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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

A homology search was conducted by BLASTx against the NR database. (A)E-value distribution of BLAST hits for matched unigene sequences. (B) Similarity distribution of top BLAST hits for each unigene. (C) Species distribution of the top BLAST hits.
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Figure 3: A homology search was conducted by BLASTx against the NR database. (A)E-value distribution of BLAST hits for matched unigene sequences. (B) Similarity distribution of top BLAST hits for each unigene. (C) Species distribution of the top BLAST hits.

Mentions: The assembled sequences were first searched against the NR protein database, and analysis indicated that 55% of the sequences ranged from 1.0E−5 to 1.0E−50, while 18,006 of sequences with an E < 10E−50 displayed strong homology (Figure 3). The distribution of identity is shown in Figure 3B. The majority pattern was 60–80% similarity (12,111) and 40–60% similarity (9812). The closest species was Setaria itallica, with 14,950 genes (45%) matched. The next closest species was Sorghum bicolor, which showed 17% homology with Zoysia. This implies that the transcripts were assembled and annotated correctly (Dang et al., 2013; Wang et al., 2013). Figure 3C shows homologies with plants in the family Poaceae. Recent research (Ahn et al., 2015) supports our data showing that the most homologous model species to Zoysia is Setaria itallica, followed by Sorghum bicolor and Zea mays. Due to the differences in tissue between cultivar and treatment, our results were not completely consistent with that research.


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)

A homology search was conducted by BLASTx against the NR database. (A)E-value distribution of BLAST hits for matched unigene sequences. (B) Similarity distribution of top BLAST hits for each unigene. (C) Species distribution of the top BLAST hits.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: A homology search was conducted by BLASTx against the NR database. (A)E-value distribution of BLAST hits for matched unigene sequences. (B) Similarity distribution of top BLAST hits for each unigene. (C) Species distribution of the top BLAST hits.
Mentions: The assembled sequences were first searched against the NR protein database, and analysis indicated that 55% of the sequences ranged from 1.0E−5 to 1.0E−50, while 18,006 of sequences with an E < 10E−50 displayed strong homology (Figure 3). The distribution of identity is shown in Figure 3B. The majority pattern was 60–80% similarity (12,111) and 40–60% similarity (9812). The closest species was Setaria itallica, with 14,950 genes (45%) matched. The next closest species was Sorghum bicolor, which showed 17% homology with Zoysia. This implies that the transcripts were assembled and annotated correctly (Dang et al., 2013; Wang et al., 2013). Figure 3C shows homologies with plants in the family Poaceae. Recent research (Ahn et al., 2015) supports our data showing that the most homologous model species to Zoysia is Setaria itallica, followed by Sorghum bicolor and Zea mays. Due to the differences in tissue between cultivar and treatment, our results were not completely consistent with that research.

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