Chin Bull Bot ›› 2015, Vol. 50 ›› Issue (2): 171-179.doi: 10.3724/SP.J.1259.2015.00171

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Transcriptome Analysis of Physcomitrella patens Response to Cadmium Stress by Bayesian Network

Zili Wu1, 2, Mengyao Yu2, Lu Chen2, Jing Wei2, Xiaoqin Wang3, Yong Hu2, Yan Yan2, Ping Wan2, *   

  1. 1Key Laboratory of Aromatic Plant Resources Exploitation and Utilization in Sichuan Higher Education, College of Life Sciences and Food Engineering, Yibin University, Yibin 644000, China
    2Beijing Key Laboratory of Plant Gene Resource and Low-carbon Environmental Biotechnology, Capital Normal University, Beijing 100048, China
    3Key Laboratory of Urban Agriculture (North) Ministry of Agriculture, Beijing University of Agriculture, Beijing 102206, China
  • Received:2014-10-27 Accepted:2015-02-02 Online:2015-04-10 Published:2015-03-01
  • Contact: Wan Ping
  • About author:

    ? These authors contributed equally to this paper


Cadmium is a non-essential heavy metal for plant growth. Cadmium stress causes cell metabolism disturbance or death in plant. Here, we performed transcriptome analysis of Physcomitrella patens during cadmium stress by RNA-Seq. We revealed a new transcriptional network of cadmium stress in plants. The functions of genes that were upregulated or downregulated under cadmium stress included microtubule-based movement, microtubule-based processing, cytoskeleton organization, DNA replication, DNA metabolic process, telomere maintenance and organization, sexual reproduction, urea metabolic process, and nitrogen cycle metabolic process. These proteins may play roles in P. patens under cadmium stress. Our study provides new information for the further research of the molecular mechanisms of plant adaptation to cadmium stress.

Figure 1

The effect of cadmium stress on Physcomitrella patens growth"

The gene regulatory network of Physcomitrella patens under cadmium stress The network consists of 704 nodes (genes) and 788 edges (regulation relation). The degree of the red node is thirteen"

Figure 3

The distribution of the node degree in Physcomitrella patens gene regulation network under cadmium stress"

Table 1

The enriched GO terms in Physcomitrella patens gene regulation network under cadmium stress"

Type GO number Biological processes P value
1 GO:0007018 Microtubule-based movement 2.80E-06
GO:0007017 Microtubule-based process 6.90E-05
GO:0007010 Cytoskeleton organization 0.018 8
2 GO:0006260 DNA replication 0.001 7
GO:0006259 DNA metabolic process 0.002 5
GO:0006302 Double-strand break repair 0.015 3
GO:0000723 Telomere maintenance 0.033 4
GO:0032200 Telomere organization 0.033 4
3 GO:0007276 Gamete generation 0.033 4
GO:0007292 Female gamete generation 0.033 4
GO:0019953 Sexual reproduction 0.033 4
4 GO:0019627 Urea metabolic process 0.033 4
GO:0071941 Nitrogen cycle metabolic process 0.033 4

Figure 4

Expression of 10 Cd-respon- sive genes"

Table 2

A list of ten genes selected for qPCR analysis"

Gene identification
The homologous gene in
Arabidopsis thaliana
Pp1s34_49V6 AT2G27290.1 Protein of unknown function (DUF1279)
Pp1s352_53V6 AT3G57060.2 Chromosome condensation
Pp1s59_160V6 AT3G44750.1 Histone deacetylase 3
Pp1s57_179V6 AT5G18140.1 Chaperone DnaJ-domain superfamily protein
Pp1s204_5V6 AT5G20935.1 Protein of unknown function
Pp1s68_291V6 AT5G57590.1 Adenosylmethionine-8-amino-7-oxononanoate transaminases
Pp1s13_454V6 AT5G54910.1 DEA (D/H)-box RNA helicase family protein
Pp1s133_35V6.1 AT1G08260.1 DNA polymerase epsilon catalytic subunit
Pp1s259_32V6.1 AT1G79690.1 Dipeptidyl-peptidase activity, hydrolase activity
Pp1s175_94V6.1 AT4G01130.1 GDSL-like Lipase/Acylhydrolase superfamily protein involved in lipid metabolic process

Figure 5

Gene regulatory sub-network of Pp1s34_49V6"

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