title: Genome-wide survey and expression analysis of the PUB family in Chinese cabbage (Brassica rapa ssp. pekinesis).
abstract: 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.
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.|Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.|Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
authors.forename: Weike
authors.initials: W
authors.lastname: Duan
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.|Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
authors.forename: Ali RamuliMaquina
authors.initials: AR
authors.lastname: Riquicho
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.|Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
authors.forename: Zange
authors.initials: Z
authors.lastname: Jing
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.|Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
authors.forename: Tongkun
authors.initials: T
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.|Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
authors.forename: Xilin
authors.initials: X
authors.lastname: Hou
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China. yingli@njau.edu.cn.|Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People's Republic of China. yingli@njau.edu.cn.
authors.forename: Ying
authors.initials: Y
authors.lastname: Li
mesh_terms: D029741:Brassica rapa / Q000235:genetics*; D032461:Chromosomes, Plant; D018745:Genome, Plant; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*
chemical_list: D010940:Plant Proteins
keywords: Abiotic stress; Chinese cabbage; Plant U-box (PUB) proteins; RNA-seq; qRT-PCR