基于盐胁迫转录组信息的蚕豆F-box基因家族分析

doi:10.3864/j.issn.0578-1752.2020.17.003

中国农业科学 ›› 2020, Vol. 53 ›› Issue (17): 3443-3454.doi: 10.3864/j.issn.0578-1752.2020.17.003

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于盐胁迫转录组信息的蚕豆F-box基因家族分析

郝树琳¹(),陈宏伟²,廖芳丽³,李莉²,刘昌燕²,刘良军²,万正煌²(),沙爱华¹()

¹长江大学农学院/主要粮食作物产业化湖北省协同创新中心,湖北荆州 434025
²湖北省农业科学院粮食作物研究所/粮食作物种质创新与遗传改良湖北省重点实验室,武汉 430064
³荆州市种子管理局,湖北荆州 434020

收稿日期:2019-12-19 接受日期:2020-03-05 出版日期:2020-09-01 发布日期:2020-09-11
联系方式: 郝树琳,E-mail：shulinlin6@163.com。
基金资助:
国家重点研发计划(2019YFD1001303/2019YFD1001300);国家现代农业产业技术体系建设项目(CARS-09);国家食用豆产业技术体系建设专项(CARS-08-G13);湖北省技术创新重大专项(2016ABA087);湖北省技术创新重大专项(2018ABA090)

Analysis of F-Box Gene Family Based on Salt-Stressed Transcriptome Sequencing in Vicia faba L.

HAO ShuLin¹(),CHEN HongWei²,LIAO FangLi³,LI Li²,LIU ChangYan²,LIU LiangJun²,WAN ZhengHuang²(),SHA AiHua¹()

¹College of Agriculture, Yangtze University/Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, Hubei
²Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430064
³Seed Authority of Jingzhou, Jingzhou 434020, Hubei

Received:2019-12-19 Accepted:2020-03-05 Published:2020-09-01 Online:2020-09-11

摘要/Abstract

摘要：

【目的】通过生物信息学方法分析蚕豆F-box基因家族成员的分布、结构及进化,研究家族成员在不同处理时间条件下的表达模式及对盐胁迫的响应,为该类基因生物学功能和盐胁迫机制的研究提供参考。【方法】基于蚕豆盐胁迫转录组测序（RNA-seq）数据,利用NR、Swiss-prot和PFAM 3个数据库和NCBI网站,对蚕豆F-box基因进行筛选注释;利用Web Logo 3、Prot Comp 9.0、MEGA-X和MEME等软件进行保守结构域、亚细胞定位、系统进化树和Motif等生物信息学分析。基于盐胁迫转录组数据分析蚕豆（yz17134耐盐和yz17078不耐盐）F-box基因家族在盐胁迫下的差异表达模式,并采用实时荧光定量PCR技术（qRT-PCR）检测部分家族成员在16和24 h的表达情况。【结果】基于盐胁迫转录组测序数据,注释得到161个蚕豆F-box基因,均含有F-box保守结构域。根据C端结构域的不同,将其分成11个亚族：FBX、FBXFBA、FBXLRR、FBXPP2、FBXKelch、FBXTUB、FBXFBD、FBXDUF、FBXACTIN、FBXWD40和FBO。保守结构域分析表明,F-box保守基序中包含1个极度保守的色氨酸残基。比较分析蚕豆F-box家族和拟南芥F-box家族共同构建的进化树,发现同一C端结构域的基因大多聚集在一起。亚细胞定位预测结果显示,124个F-box基因定位于细胞外,37个定位于细胞核中。基因结构分析表明,蚕豆F-box家族基因的DNA序列中均无内含子,且均由UTR区和CDS区组成。基于盐胁迫转录组数据的F-box差异表达模式分析表明,蚕豆F-box基因在2个不同处理时间点上的表达各不相同,在盐处理16 h的表达较为明显。qRT-PCR分析结果表明,在F-box家族成员中,共存在5个差异基因。其中Vf056266.1、Vf062764.1和Vf024236.1在盐处理16 h的表达量均上调,Vf060904.1和Vf045761.1在盐处理16 h的表达量均下调。【结论】蚕豆F-box基因家族注释得到161个蚕豆F-box基因,分为11个亚族。其中5个重要的F-box基因在不同盐处理时间的表达量存在差异。

关键词: 蚕豆, 转录组测序, F-box家族, 盐胁迫, 表达模式

Abstract:

