| 引用本文: | 王明强,高贝,张道远.2个银叶真藓HSP70序列的生物信息学相关分析[J].生物信息学,2015,13(1):1-8. |
| WANG Mingqiang,GAO Bei,ZHANG Daoyuan.Bioinformatics relevant analysis of two heat shock protein 70 sequence from Bryum argenteum[J].Chinese Journal of Bioinformatics,2015,13(1):1-8. |
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| 摘要: |
| 从银叶真藓(Bryum argenteum)转录组数据库出发,使用Pfam数据库提供的HMM模型共得到33条长度大于200aa,注释的热休克蛋白BaHSP70；其中2条(BaHSP70-1, BaHSP70-2)具有完整ORF,NCBI核酸数据库登录号为KP087877和KP087878。使用生物信息学在线分析工具和软件,对真藓HSP70的两条蛋白质序列从氨基酸组成、保守结构域、理化性质、疏水性/亲水性、信号肽、蛋白质结构、模体的识别及同源性分析等方面进行了预测和分析。结果表明:2条BaHSP70s基因序列ORF全长分别为2 396 bp和2 356 bp,分别编码649aa和650aa。序列模体分析表明BaHSP70s和其它报道的植物HSP70均含有4个相同的模体,并且各模体在蛋白质序列上顺序一致。通过对2条BaHSP70s进行氨基酸多序列比对及基因树分析,发现BaHSP70-1和BaHSP70-2雪莲相似度最高,分别是91.2%和86.6%。本研究为进一步研究HSP70基因的克隆和功能验证奠定了基础。 |
| 关键词: 真藓 热激蛋白70 RNA-Seq 生物信息学 |
| DOI：10.3969/j.issn.1672-5565.2015.01.01 |
| 分类号:Q811.4 |
| 基金项目:NSFC-新疆青年人才联合项目(U1403302)。 |
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| Bioinformatics relevant analysis of two heat shock protein 70 sequence from Bryum argenteum |
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WANG Mingqiang1,2, GAO Bei1, ZHANG Daoyuan1
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(1.Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011,China ; 2.University of Chinese Academy of Sciences, Beijing 10049, China)
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| Abstract: |
| Our study utilizes the RNA-seq technology which is based on the Hi-seq 2000 sequencing platform from BGI to acquire the RNA sequences data from Bryum argenteumdealt with dehydration and rehydration stress. Using the Hidden Markov Model provided by the Pfam database, we have identified 33 HSP70 sequences with the length longer than 200aa. Two of them (BaHSP70-1,BaHSP70-2) contain Open Reading Frame, the Accession No. in NCBI nucleotide database are KP087877 and KP087878, respectively. Applying web-based bioinformatics tools and softwares, we predicted and analyzed B. argenteumHeat Shock Protein 70 sequences from the following aspects: amino acid component, conserved domain, physicochemical property, hydrophobicity and hydrophily, singal peptide, protein structure, motif recognition, homologous analysis. The result showed the length of two possessed complete ORF HSP70s are 649aa and 650aa respectively. The length of corresponding anscripts in the transcriptome database are 2 396 bp and 2 356 bp. Sequence motif analysis indicates B. argenteumand other plant species have 4 identical motifs. Meanwhile, the order of the motifs arranged in protein sequence is the same in all selected species. Multiple sequence alignment and homologous analysis demonstrated that HSP70-1 and HSP70-2 are most similar to Saussureaup to the similarity of 91.2% and 86.6% respectively. This study laid fundation for the B.argenteumfurther research in gene clone and functional confirmation. |
| Key words: Bryum argenteum Heat shock protein 70 RNA-Seq Bioinformatics |
