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De novo assembly of the Japanese lawngrass (Zoysia japonica Steud.) root transcriptome and identification of candidate unigenes related to early responses under salt stress.

Xie Q, Niu J, Xu X, Xu L, Zhang Y, Fan B, Liang X, Zhang L, Yin S, Han L - Front Plant Sci (2015)

Bottom Line: Compared with the control, 6035 genes were significantly different (false discovery rate ≤0.01, /log2Ratio/≥1) in the NaCl-treated samples.Using high-throughput next-generation sequencing, we built a database as a global transcript resource for Z. japonica Steud. roots.The results of this study will advance our understanding of the early salt response in Japanese lawngrass roots.

View Article: PubMed Central - PubMed

Affiliation: Institute of Turfgrass Science, College of Forestry, Beijing Forestry University Beijing, China.

ABSTRACT
Japanese lawngrass (Zoysia japonica Steud.) is an important warm-season turfgrass that is able to survive in a range of soils, from infertile sands to clays, and to grow well under saline conditions. However, little is known about the molecular mechanisms involved in its resistance to salt stress. Here, we used high-throughput RNA sequencing (RNA-seq) to investigate the changes in gene expression of Zoysia grass at high NaCl concentrations. We first constructed two sequencing libraries, including control and NaCl-treated samples, and sequenced them using the Illumina HiSeq™ 2000 platform. Approximately 157.20 million paired-end reads with a total length of 68.68 Mb were obtained. Subsequently, 100,800 unigenes with an N50 length of 1104 bp were assembled using Trinity, among which 70,127 unigenes were functionally annotated (E ≤ 10(-5)) in the non-redundant protein (NR) database. Furthermore, three public databases, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Swiss-prot, and Clusters of Orthologous Groups (COGs), were used for gene function analysis and enrichment. The annotated genes included 46 Gene Ontology (GO) terms, 120 KEGG pathways, and 25 COGs. Compared with the control, 6035 genes were significantly different (false discovery rate ≤0.01, /log2Ratio/≥1) in the NaCl-treated samples. These genes were enriched in 10 KEGG pathways and 58 GO terms, and subjected to 25 COG categories. Using high-throughput next-generation sequencing, we built a database as a global transcript resource for Z. japonica Steud. roots. The results of this study will advance our understanding of the early salt response in Japanese lawngrass roots.

No MeSH data available.


Related in: MedlinePlus

Identification of DEGs between the CK (control) and Case (salt-stressed) samples. (A) Volcano plot: The x-axis is the log of the fold change between the two conditions; the y-axis is the negative logarithm of the FDR. (B) MA plot: The x-axis is the average expression (log scale) level between the two conditions, indicating the basal expression level. The y-axis is the fold change (log scale), which indicates the difference between the two. (C) Each column represents a different sample. Each line represents a different gene. Each color represents a different gene expression level.
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Figure 4: Identification of DEGs between the CK (control) and Case (salt-stressed) samples. (A) Volcano plot: The x-axis is the log of the fold change between the two conditions; the y-axis is the negative logarithm of the FDR. (B) MA plot: The x-axis is the average expression (log scale) level between the two conditions, indicating the basal expression level. The y-axis is the fold change (log scale), which indicates the difference between the two. (C) Each column represents a different sample. Each line represents a different gene. Each color represents a different gene expression level.

Mentions: We used the RPKM method (RPKM > 0.1) to calculate the expression levels of unigenes in the control and salt-treated samples. Using DESeq software (FDR < 0.01, FC > 2) to analyze the DEGs between salt- and control-treated root samples, a total of 1648 differentially expressed unigenes (Figure 4) were obtained. Among those genes, 948 were upregulated and 700 were downregulated (Supplementary File 4).


De novo assembly of the Japanese lawngrass (Zoysia japonica Steud.) root transcriptome and identification of candidate unigenes related to early responses under salt stress.

Xie Q, Niu J, Xu X, Xu L, Zhang Y, Fan B, Liang X, Zhang L, Yin S, Han L - Front Plant Sci (2015)

Identification of DEGs between the CK (control) and Case (salt-stressed) samples. (A) Volcano plot: The x-axis is the log of the fold change between the two conditions; the y-axis is the negative logarithm of the FDR. (B) MA plot: The x-axis is the average expression (log scale) level between the two conditions, indicating the basal expression level. The y-axis is the fold change (log scale), which indicates the difference between the two. (C) Each column represents a different sample. Each line represents a different gene. Each color represents a different gene expression level.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542685&req=5

Figure 4: Identification of DEGs between the CK (control) and Case (salt-stressed) samples. (A) Volcano plot: The x-axis is the log of the fold change between the two conditions; the y-axis is the negative logarithm of the FDR. (B) MA plot: The x-axis is the average expression (log scale) level between the two conditions, indicating the basal expression level. The y-axis is the fold change (log scale), which indicates the difference between the two. (C) Each column represents a different sample. Each line represents a different gene. Each color represents a different gene expression level.
Mentions: We used the RPKM method (RPKM > 0.1) to calculate the expression levels of unigenes in the control and salt-treated samples. Using DESeq software (FDR < 0.01, FC > 2) to analyze the DEGs between salt- and control-treated root samples, a total of 1648 differentially expressed unigenes (Figure 4) were obtained. Among those genes, 948 were upregulated and 700 were downregulated (Supplementary File 4).

Bottom Line: Compared with the control, 6035 genes were significantly different (false discovery rate ≤0.01, /log2Ratio/≥1) in the NaCl-treated samples.Using high-throughput next-generation sequencing, we built a database as a global transcript resource for Z. japonica Steud. roots.The results of this study will advance our understanding of the early salt response in Japanese lawngrass roots.

View Article: PubMed Central - PubMed

Affiliation: Institute of Turfgrass Science, College of Forestry, Beijing Forestry University Beijing, China.

ABSTRACT
Japanese lawngrass (Zoysia japonica Steud.) is an important warm-season turfgrass that is able to survive in a range of soils, from infertile sands to clays, and to grow well under saline conditions. However, little is known about the molecular mechanisms involved in its resistance to salt stress. Here, we used high-throughput RNA sequencing (RNA-seq) to investigate the changes in gene expression of Zoysia grass at high NaCl concentrations. We first constructed two sequencing libraries, including control and NaCl-treated samples, and sequenced them using the Illumina HiSeq™ 2000 platform. Approximately 157.20 million paired-end reads with a total length of 68.68 Mb were obtained. Subsequently, 100,800 unigenes with an N50 length of 1104 bp were assembled using Trinity, among which 70,127 unigenes were functionally annotated (E ≤ 10(-5)) in the non-redundant protein (NR) database. Furthermore, three public databases, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Swiss-prot, and Clusters of Orthologous Groups (COGs), were used for gene function analysis and enrichment. The annotated genes included 46 Gene Ontology (GO) terms, 120 KEGG pathways, and 25 COGs. Compared with the control, 6035 genes were significantly different (false discovery rate ≤0.01, /log2Ratio/≥1) in the NaCl-treated samples. These genes were enriched in 10 KEGG pathways and 58 GO terms, and subjected to 25 COG categories. Using high-throughput next-generation sequencing, we built a database as a global transcript resource for Z. japonica Steud. roots. The results of this study will advance our understanding of the early salt response in Japanese lawngrass roots.

No MeSH data available.


Related in: MedlinePlus