【Objective】The distribution structure and evolution of F-box gene family members in Vicia faba were analyzed by bioinformatics method to study the expression patterns of family members and their responses to salt stress under different treatment times. It can provide a reference for the study of the biological function and the mechanism of F-box genes.【Method】Based on the salt-stressed transcriptome sequencing (RNA-seq) data, the NR, Swiss-Prot, PFAM and NCBI websites were used at the same time to screen and annotate the F-box genes of Vicia faba. The softwares including Web Logo 3, Prot Comp 9.0, MEGA-X and MEME were also applied to analyze the bioinformatics of conserved domain, subcellular localization, phylogenetic tree and Motif. Based on salt stress transcriptome data, the differential expression patterns of F-box gene family in Vicia faba (yz17134 salt tolerance and yz17078 salt intolerance) under salt stress were analyzed, and real-time fluorescence quantitative PCR (qRT-PCR) was used to verify the specific expression of part family members at 16 h and 24 h.【Result】Based on salt-stressed transcriptome sequencing (RNA-seq) data, 161 Vicia faba F-box genes were annotated and all contain F-box conserved domain. According to different C-terminal domains, they were divided into 11 subfamilies (FBX, FBXFBA, FBXLRR, FBXPP2, FBXKelch, FBXTUB, FBXFBD, FBXDUF, FBXACTIN, FBXWD40, and FBO). The analysis of the conserved domain showed that the F-box conserved Motif contained an extremely conserved tryptophan residue. By comparing and analyzing the evolutionary tree constructed by the F-box family of Vicia faba and the F-box family of Arabidopsis thaliana, it was found that most of the genes in the same C-terminal domain were clustered together. The results of subcellular localization prediction showed that 124 F-box genes were located outside the cell, and 37 F-box genes were located in the nucleus. The analysis of gene structure showed that there were no introns in the DNA sequences of the F-box family genes of Vicia faba, and all of them were composed of UTR zone and CDS zone. Analysis of F-box differential expression patterns based on salt-stressed transcriptome data showed that F-box gene expression in Vicia faba was diverse from each other at two different processing time points, the expression was more obvious at 16 hours after salt treatment. The results of qRT-PCR analysis showed that there were five different genes in the F-box family. The expressions of Vf056266.1, Vf062764.1 and Vf024236.1 were all up-regulated at 16 hours after salt treatment, Vf060904.1 and Vf045761.1 were both down-regulated at 16 hours after salt treatment.【Conclusion】161 Vicia faba F-box genes were identified by family annotation, and they were identified by family annotation, which were Evolutionarily divided into 11 subfamilies. 5 important genes were obtained through a series of bioinformatics analysis. What’s more, there exist difference among the expressions in diverse salt treatment time.

Key words: Vicia faba L., RNA-seq, F-box gene family, salt stress, expression pattern

郝树琳,陈宏伟,廖芳丽,李莉,刘昌燕,刘良军,万正煌,沙爱华. 基于盐胁迫转录组信息的蚕豆F-box基因家族分析[J]. 中国农业科学, 2020, 53(17): 3443-3454.

HAO ShuLin,CHEN HongWei,LIAO FangLi,LI Li,LIU ChangYan,LIU LiangJun,WAN ZhengHuang,SHA AiHua. Analysis of F-Box Gene Family Based on Salt-Stressed Transcriptome Sequencing in Vicia faba L.[J]. Scientia Agricultura Sinica, 2020, 53(17): 3443-3454.

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基因Gene	正向引物序列Forward primer sequence (5′-3′)	反向引物序列Reverse primer sequence (5′-3′)
Vf056266.1	CACGCCCAAAATCTCAAGGT	AAGTTGCTAGGCCTTCCAGT
Vf060904.1	TGAACGAAACTGGCTTGA	CGATGGTGCGATAGAGGA
Vf062764.1	TTACCAATAACCCTTCCAC	TCAATACGATTAGCACCCT
Vf024236.1	CTGCTGCTGTTGTGAAGA	AACCAAACGGGAGAAGAT
Vf045761.1	CCGTCTCATACTATCGTCTGTT	GGGTCGGCTTGGGAGGAAT
VfNADHD4	AGGGTTAGTGAGCACCATGC	ATAGCCAAAGGGAATACGCC

基于盐胁迫转录组信息的蚕豆F-box基因家族分析

Analysis of F-Box Gene Family Based on Salt-Stressed Transcriptome Sequencing in Vicia faba L.

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