园艺学报 ›› 2021, Vol. 48 ›› Issue (5): 947-959.doi: 10.16420/j.issn.0513-353x.2020-0800
牛西强1, 罗潇云1, 康凯程2, 黄先忠1,2,*(), 胡能兵1, 隋益虎1, 艾昊1
收稿日期:
2020-12-07
修回日期:
2021-03-21
出版日期:
2021-05-25
发布日期:
2021-06-07
通讯作者:
黄先忠
E-mail:huangxz@ahstu.edu.cn
基金资助:
NIU Xiqaing1, LUO Xiaoyun1, KANG Kaicheng2, HUANG Xianzhong1,2,*(), HU Nengbing1, SUI Yihu1, AI Hao1
Received:
2020-12-07
Revised:
2021-03-21
Online:
2021-05-25
Published:
2021-06-07
Contact:
HUANG Xianzhong
E-mail:huangxz@ahstu.edu.cn
摘要:
植物磷脂酰乙醇胺结合蛋白(Phosphatidyl ethanolamine-binding protein,PEBP)分为MFT、FT和TFL1共3个亚家族,其中FT和TFL1亚家族蛋白构成了植物的成花激素—抗成花激素系统,调控开花时间和株形结构。基于辣椒(Capsicum annuum)全基因组数据,对辣椒PEBP基因家族进行鉴定,并对基因和蛋白结构、比较进化、共线性和组织表达特征等进行了分析。结果表明,辣椒基因组包含9个PEBP成员,并且9个基因均含有4个外显子和3个内含子,定位在6条染色体上,其编码蛋白质定位在细胞质和细胞核中。与番茄PEBP同源基因的比较进化分析表明,辣椒的PEBP基因受纯化选择,其中CaFT2和CaFT4在进化中较稳定,辣椒和番茄之间存在8对共线性基因。qRT-PCR分析表明CaPEBP基因在所检测的组织中明显差异表达,如CaMFT/CaTFL1-1在果实中高表达,CaFT1在叶片中相对表达量最高,CaFT3在顶端分生组织和花中表达量最高,CaTFL1-4在根中特异表达。
中图分类号:
牛西强, 罗潇云, 康凯程, 黄先忠, 胡能兵, 隋益虎, 艾昊. 辣椒PEBP基因家族的全基因组鉴定、比较进化与组织表达分析[J]. 园艺学报, 2021, 48(5): 947-959.
NIU Xiqaing, LUO Xiaoyun, KANG Kaicheng, HUANG Xianzhong, HU Nengbing, SUI Yihu, AI Hao. Genome-wide Identification,Comparative Evolution and Expression Analysis of PEBP Gene Family from Capsicum annuum[J]. Acta Horticulturae Sinica, 2021, 48(5): 947-959.
基因 Gene | 上游引物序列(5′-3′) Forward primer sequence | 下游引物序列(5′-3′) Reverse primer sequence |
---|---|---|
CaMFT | GCTCCAAGTCCAAGTGAACC | CCGAGATCAAGATGCTGTGC |
CaFT1 | CAATGCGCCAGACATAATTG | AGACGACGACCACCAGTACC |
CaFT2 | GGTTCATATTGGAGGCAACG | TGCTGGGATATCTGTGACCA |
CaFT3 | TGGTACTGATTTGAGGCCTTCT | CTCAAATTTGGGTTGCTAGGAC |
CaFT4 | TGGTACAAATTTGAGGCCTTCT | GCATTTCCAAAGGTTACTCCTG |
CaTFL1-1 | ACCTCCACTGGATTGTGACAG | CATTCTCTGCAGCAAACCTTC |
CaTFL1-2 | TAGAGGGGCTTGTGAACCAC | TCTTCACCCCCAATCTCAAC |
CaTFL1-3 | ACGGACATTCCAGGCACTAC | CAGAATCGATCCCTGGAGAG |
CaTFL1-4 | AGATCCTGATGTTCCTGGCC | CTGAACTCCGACGTTTCTGC |
CaUBI3 | TGTCCATCTGCTCTCTGTTG | CACCCCAAGCACAATAAGAC |
表1 辣椒PEBP基因家族基因表达分析的实时荧光定量PCR引物
Table 1 qRT-PCR primers for expression analysis of PEBP in Capsicum annuum
基因 Gene | 上游引物序列(5′-3′) Forward primer sequence | 下游引物序列(5′-3′) Reverse primer sequence |
---|---|---|
CaMFT | GCTCCAAGTCCAAGTGAACC | CCGAGATCAAGATGCTGTGC |
CaFT1 | CAATGCGCCAGACATAATTG | AGACGACGACCACCAGTACC |
CaFT2 | GGTTCATATTGGAGGCAACG | TGCTGGGATATCTGTGACCA |
CaFT3 | TGGTACTGATTTGAGGCCTTCT | CTCAAATTTGGGTTGCTAGGAC |
CaFT4 | TGGTACAAATTTGAGGCCTTCT | GCATTTCCAAAGGTTACTCCTG |
CaTFL1-1 | ACCTCCACTGGATTGTGACAG | CATTCTCTGCAGCAAACCTTC |
CaTFL1-2 | TAGAGGGGCTTGTGAACCAC | TCTTCACCCCCAATCTCAAC |
CaTFL1-3 | ACGGACATTCCAGGCACTAC | CAGAATCGATCCCTGGAGAG |
CaTFL1-4 | AGATCCTGATGTTCCTGGCC | CTGAACTCCGACGTTTCTGC |
CaUBI3 | TGTCCATCTGCTCTCTGTTG | CACCCCAAGCACAATAAGAC |
基因 Gene | 基因登录号 GenBank ID | 染色体 Chr. No. | 开放阅读 框长度/bp ORF | 氨基酸数/aa Amino acid | 分子量/kD Molecular weight | 等电点 pI | 亚细胞定位 Subcellular location |
---|---|---|---|---|---|---|---|
