnaA07g13760D A07 12144138 12147369 684 9.68 79.43 -0.102 质膜Plasma membrane
BnCNGC22 BnaA07g17630D A07 14705083 14708986 688 8.68 78.43 -0.092 质膜Plasma membrane
BnCNGC23 BnaA09g41300D A09 28879650 28883074 715 8.85 82.39 -0.110 质膜Plasma membrane
BnCNGC24 BnaA09g41750D A09 29111335 29114828 737 9.44 84.65 -0.181 质膜Plasma membrane
BnCNGC25 BnaA10g06480D A10 4931547 4934085 720 9.57 83.90 -0.194 质膜Plasma membrane
BnCNGC26 BnaA10g07330D A10 5759951 5765207 699 8.60 80.72 -0.173 质膜Plasma membrane
BnCNGC27 BnaA10g18740D A10 13494368 13497571 719 9.56 82.00 0.012 质膜Plasma membrane
BnCNGC28 BnaA10g19030D A10 13658839 13663652 973 7.24 110.58 -0.284 质膜Plasma membrane
BnCNGC29 BnaC01g08020D C01 4234002 4238184 705 9.01 81.88 -0.185 质膜Plasma membrane
BnCNGC30 BnaC01g34960D C01 34227372 34232651 734 9.20 82.98 0.033 质膜Plasma membrane
BnCNGC31 BnaC02g11090D C02 6416508 6419623 721 9.21 82.52 -0.122 质膜Plasma membrane
BnCNGC32 BnaC02g14560D C02 10092252 10095260 711 9.35 82.54 -0.179 质膜Plasma membrane
BnCNGC33 BnaC03g31720D C03 19518056 19522572 704 9.18 81.33 -0.212 质膜Plasma membrane
BnCNGC34 BnaC03g40070D C03 25130865 25135231 413 6.10 47.62 -0.098 质膜Plasma membrane
BnCNGC35 BnaC04g01250D C04 984082 987459 701 9.40 80.79 -0.137 质膜Plasma membrane
BnCNGC36 BnaC04g16000D C04 14008149 14011414 684 9.68 79.49 -0.108 质膜Plasma membrane
BnCNGC37 BnaC04g36270D C04 37794024 37797281 714 9.16 82.28 -0.081 质膜Plasma membrane
BnCNGC38 BnaC04g36890D C04 38310006 38313393 745 9.45 85.22 -0.184 质膜Plasma membrane
CNGC蛋白
CNGC
protein		 基因号
Gene ID		 染色体
Chr.		 起始位置
Initial
position		 终止位置
End
position		 氨基酸数
Amino acid amounts		 等电点
pI		 分子量
MW (kD)		 总平均
亲水性
GRAVY		 亚细胞定位
Subcellular localization
BnCNGC39 BnaC04g38170D C04 39436436 39439178 647 9.50 74.82 -0.016 质膜Plasma membrane
BnCNGC40 BnaC05g12210D C05 7083786 7086776 722 9.50 82.84 -0.207 质膜Plasma membrane
BnCNGC41 BnaC05g35840D C05 35081609 35084991 750 9.60 85.61 -0.072 质膜Plasma membrane
BnCNGC42 BnaC05g35850D C05 35087166 35090279 750 9.20 86.57 -0.201 质膜Plasma membrane
BnCNGC43 BnaC05g35860D C05 35092931 35096102 762 9.88 87.76 -0.163 质膜Plasma membrane
BnCNGC44 BnaC07g42730D C07 42093754 42097033 741 9.29 84.49 -0.169 质膜Plasma membrane
BnCNGC45 BnaC08g33890D C08 32189874 32193318 715 8.85 82.34 -0.111 质膜Plasma membrane
BnCNGC46 BnaC09g29350D C09 31884192 31886408 600 9.45 70.24 -0.169 质膜Plasma membrane
BnCNGC47 BnaC09g30630D C09 33625801 33632938 698 8.42 80.76 -0.192 质膜Plasma membrane
BnCNGC48 BnaC09g42460D C09 44006544 44009743 719 9.58 82.17 0.002 质膜Plasma membrane
BnCNGC49 BnaC09g42720D C09 44128700 44131819 714 8.60 81.30 -0.139 质膜Plasma membrane

图3

甘蓝、白菜、番茄、甘蓝型油菜(●)、拟南芥和水稻CNGC家族的系统进化树"

图4

甘蓝型油菜BnCNGC家族的基因结构"

图5

甘蓝型油菜BnCNGC蛋白保守结构域"

表3

甘蓝型油菜BnCNGC基因家族启动子顺式作用元件预测"

