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

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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.

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Acknowledgments

This work is supported by the Specialized Research Fund for the Doctoral Program of Higher Education (SRFDP, BO201300666), the National Basic Research Program of China (973 Program, 2012CB113903), the National Natural Science Foundation of China (31471886) and the Jiangsu Province Natural Science Foundation (BK20130673). This study was funded by the Specialized Research Fund for the Doctoral Program of Higher Education (SRFDP, BO201300666), the National Basic Research Program of China (973 Program, 2012CB113903), the National Natural Science Foundation of China (31471886) and the Jiangsu Province Natural Science Foundation (BK20130673).

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    Authors and Affiliations

    1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095, People’s Republic of China

      Cheng Wang, Weike Duan, Ali RamuliMaquina Riquicho, Zange Jing, Tongkun Liu, Xilin Hou & Ying Li

    2. 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

      Cheng Wang, Weike Duan, Ali RamuliMaquina Riquicho, Zange Jing, Tongkun Liu, Xilin Hou & Ying Li

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    1. Cheng Wang
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    3. Ali RamuliMaquina Riquicho
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    Correspondence to Ying Li.

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    Communicated by S. Hohmann.

    C. Wang and W. Duan contributed equally to this work.

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    438_2015_1075_MOESM1_ESM.png

    Supplementary material 1 (PNG 202 kb) Supplementary Fig. 1. Phylogenetic relationships and subgroup designations in U-box proteins from Arabidopsis

    438_2015_1075_MOESM2_ESM.png

    Supplementary material 2 (PNG 1156 kb) Supplementary Fig. 2. Sequence logos of PUB domains in B. rapa. The overall height of the stack indicates the level of sequence conservation. The height of residues within the stack indicates the relative frequency of each residue at that position

    438_2015_1075_MOESM3_ESM.png

    Supplementary material 3 (PNG 44 kb) Supplementary Fig. 3. Retention by number of homologous copies in the syntenic region between Arabidopsis and B. rapa

    438_2015_1075_MOESM4_ESM.png

    Supplementary material 4 (PNG 528 kb) Supplementary Fig. 4. The networks of PUB genes in B. rapa and Arabidopsis. This interrelation network has been constructed using B. rapa and Arabidopsis orthologous gene pairs. (a) One orthologous gene pair between B. rapa and Arabidopsis. (b) Two orthologous gene pairs between B. rapa and Arabidopsis. (c) Three or more than three orthologous gene pairs between B. rapa and Arabidopsis

    438_2015_1075_MOESM5_ESM.png

    Supplementary material 5 (PNG 197 kb) Supplementary Fig. 5. Expression analyses of B. rapa PUB-ARM genes under six abiotic stresses. Heat map representation and hierarchical clustering of BrPUB-ARM genes during GA, ABA, NaCl, PEG, heat and cold stresses. Every stress contains three durations: 1 h, 4 h and 12 h. The relative expression levels of BrPUB-ARMs in leaves under these stresses were quantified against the control transcript levels. The bar at the bottom of each heat map represents relative expression values

    Supplementary material 6 (XLSX 119 kb)

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    Wang, C., Duan, W., Riquicho, A.R. et al. Genome-wide survey and expression analysis of the PUB family in Chinese cabbage (Brassica rapa ssp. pekinesis). Mol Genet Genomics 290, 2241–2260 (2015). https://doi.org/10.1007/s00438-015-1075-x

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