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

doi:10.3724/SP.J.1259.2015.00171

Abstract

Abstract: 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.

Key words: Bayesian network, cadmium stress, high-throughput sequencing, Physcomitrella patens, regulatory mechanism

Zili Wu, Mengyao Yu, Lu Chen, Jing Wei, Xiaoqin Wang, Yong Hu, Yan Yan, Ping Wan. Transcriptome Analysis of Physcomitrella patens Response to Cadmium Stress by Bayesian Network[J]. Chinese Bulletin of Botany, 2015, 50(2): 171-179.

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URL: https://www.chinbullbotany.com/EN/10.3724/SP.J.1259.2015.00171

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Figures/Tables 7

References 36

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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
4	GO:0071941	Nitrogen cycle metabolic process	0.033 4

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
4	GO:0071941	Nitrogen cycle metabolic process	0.033 4

Gene identification number	The homologous gene in Arabidopsis thaliana	Function
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

Gene identification number	The homologous gene in Arabidopsis thaliana	Function
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

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