元件类型
Element type		 特性
Characteristic		 基因
Gene
CGTCA-motif 茉莉酸甲酯响应元件
cis-acting regulatory element involved
in the MeJA-responsiveness		 BnCNGC1-BnCNGC6, BnCNGC10, BnCNGC12-BnCNGC15, BnCNGC17, BnCNGC18-BnCNGC20, BnCNGC23-BnCNGC26, BnCNGC29, BnCNGC31-BnCNGC39, BnCNGC42-BnCNGC45, BnCNGC49
MBS 干旱响应元件
MYB binding site involved in drought-inducibility		 BnCNGC2, BnCNGC5, BnCNGC12, BnCNGC16, BnCNGC17, BnCNGC21, BnCNGC29, BnCNGC31, BnCNGC34, BnCNGC36, BnCNGC37, BnCNGC41, BnCNGC46, BnCNGC47
元件类型
Element type		 特性
Characteristic		 基因
Gene
ABRE 脱落酸响应元件
cis-acting element involved in abscisic
acid responsiveness		 BnCNGC3, BnCNGC4, BnCNGC6, BnCNGC8, BnCNGC10, BnCNGC12, BnCNGC13, BnCNGC18-BnCNGC25, BnCNGC27, BnCNGC28, BnCNGC30, BnCNGC33, BnCNGC34, BnCNGC36, BnCNGC39-BnCNGC41, BnCNGC43, BnCNGC46-BnCNGC49
GARE-motif 赤霉素响应元件
Gibberellin-responsive element		 BnCNGC6, BnCNGC20-BnCNGC22, BnCNGC27, BnCNGC36, BnCNGC38, BnCNGC48
WUN-motif 损伤响应元件
Wound-responsive element		 BnCNGC1, BnCNGC3, BnCNGC4, BnCNGC9, BnCNGC11, BnCNGC14, BnCNGC16, BnCNGC21, BnCNGC22, BnCNGC25, BnCNGC27, BnCNGC29, BnCNGC32, BnCNGC33, BnCNGC38, BnCNGC41-BnCNGC43, BnCNGC48
TCA-element 水杨酸响应元件
cis-acting element involved in salicylic
acid responsiveness		 BnCNGC15, BnCNGC16, BnCNGC18, BnCNGC23, BnCNGC25, BnCNGC27, BnCNGC28, BnCNGC31, BnCNGC35-BnCNGC39, BnCNGC41, BnCNGC43, BnCNGC46
TGA-element 生长素响应元件
Auxin-responsive element		 BnCNGC1-BnCNGC3, BnCNGC11, BnCNGC20, BnCNGC21, BnCNGC26, BnCNGC30, BnCNGC32, BnCNGC39, BnCNGC40, BnCNGC46, BnCNGC47
TC-rich repeats 逆境与防御反应响应元件
cis-acting element involved in stress and defense responsiveness		 BnCNGC1, BnCNGC7, BnCNGC8, BnCNGC11, BnCNGC14, BnCNGC19, BnCNGC21, BnCNGC25, BnCNGC29, BnCNGC30, BnCNGC33, BnCNGC36, BnCNGC38, BnCNGC40, BnCNGC43, BnCNGC44
AT-rich sequence 诱导子激活元件
Element for maximal elicitor-mediated activation		 BnCNGC2, BnCNGC3, BnCNGC8, BnCNGC9, BnCNGC12, BnCNGC17, BnCNGC19, BnCNGC20, BnCNGC25, BnCNGC44

附表1

核盘菌侵染甘蓝型油菜叶片的CNGC转录组数据"

基因名称
Gene name		 FPKM-0 FPKM-12 FPKM-24 FPKM-48
BnCNGC2 0.76 0.30 0.53 0.10
BnCNGC32 1.65 1.89 0.65 0.54
BnCNGC24 0.88 1.06 0.40 0.72
BnCNGC29 1.50 1.79 1.68 1.59
BnCNGC5 0.23 0.67 0.40 0.20
BnCNGC31 0.49 2.49 1.37 0.45
BnCNGC33 1.86 1.67 2.55 7.20
BnCNGC36 0.72 0.21 0.31 0.14
BnCNGC7 2.84 3.53 3.42 1.53
BnCNGC1 1.74 2.32 2.52 3.08
BnCNGC39 0.64 1.34 1.15 1.42
BnCNGC11 0.47 0.31 0.31 0.90
BnCNGC35 4.15 1.78 5.82 1.25
BnCNGC41 3.41 3.07 3.13 0.73
BnCNGC48 10.25 17.10 12.49 1.61
BnCNGC9 4.33 2.21 4.62 0.35
BnCNGC8 3.43 2.86 3.71 12.18
BnCNGC34 0.03 0.04 2.31 18.35
BnCNGC38 2.04 4.54 3.49 4.11
BnCNGC16 2.12 1.77 2.49 0.15
BnCNGC47 3.84 5.64 5.52 1.17
BnCNGC15 6.09 4.69 10.52 4.13

图6

基于转录组数据的甘蓝型油菜BnCNGC家族基因在PEG模拟干旱和核盘菌侵染下的表达水平 图中不同颜色的方格代表每个基因转录组测序所得的FPKM, 并取以2为底数的对数值。A和B为PEG模拟干旱胁迫下BnCNGC家族基因的表达模式, 数据源分别为PRJNA273932、PRJNA389508; PEG1、PEG2代表在PEG模拟干旱胁迫下具有低呼吸效率和高NADH含量的2个植株, PEG-12 h表示PEG模拟干旱处理12 h的植株。C: NCBI项目登录编号为PRJNA274853, 为核盘菌胁迫下甘蓝型油菜叶片BnCNGC家族基因的表达模式。D: 由本实验室前期测定的核盘菌侵染油菜叶片的转录组数据(附表1)筛选得到的BnCNGC家族基因的表达模式。"

图7

甘蓝型油菜BnCNGC部分成员在核盘菌侵染或PEG模拟干旱处理条件下的相对表达量 A: 核盘菌侵染(S. s); B: PEG模拟干旱(sd)。误差线代表3个生物学重复的标准偏差, * 代表同一时间点处理与对照间差异显著(P < 0.05), ns代表同一时间点处理与对照间显著不差异。"

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