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Transcriptome-based gene profiling provides novel insights into the characteristics of radish root response to Cr stress with next-generation sequencing.

Xie Y, Ye S, Wang Y, Xu L, Zhu X, Yang J, Feng H, Yu R, Karanja B, Gong Y, Liu L - Front Plant Sci (2015)

Bottom Line: Differential gene analysis revealed that 2985 uingenes were significantly differentially expressed between Cr-free (CK) and Cr-treated (Cr600) libraries, among which 1424 were up-regulated and 1561 down-regulated.RT-qPCR analysis showed that the expression patterns of 12 randomly selected DEGs were highly accordant with the results from RNA-seq.These results would provide novel insight into molecular mechanism underlying plant responsiveness to Cr stress and facilitate further genetic manipulation on Cr uptake and accumulation in radish.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University Nanjing, China.

ABSTRACT
Radish (Raphanus sativus L.) is an important worldwide root vegetable crop with high nutrient values and is adversely affected by non-essential heavy metals including chromium (Cr). Little is known about the molecular mechanism underlying Cr stress response in radish. In this study, RNA-Seq technique was employed to identify differentially expressed genes (DEGs) under Cr stress. Based on de novo transcriptome assembly, there were 30,676 unigenes representing 60,881 transcripts isolated from radish root under Cr stress. Differential gene analysis revealed that 2985 uingenes were significantly differentially expressed between Cr-free (CK) and Cr-treated (Cr600) libraries, among which 1424 were up-regulated and 1561 down-regulated. Gene ontology (GO) analysis revealed that these DEGs were mainly involved in primary metabolic process, response to abiotic stimulus, cellular metabolic process and small molecule metabolic process. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that the DEGs were mainly involved in protein processing in endoplasmic reticulum, starch and sucrose metabolism, amino acid metabolism, glutathione metabolism, drug and xenobiotics by cytochrome P450 metabolism. RT-qPCR analysis showed that the expression patterns of 12 randomly selected DEGs were highly accordant with the results from RNA-seq. Furthermore, many candidate genes including signaling protein kinases, transcription factors and metal transporters, chelate compound biosynthesis and antioxidant system, were involved in defense and detoxification mechanisms of Cr stress response regulatory networks. These results would provide novel insight into molecular mechanism underlying plant responsiveness to Cr stress and facilitate further genetic manipulation on Cr uptake and accumulation in radish.

No MeSH data available.


The length distribution of the assembled transcripts.
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Figure 1: The length distribution of the assembled transcripts.

Mentions: A total of 37.95M and 27.45M raw reads were generated from CK and Cr600 library with Illumina Solexa sequencing technology, respectively. Before mapping these sequencing reads to the reference genome, the reads with connectors, filtered low-length reads and low-quality reads were removed. A total of 26.38M (69.52%) and 15.03M (54.74%) 101-nt clean reads were generated in cDNA libraries of CK and Cr600, respectively (Table 1). The sequencing reads were aligned against the combined radish reference database, and a total of 60,881 isogenes or 30,676 unigenes with 71,526,014 nt were filtered out for the differential expression analysis. Moreover, the average length of the isogene was 1,174.85 bp, and the largest and shortest isogene was 15,585 and 306 bp, respectively. The sequence length of these assembled transcripts was mainly distributed between 306 and 3000 bp with 401 and 600 bp length in the highest abundance (Figure 1).


Transcriptome-based gene profiling provides novel insights into the characteristics of radish root response to Cr stress with next-generation sequencing.

Xie Y, Ye S, Wang Y, Xu L, Zhu X, Yang J, Feng H, Yu R, Karanja B, Gong Y, Liu L - Front Plant Sci (2015)

The length distribution of the assembled transcripts.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379753&req=5

Figure 1: The length distribution of the assembled transcripts.
Mentions: A total of 37.95M and 27.45M raw reads were generated from CK and Cr600 library with Illumina Solexa sequencing technology, respectively. Before mapping these sequencing reads to the reference genome, the reads with connectors, filtered low-length reads and low-quality reads were removed. A total of 26.38M (69.52%) and 15.03M (54.74%) 101-nt clean reads were generated in cDNA libraries of CK and Cr600, respectively (Table 1). The sequencing reads were aligned against the combined radish reference database, and a total of 60,881 isogenes or 30,676 unigenes with 71,526,014 nt were filtered out for the differential expression analysis. Moreover, the average length of the isogene was 1,174.85 bp, and the largest and shortest isogene was 15,585 and 306 bp, respectively. The sequence length of these assembled transcripts was mainly distributed between 306 and 3000 bp with 401 and 600 bp length in the highest abundance (Figure 1).

Bottom Line: Differential gene analysis revealed that 2985 uingenes were significantly differentially expressed between Cr-free (CK) and Cr-treated (Cr600) libraries, among which 1424 were up-regulated and 1561 down-regulated.RT-qPCR analysis showed that the expression patterns of 12 randomly selected DEGs were highly accordant with the results from RNA-seq.These results would provide novel insight into molecular mechanism underlying plant responsiveness to Cr stress and facilitate further genetic manipulation on Cr uptake and accumulation in radish.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University Nanjing, China.

ABSTRACT
Radish (Raphanus sativus L.) is an important worldwide root vegetable crop with high nutrient values and is adversely affected by non-essential heavy metals including chromium (Cr). Little is known about the molecular mechanism underlying Cr stress response in radish. In this study, RNA-Seq technique was employed to identify differentially expressed genes (DEGs) under Cr stress. Based on de novo transcriptome assembly, there were 30,676 unigenes representing 60,881 transcripts isolated from radish root under Cr stress. Differential gene analysis revealed that 2985 uingenes were significantly differentially expressed between Cr-free (CK) and Cr-treated (Cr600) libraries, among which 1424 were up-regulated and 1561 down-regulated. Gene ontology (GO) analysis revealed that these DEGs were mainly involved in primary metabolic process, response to abiotic stimulus, cellular metabolic process and small molecule metabolic process. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that the DEGs were mainly involved in protein processing in endoplasmic reticulum, starch and sucrose metabolism, amino acid metabolism, glutathione metabolism, drug and xenobiotics by cytochrome P450 metabolism. RT-qPCR analysis showed that the expression patterns of 12 randomly selected DEGs were highly accordant with the results from RNA-seq. Furthermore, many candidate genes including signaling protein kinases, transcription factors and metal transporters, chelate compound biosynthesis and antioxidant system, were involved in defense and detoxification mechanisms of Cr stress response regulatory networks. These results would provide novel insight into molecular mechanism underlying plant responsiveness to Cr stress and facilitate further genetic manipulation on Cr uptake and accumulation in radish.

No MeSH data available.