WANG An,PANG Wenyu,QIN Ning,et al.Bioinformatics Analysis of PUP Gene Family in Chinese Cabbage (Brassica rapa ssp.pekinensis)[J].Northern Horticulture,2018,42(19):8-16.[doi:10.11937/bfyy.20180615]
大白菜PUP基因家族的生物信息学分析
- Title:
- Bioinformatics Analysis of PUP Gene Family in Chinese Cabbage (Brassica rapa ssp.pekinensis)
- Keywords:
- Chinese cabbage (Brassica rapa ssp.pekinensis); purine permeases; gene family; bioinformatic
- 文献标志码:
- A
- 摘要:
- 为深入研究大白菜PUP基因家族的功能，采用生物信息学方法对大白菜基因组中PUP基因家族成员进行了鉴定，并对其基因组信息、蛋白生理生化特征、基因结构、保守结构域、系统进化树和表达模式等方面进行了研究。结果表明：在大白菜基因组中共鉴定出了24个PUP基因，可以聚类到3个分支，Clade I、Clade II和Clade III；PUP基因在大白菜10条染色体上不均匀分布，而且存在明显的串联重复现象并在染色体上呈现5个串联重复基因簇，说明串联复制是PUP基因家族基因扩增的主要方式；对BrPUP蛋白氨基酸序列多重比对和蛋白跨膜域的分析表明BrPUP蛋白一般存在10个跨膜域，为典型的跨膜蛋白；通过MEME软件对BrPUP蛋白motif的预测还发现了10个比较保守的motif；最后利用Unigene数据库中的EST表达数据对BrPUPs的表达模式进行了初步研究。上述研究结果为大白菜PUP基因功能的研究奠定了基础。
- Abstract:
- To further research the PUP gene family functions of Chinese cabbage,bioinformatics tools were conducted to identify the PUP gene family members in the Chinese cabbage genome,and genome annotation,physiological and biochemical characteristics of proteins,gene structures,conserved domains,phylogenetic trees and expression patterns were also analyzed.The results showed that 24 PUP genes were identified in the whole genome level,which could be clustered into 3 clades,Clade I，Clade II and Clade III;BrPUP genes were unevenly distributed in the 10 chromosomes,and tandem duplications were apparently observed in 5 tandem duplicated gene clusters,it indicated that tandem duplication was the primary approach of gene amplifications for the PUP gene family.Multiple alignment of protein sequences and protein transmembrane analysis showed BrPUP proteins were typical transmembrane proteins with general 10 transmembrane helics;10 conserved motifs were also predicted among BrPUP proteins by MEME analysis.Besides,expression patterns of BrPUPs were primarily investigated based on EST data in Unigene database.These results established a certain foundation for PUP gene functions in Chinese cabbage.
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备注/Memo
第一作者简介：王安（1995-），女，硕士研究生，研究方向为蔬菜分子生物学。E-mail:wangan@lyu.edu.cn.责任作者：刘振宁（1988-），男，博士，教授，研究方向为蔬菜分子生物学与遗传育种。E-mail:liuzhenning@lyu.edu.cn.基金项目：国家自然科学基金资助项目（31700272）；山东省自然科学基金资助项目（ZR2017PC012）。收稿日期：2018-04-12