CaMFT | PHT88651.1 | Chr03 | 522 | 173 | 18.98 | 9.20 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaFT1 | PHT82416.1 | Chr05 | 531 | 176 | 19.69 | 6.82 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaFT2 | PHT82541.1 | Chr05 | 528 | 175 | 19.81 | 7.76 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaFT3 | PHT65068.1 | Chr12 | 534 | 177 | 19.98 | 8.64 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaFT4 | PHT61065.1 | Sca. 2174 | 531 | 176 | 19.71 | 6.73 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaTFL1-1 | PHT94378.1 | Chr01 | 534 | 177 | 19.92 | 9.01 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaTFL1-2 | PHT87214.1 | Chr03 | 528 | 175 | 19.54 | 9.07 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaTFL1-3 | PHT80015.1 | Chr06 | 528 | 175 | 19.93 | 8.64 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaTFL1-4 | PHT71587.1 | Chr09 | 519 | 172 | 19.55 | 7.97 | 细胞质和细胞核 Cytoplasmic and nuclear |
表2 辣椒(Capsicum annuum)PEBP基因家族信息
Table 2 The information of PEBP gene family in Capsicum annuum
基因 Gene | 基因登录号 GenBank ID | 染色体 Chr. No. | 开放阅读 框长度/bp ORF | 氨基酸数/aa Amino acid | 分子量/kD Molecular weight | 等电点 pI | 亚细胞定位 Subcellular location |
---|---|---|---|---|---|---|---|
CaMFT | PHT88651.1 | Chr03 | 522 | 173 | 18.98 | 9.20 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaFT1 | PHT82416.1 | Chr05 | 531 | 176 | 19.69 | 6.82 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaFT2 | PHT82541.1 | Chr05 | 528 | 175 | 19.81 | 7.76 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaFT3 | PHT65068.1 | Chr12 | 534 | 177 | 19.98 | 8.64 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaFT4 | PHT61065.1 | Sca. 2174 | 531 | 176 | 19.71 | 6.73 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaTFL1-1 | PHT94378.1 | Chr01 | 534 | 177 | 19.92 | 9.01 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaTFL1-2 | PHT87214.1 | Chr03 | 528 | 175 | 19.54 | 9.07 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaTFL1-3 | PHT80015.1 | Chr06 | 528 | 175 | 19.93 | 8.64 | 细胞质和细胞核 Cytoplasmic and nuclear |
CaTFL1-4 | PHT71587.1 | Chr09 | 519 | 172 | 19.55 | 7.97 | 细胞质和细胞核 Cytoplasmic and nuclear |
图1 拟南芥、番茄和辣椒PEBP氨基酸多重序列比对 三角形表示决定FT-like和TFL1-like功能的关键氨基酸,方框表示[FYL]-x-[LVM]-[LIVF]-x-[TIVM]-[DC]-P-D-x-P-[SNG]-x(10)-H和G-X-H-R保守基序。At:拟南芥;Sl:番茄;Ca:辣椒。
Fig. 1 Multiple amino acid sequence alignment of PEBP proteins from Arabidopsis thaliana,Solanum lycopersicum and Capsicum annuum The red triangles represent the key amino acids that determine the functions of FT-like and TFL1-like,the rectangles represent [FYL]-x-[LVM]-[LIVF]-X-[TIVM]-[DC]-P-d-x-P-[SNG]-x(10)-H and G-X-H-R conserved motif. At:Arabidopsis thaliana;Sl:Solanum lycopersicum;Ca:Capsicum annuum.
图2 CaPEBP进化树分析、辣椒PEBP基因外显子-内含子结构和motif分析 分支上的数值表示自展值;标尺表示分支长度。
Fig. 2 Phylogentic tree of CaPEBP,gene intron/exon structure and conserved motif analysis of the PEBP genes in Capsicum annuum The number in the tree represents boots value. The scale bar represents branch length.
