Genome-wide survey and expression analysis of the PUB family in Chinese cabbage (Brassica rapa ssp. pekinesis)

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• 作者：Cheng Wang ; Weike Duan ; Ali RamuliMaquina Riquicho…
• 关键词：Chinese cabbage ; Plant U ; box (PUB) proteins ; Abiotic stress ; RNA ; seq ; qRT ; PCR
• 刊名：Molecular Genetics and Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：290
• 期：6
• 页码：2241-2260
• 全文大小：7,307 KB
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• 作者单位：Cheng Wang (1) (2)
  Weike Duan (1) (2)
  Ali RamuliMaquina Riquicho (1) (2)
  Zange Jing (1) (2)
  Tongkun Liu (1) (2)
  Xilin Hou (1) (2)
  Ying Li (1) (2)
  
  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People鈥檚 Republic of China
  2. Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People鈥檚 Republic of China
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Cell Biology
  Biochemistry
  Microbial Genetics and Genomics
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1617-4623

文摘

U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. Plant U-box (PUB) proteins play crucial regulatory roles in various developmental and physiological processes. Previously, 64 and 77 PUB genes have been identified in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), respectively. In this study, 101 putative PUB genes were identified in the Chinese cabbage (Brassica rapa ssp. pekinensis line Chiifu-401-42) genome and compared with other 15 representative plants. By specific protein domains and a phylogenetic analysis, the B. rapa PUB (BrPUB) gene family was subdivided into 10 groups. Localization of BrPUB genes showed an uneven distribution on the ten chromosomes of B. rapa. The orthologous and co-orthologous PUB gene pairs were identified between B. rapa and A. thaliana. RNA-seq transcriptome data of different tissues revealed tissue-specific and differential expression profiles of the BrPUBs, and quantitative real-time PCR analysis showed inverse gene expression patterns of the BrPUB-ARMs in response to cold and heat stresses. Altogether, the identification, classification, phylogenetic analysis, chromosome distribution, conserved motifs, and expression patterns of BrPUBs were predicted and analysed. Importantly, this study of BrPUBs provides a rich resource that will aid in the determination of PUB functions in plant development. Keywords Chinese cabbage Plant U-box (PUB) proteins Abiotic stress RNA-seq qRT-PCR