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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

Random distribution of the assembled unigenes. The x-axis indicates the length of the unigenes. The y-axis indicates the number of unigenes.
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Figure 2: Random distribution of the assembled unigenes. The x-axis indicates the length of the unigenes. The y-axis indicates the number of unigenes.

Mentions: The Trinity method can generate full-length transcripts without reference genomes (Grabherr et al., 2011; Haas et al., 2013). Using this method for de novo assembly, all high-quality clean reads were assembled into 719,182 contigs (Supplementary File 2) with an average length of 201.56 bp. Contigs of 100–500 bp were most frequent, accounting for 94% of the total. Subsequently, the contigs were clustered into 32,849 unigenes of which the mean length was 1107 bp and the N50 value was 1781 bp (Table 1B). There were 20,499 unigenes of ≥500 bp, and 5224 unigenes of ≥2000 bp. Most unigenes were in the range 200–500 bp (37.59%). Among these genes, the longest and shortest were 15,772 and 201 bp, respectively. The unigene lengths facilitated annotation and classification. The random distribution of the unigenes is presented in Figure 2.


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)

Random distribution of the assembled unigenes. The x-axis indicates the length of the unigenes. The y-axis indicates the number of unigenes.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Random distribution of the assembled unigenes. The x-axis indicates the length of the unigenes. The y-axis indicates the number of unigenes.
Mentions: The Trinity method can generate full-length transcripts without reference genomes (Grabherr et al., 2011; Haas et al., 2013). Using this method for de novo assembly, all high-quality clean reads were assembled into 719,182 contigs (Supplementary File 2) with an average length of 201.56 bp. Contigs of 100–500 bp were most frequent, accounting for 94% of the total. Subsequently, the contigs were clustered into 32,849 unigenes of which the mean length was 1107 bp and the N50 value was 1781 bp (Table 1B). There were 20,499 unigenes of ≥500 bp, and 5224 unigenes of ≥2000 bp. Most unigenes were in the range 200–500 bp (37.59%). Among these genes, the longest and shortest were 15,772 and 201 bp, respectively. The unigene lengths facilitated annotation and classification. The random distribution of the unigenes is presented in Figure 2.

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