基序 Motif | 长度/aa Length | 氨基酸保守序列 Amino acid conserved sequence |
---|---|---|
motif 1 | 29 | DPLVVGRVIGDVVDPFTPSVKMSVVYNNR |
motif 2 | 31 | YNGHELRPSQIAAQPRVEIGGNDLRTFYTLI |
motif 3 | 50 | MTDPDAPSPSBPYLREYLHWJVTDIPGTTDVSFGNEIVCYESPRPSIGIH |
motif 4 | 11 | RYVFVLFRQLG |
motif 5 | 41 | VYAPTWRDHFNTRDFAEENNLGSPVAAVYFNCQRETATRRR |
表3 辣椒PEBP蛋白氨基酸保守序列
Table 3 Conserved motifs of the PEBP proteins in Capsicum annuum
基序 Motif | 长度/aa Length | 氨基酸保守序列 Amino acid conserved sequence |
---|---|---|
motif 1 | 29 | DPLVVGRVIGDVVDPFTPSVKMSVVYNNR |
motif 2 | 31 | YNGHELRPSQIAAQPRVEIGGNDLRTFYTLI |
motif 3 | 50 | MTDPDAPSPSBPYLREYLHWJVTDIPGTTDVSFGNEIVCYESPRPSIGIH |
motif 4 | 11 | RYVFVLFRQLG |
motif 5 | 41 | VYAPTWRDHFNTRDFAEENNLGSPVAAVYFNCQRETATRRR |
辣椒基因 Gene ID in C. annuum | 番茄基因 Gene ID in S. lycopersicum | 基因模型 Gene model | 非同义突变频/Ka | 同义突变频率/Ks | Ka/Ks |
---|---|---|---|---|---|
CaMFT | SlMFT | MFT-like | 0.07 | 0.44 | 0.17 |
CaFT1 | SlSP5G | FT-like | 0.03 | 0.39 | 0.09 |
CaFT2 | SlSP6A | FT-like | 0.06 | 0.24 | 0.27 |
CaFT3 | SlSP5G3 | FT-like | 0.03 | 0.29 | 0.11 |
CaFT4 | SlSP5G1 | FT-like | 0.18 | 0.48 | 0.37 |
CaTFL1-1 | SlCEN1.3 | TFL1-like | 0.06 | 0.56 | 0.11 |
CaTFL1-2 | SlCEN1.1 | TFL1-like | 0.04 | 0.57 | 0.08 |
CaTFL1-3 | SlSP | TFL1-like | 0.03 | 0.22 | 0.15 |
SlCEN1.3 | TFL1-like | 0.26 | 1.16 | 0.22 | |
CaTFL1-4 | SlSP9D | TFL1-like | 0.05 | 0.36 | 0.13 |
表4 辣椒和番茄PEBP同源基因的Ka/Ks
Table 4 Ka/Ks values of PEBP genes between Capsicum annuum and Solanum lycopersicum
辣椒基因 Gene ID in C. annuum | 番茄基因 Gene ID in S. lycopersicum | 基因模型 Gene model | 非同义突变频/Ka | 同义突变频率/Ks | Ka/Ks |
---|---|---|---|---|---|
CaMFT | SlMFT | MFT-like | 0.07 | 0.44 | 0.17 |
CaFT1 | SlSP5G | FT-like | 0.03 | 0.39 | 0.09 |
CaFT2 | SlSP6A | FT-like | 0.06 | 0.24 | 0.27 |
CaFT3 | SlSP5G3 | FT-like | 0.03 | 0.29 | 0.11 |
CaFT4 | SlSP5G1 | FT-like | 0.18 | 0.48 | 0.37 |
CaTFL1-1 | SlCEN1.3 | TFL1-like | 0.06 | 0.56 | 0.11 |
CaTFL1-2 | SlCEN1.1 | TFL1-like | 0.04 | 0.57 | 0.08 |
CaTFL1-3 | SlSP | TFL1-like | 0.03 | 0.22 | 0.15 |
SlCEN1.3 | TFL1-like | 0.26 | 1.16 | 0.22 | |
CaTFL1-4 | SlSP9D | TFL1-like | 0.05 | 0.36 | 0.13 |
图3 番茄和辣椒的PEBP基因的共线性分析 红色线条表示种间PEBP共线性关系;灰色线条代表种间所有基因成员的共线性关系。
Fig. 3 Collinearity analysis of orthologous PEBP gene pairs betweenSolanum lycopersicum andCapsicum annuum The red lines representPEBP collinearity between species,and the gray lines are collinearity of all gene members between species.
图4 辣椒根、茎、叶、顶端分生组织(SAM)、花和果(果实发育的第6时期)中PEBP基因表达的qRT-PCR分析
Fig. 4 Expression analysis of CaPEBP genes by qRT-PCR in roots,stems,leaves,shoot apical meristems(SAM),flowers and fruit(6th stage of fruit development)of pepper
图6 辣椒果实发育(果1 ~ 果6分别表示果实发育的不同阶段)中4个CaPEBP基因的表达特征
Fig. 6 Expression profiles of four CaPEBPgenes at different developmental stages(Fruit 1-6)in fruit of Capsicum annuum
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