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

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, 32,849 unigenes with an N50 length of 1781 bp were assembled using Trinity. 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 57 Gene Ontology (GO) terms, 120 KEGG pathways, and 24 COGs. Compared with the control, 1455 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 73 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.

RNA-Seq analysis of Clerodendrum inerme (L.) roots in response to salt stress

“…In Populus tomentosa, the accumulation of H 2 O 2 and concentration of hormones changed significantly at 6 h, 12 h, and 24 h, and root samples at those time points were subjected to RNA-seq analysis to understand the short-term salt stress response, revealing the high enrichment of DEGs involved in H 2 O 2 and hormone production [51]. In Zoysia japonica, oxidative stress caused by H 2 O 2 was visible throughout roots after 30 min exposure to NaCl, and numerous candidate genes related to early responses to salt stress were revealed by de novo assembly of the Japanese lawngrass root transcriptome [52]. The activity of antioxidant enzymes in plants is closely related with tolerance to salt [53,54].…”

Mechanisms of Environmental Stress Tolerance in Turfgrass

“…Investigating the salt stress response at the molecular level is a possible way to further understand salt tolerance mechanism of bermudagrass. Transcriptome profilings of Kentucky bluegrass, zoysiagrass, and salt couch grass (Sporobolus virginicus) have been analyzed comprehensively, and a number of candidate unigenes related to salt stress responses were identified [49][50][51]; putatively, a total of 36,587, 1455 and 8340 differentially expressed genes were detected for these species, respectively. Functional annotation indicated that the detected genes were related to transcription factors, processes and pathways such as oxidation-reduction process, ion transport and ROS scavenging.…”

Molecular cloning and characterization of a chlorophyll degradation regulatory gene (ZjSGR) from Zoysia japonica

“…Nevertheless, a barrier to spread its use more widely is the de-greening phenotype that occurs during harsh seasons. To date, limited genetic resources are available for zoysiagrass (Wei et al, 2015;Xie et al, 2015). Further investigation of the possible genetic factors regulating chlorophyll degradation and senescence would contribute to the application of zoysiagrass.…”