Plant Molecular Biology Reporter

, Volume 36, Issue 2, pp 210–224 | Cite as

Genome-Wide Identification, Classification, and Expression Analysis of SNARE Genes in Chinese Cabbage (Brassica rapa ssp. pekinensis) Infected by Turnip mosaic virus

  • Changwei Zhang
  • Shanwu Lyu
  • Liwei Gao
  • Xiaoming Song
  • Yanxiao Li
  • Xilin HouEmail author
Original Paper


Turnip mosaic virus (TuMV) is a widely distributed pathogen that seriously affects the yield and quality of brassica crops. The SNARE genes in the host encode proteins that are very important for virus replication and movement. However, systematic and comprehensive analyses of these genes have not been reported for Chinese cabbage. In the present study, 78 BrSNARE genes were identified in Chinese cabbage. We analyzed the classification of these genes, their phylogenetic relationships (including their orthologous and paralogous relationships with those in Arabidopsis and rice), conserved motifs, and distribution on the ten chromosomes of Chinese cabbage. Of the 78 BrSNAREs, 77 were unevenly distributed among ten chromosomes. In the phylogenetic analyses of SNARES from Chinese cabbage, Arabidopsis, and rice, the 78 BrSNAREs were classified into four subfamilies. Analyses of the transcript levels of BrSNAREs in six different tissues revealed tissue-specific expression of some BrSNARE genes. We detected the expression of 55 BrSNAREs and grouped them according to their change trends and subcellular location in different organelles. On the basis of our analyses, we concluded that nine BrSNAREs may be associated with cell-to-cell movement and 15 BrSNAREs may be associated with long-distance transport. These results indicate that many BrSNAREs have evolved in Chinese cabbage and that some of them are related to TuMV infection.


Genome-wide analysis SNARE genes Turnip mosaic virus (TuMV) Expression pattern Chinese cabbage 





endoplasmic reticulum


kilobase of exon model per million mapped reads

GET pathway

guided entry of tail-anchored protein pathway


Golgi apparatus


least fractionated


medium fractionated


most fractionated


prevacuolar compartment


quantitative real-time PCR


syntaxin of plants


trans-Golgi network


Turnip mosaic virus




cell plate during cytokinesis


multivesicular body




plasma membrane


Authors’ Contributions

CZ, SL, LG, YL, XS, and XH conceived the study. CZ, SL, and LG completed the experiments. YL and XS contributed to data analysis and manuscript preparation. CZ and XH participated in the planning of experiments and revising the manuscript. All authors had read and approved the final version of the manuscript.

Funding Information

This work was supported by the grants from the National Natural Science Foundation of China (31272172), the Fundamental Research Funds for the Central Universities (KYTZ201401), and the Nature Science Foundation of Jiangsu Province (BK20141364).

Compliance with Ethical Standards

Competing Interests

The authors declare that they have no competing interests.

Supplementary material

11105_2017_1060_MOESM1_ESM.pdf (313 kb)
Figure S1 Cluster analysis of expression profile of SNARE family genes in Chinese cabbage. Gene expression levels represent log2-transformedFPKM values in six tissues (flower, leaf, seed, bud, silique and root). (PDF 312 kb)
11105_2017_1060_MOESM2_ESM.pdf (6.4 mb)
Figure S2 Distribution of vascular bundle in petiole. Transverse sections of petiole are shown. Left: 40× magnification. Right: 100× magnifications (bars at top right). p: phloem, x: xylem. (PDF 6593 kb)
11105_2017_1060_MOESM3_ESM.xls (132 kb)
ESM 1 (XLS 131 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Changwei Zhang
    • 1
  • Shanwu Lyu
    • 1
  • Liwei Gao
    • 1
  • Xiaoming Song
    • 2
  • Yanxiao Li
    • 1
  • Xilin Hou
    • 1
    • 3
    Email author
  1. 1.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of HorticultureNanjing Agricultural UniversityNanjingPeople’s Republic of China
  2. 2.Department of Life SciencesNorth China University of Science and TechnologyTangshanChina
  3. 3.Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of AgricultureNanjing Agricultural UniversityNanjingPeople’s Republic of China

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