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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

The fold changes in the DEGs as determined using RNA-seq and RT-qPCR are shown. (A) The first line represents the unigene ID; the second line represents the fold change in the DEG; the third line represents the RT-qPCR result; the fourth line represents the length of the unigene; and the fifth line represents the FDR of the unigene. (B) The x-axis represents the unigene ID while the y-axis represents the fold change in expression of the unigenes.
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Figure 6: The fold changes in the DEGs as determined using RNA-seq and RT-qPCR are shown. (A) The first line represents the unigene ID; the second line represents the fold change in the DEG; the third line represents the RT-qPCR result; the fourth line represents the length of the unigene; and the fifth line represents the FDR of the unigene. (B) The x-axis represents the unigene ID while the y-axis represents the fold change in expression of the unigenes.

Mentions: We identified nine ERFs with significant changes; their lengths varied from 260 to 873 bp (Figure 6). PCR amplification showed that all RT-qPCR primers (Supplementary File 10) used produced only single fragments of the expected lengths (100–250 bp; 100% success rate). All positive clones from the validation studies were subjected to Sanger sequencing, and the results confirmed those obtained using the Illumina method. Our qPCR results for the nine unigenes are in agreement with those from the DESeq analysis of our RNA-seq data.


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)

The fold changes in the DEGs as determined using RNA-seq and RT-qPCR are shown. (A) The first line represents the unigene ID; the second line represents the fold change in the DEG; the third line represents the RT-qPCR result; the fourth line represents the length of the unigene; and the fifth line represents the FDR of the unigene. (B) The x-axis represents the unigene ID while the y-axis represents the fold change in expression of the unigenes.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 6: The fold changes in the DEGs as determined using RNA-seq and RT-qPCR are shown. (A) The first line represents the unigene ID; the second line represents the fold change in the DEG; the third line represents the RT-qPCR result; the fourth line represents the length of the unigene; and the fifth line represents the FDR of the unigene. (B) The x-axis represents the unigene ID while the y-axis represents the fold change in expression of the unigenes.
Mentions: We identified nine ERFs with significant changes; their lengths varied from 260 to 873 bp (Figure 6). PCR amplification showed that all RT-qPCR primers (Supplementary File 10) used produced only single fragments of the expected lengths (100–250 bp; 100% success rate). All positive clones from the validation studies were subjected to Sanger sequencing, and the results confirmed those obtained using the Illumina method. Our qPCR results for the nine unigenes are in agreement with those from the DESeq analysis of our RNA-seq data.

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