Genome-wide Identification,Comparative Evolution and Expression Analysis of PEBP Gene Family from Capsicum annuum

doi:10.16420/j.issn.0513-353x.2020-0800

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (5): 947-959.doi: 10.16420/j.issn.0513-353x.2020-0800

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Genome-wide Identification,Comparative Evolution and Expression Analysis of PEBP Gene Family from Capsicum annuum

NIU Xiqaing¹, LUO Xiaoyun¹, KANG Kaicheng², HUANG Xianzhong¹^,²^,^*(), HU Nengbing¹, SUI Yihu¹, AI Hao¹

¹College of Agriculture,Anhui Science and Technology University,Fengyang,Anhui 233100,China
²Plant Genomics Laboratory,College of Life Sciences,Shihezi University,Shihezi,Xinjiang 832003,China

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

Abstract

Abstract:

The plant phosphatidyl ethanolamine-binding protein(PEBP)is divided into three subfamilies:MFT-like,FT-like,and TFL1-like. The FT and TFL1 subfamilies comprise the florigen-antiflorigen system of plants that regulate flowering time and plant architecture. Here,the PEBP gene family was identified by genome-wide identification of the whole genome data of the annual pepper (Capsicum annuum),and the structures of gene and protein,comparative evolution,collinearity and tissue expression profile were analyzed. The results showed that the C. annuum genome contains nine PEBP genes,including one MFT,four FT,and four TFL1 genes. All the nine PEBPgenes contain four exons and three introns,which are located on six chromosomes. Moreover,these nine PEBP proteins are located in the cytoplasm and nucleus. Comparative evolution analysis between C. annuum and Solanum lycopersicum showed that CaPEBP genes were subjected to purification selection during evolution. Among them,CaFT2 and CaFT4 were relatively stable during evolution;there were eight pairs of collinearity genes between pepper and tomato. The qRT-PCR expression profile ofCaPEBP genes were significantly differentially expressed in the tissues tested. For example,CaMFT/CaTFL1-1 was highly expressed in fruits,and CaFT1 had the highest relative expression level in leaves;the expression of CaFT3 was the highest in shoot apical meristem and flower,while CaTFL1-4 was specifically expressed in roots.

Key words: Capsicum annuum, florigen, PEBP gene family, genome-wide analysis, flowering regulation, gene expression

CLC Number:

S641.3

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.

Figures/Tables 10

References 35

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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	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

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

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

Genome-wide Identification,Comparative Evolution and Expression Analysis of PEBP Gene Family from Capsicum annuum

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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
CaTFL1-3	SlCEN1.3	TFL1-like	0.26	1.16	0.22
CaTFL1-4	SlSP9D	TFL1-like	0.05	0.36	0.13

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