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De novo sequencing, assembly, and analysis of the Taxodium 'Zhongshansa' roots and shoots transcriptome in response to short-term waterlogging.

Qi B, Yang Y, Yin Y, Xu M, Li H - BMC Plant Biol. (2014)

Bottom Line: There were 2090 differentially expressed genes (DEGs) found in roots and 394 in shoots, with 174 shared by both of them, indicating that the aerial parts were also affected.As respiration was inhibited and ATP decreased, another quick coping mechanism was repressing the energy-consuming biosynthetic processes through the whole plant.Moreover, the gene expression pattern of 5 unigenes involving in the glycolysis pathway revealed by qRT-PCR confirmed the RNA-Seq data.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Taxodium is renowned for its strong tolerance to waterlogging stress, thus it has great ecological and economic potential. However, the scant genomic resources in genus Taxodium have greatly hindered further exploration of its underlying flood-tolerance mechanism. Taxodium 'Zhongshansa' is an interspecies hybrid of T. distichum and T. mucronatum, and has been widely planted in southeastern China. To understand the genetic basis of its flood tolerance, we analyzed the transcriptomes of Taxodium 'Zhongshansa' roots and shoots in response to short-term waterlogging.

Results: RNA-seq was used to analyze genome-wide transcriptome changes of Taxodium 'Zhongshansa 406' clone root and shoot treated with 1 h of soil-waterlogging stress. After de novo assembly, 108,692 unigenes were achieved, and 70,260 (64.64%) of them were annotated. There were 2090 differentially expressed genes (DEGs) found in roots and 394 in shoots, with 174 shared by both of them, indicating that the aerial parts were also affected. Under waterlogging stress, the primary reaction of hypoxic-treated root was to activate the antioxidative defense system to prevent cells experiencing reactive oxygen species (ROS) poisoning. As respiration was inhibited and ATP decreased, another quick coping mechanism was repressing the energy-consuming biosynthetic processes through the whole plant. The glycolysis and fermentation pathway was activated to maintain ATP production in the hypoxic root. Constantly, the demand for carbohydrates increased, and carbohydrate metabolism were accumulated in the root as well as the shoot, possibly indicating that systemic communications between waterlogged and non-waterlogged tissues facilated survival. Amino acid metabolism was also greatly influenced, with down-regulation of genes involvedin serine degradation and up-regulation of aspartic acid degradation. Additionally, a non-symbiotic hemoglobin class 1 gene was up-regulated, which may also help the ATP production. Moreover, the gene expression pattern of 5 unigenes involving in the glycolysis pathway revealed by qRT-PCR confirmed the RNA-Seq data.

Conclusions: We conclude that ROS detoxification and energy maintenance were the primary coping mechanisms of 'Zhongshansa' in surviving oxygen deficiency, which may be responsible for its remarkable waterlogging tolerance. Our study not only provided the first large-scale assessment of genomic resources of Taxodium but also guidelines for probing the molecular mechanism underlying 'Zhongshansa' waterlogging tolerance.

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Length distribution of assembled unigenes.
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Figure 1: Length distribution of assembled unigenes.

Mentions: Illumina sequencing data from ‘Zhongshansa’ roots and shoots were deposited in the NCBI SRA database under accession number SRP043177. In total, 174,958,744 Illumina PE raw reads were generated (Table 1). After removing adaptor sequences, ambiguous nucleotides and low-quality sequences, there were 153,993,822 million clean reads remaining. Assembly of clean reads resulted in 108,692 unigenes in the range of 201–14,489 bp with a N50 length of 1123 bp (Figure 1).


De novo sequencing, assembly, and analysis of the Taxodium 'Zhongshansa' roots and shoots transcriptome in response to short-term waterlogging.

Qi B, Yang Y, Yin Y, Xu M, Li H - BMC Plant Biol. (2014)

Length distribution of assembled unigenes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4222663&req=5

Figure 1: Length distribution of assembled unigenes.
Mentions: Illumina sequencing data from ‘Zhongshansa’ roots and shoots were deposited in the NCBI SRA database under accession number SRP043177. In total, 174,958,744 Illumina PE raw reads were generated (Table 1). After removing adaptor sequences, ambiguous nucleotides and low-quality sequences, there were 153,993,822 million clean reads remaining. Assembly of clean reads resulted in 108,692 unigenes in the range of 201–14,489 bp with a N50 length of 1123 bp (Figure 1).

Bottom Line: There were 2090 differentially expressed genes (DEGs) found in roots and 394 in shoots, with 174 shared by both of them, indicating that the aerial parts were also affected.As respiration was inhibited and ATP decreased, another quick coping mechanism was repressing the energy-consuming biosynthetic processes through the whole plant.Moreover, the gene expression pattern of 5 unigenes involving in the glycolysis pathway revealed by qRT-PCR confirmed the RNA-Seq data.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Taxodium is renowned for its strong tolerance to waterlogging stress, thus it has great ecological and economic potential. However, the scant genomic resources in genus Taxodium have greatly hindered further exploration of its underlying flood-tolerance mechanism. Taxodium 'Zhongshansa' is an interspecies hybrid of T. distichum and T. mucronatum, and has been widely planted in southeastern China. To understand the genetic basis of its flood tolerance, we analyzed the transcriptomes of Taxodium 'Zhongshansa' roots and shoots in response to short-term waterlogging.

Results: RNA-seq was used to analyze genome-wide transcriptome changes of Taxodium 'Zhongshansa 406' clone root and shoot treated with 1 h of soil-waterlogging stress. After de novo assembly, 108,692 unigenes were achieved, and 70,260 (64.64%) of them were annotated. There were 2090 differentially expressed genes (DEGs) found in roots and 394 in shoots, with 174 shared by both of them, indicating that the aerial parts were also affected. Under waterlogging stress, the primary reaction of hypoxic-treated root was to activate the antioxidative defense system to prevent cells experiencing reactive oxygen species (ROS) poisoning. As respiration was inhibited and ATP decreased, another quick coping mechanism was repressing the energy-consuming biosynthetic processes through the whole plant. The glycolysis and fermentation pathway was activated to maintain ATP production in the hypoxic root. Constantly, the demand for carbohydrates increased, and carbohydrate metabolism were accumulated in the root as well as the shoot, possibly indicating that systemic communications between waterlogged and non-waterlogged tissues facilated survival. Amino acid metabolism was also greatly influenced, with down-regulation of genes involvedin serine degradation and up-regulation of aspartic acid degradation. Additionally, a non-symbiotic hemoglobin class 1 gene was up-regulated, which may also help the ATP production. Moreover, the gene expression pattern of 5 unigenes involving in the glycolysis pathway revealed by qRT-PCR confirmed the RNA-Seq data.

Conclusions: We conclude that ROS detoxification and energy maintenance were the primary coping mechanisms of 'Zhongshansa' in surviving oxygen deficiency, which may be responsible for its remarkable waterlogging tolerance. Our study not only provided the first large-scale assessment of genomic resources of Taxodium but also guidelines for probing the molecular mechanism underlying 'Zhongshansa' waterlogging tolerance.

Show MeSH
Related in: MedlinePlus