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Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress.

Wei S, Du Z, Gao F, Ke X, Li J, Liu J, Zhou Y - PLoS ONE (2015)

Bottom Line: Zoysiagrasses (Zoysia spp.In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated.GA metabolism, ABA and JA stimulus response were affected under cold exposure.

View Article: PubMed Central - PubMed

Affiliation: College of Life & Environmental Sciences, Minzu University of China, Beijing, PR China.

ABSTRACT
A long green period is essential for a turfgrass species with high ornamental value and a wide area of use. Zoysiagrasses (Zoysia spp. Willd.) are perennial turfgrass species popular in tropical, subtropical and temperate zones, possessing many properties necessary to be economically useful turfgrass. They do not have a long green period because of cold sensitivity. A main focus in zoysiagrass research is to develop cold tolerant cultivars. Understanding the cold response in zoysiagrass is a fundamental area of research. In the present study, 'Meyer' zoysiagrass (Zoysia japonica), a widely cultivated variety in the genus, is used. We employed RNA-Seq to investigate genome-wide gene expression profiles in leaves under cold stress (4°C). Using the Illumina sequencing platform, we obtained approximately 206 million high-quality paired-end reads from three libraries (0 h, 2 h, and 72 h cold treatment at 4°C). After de novo assembly and quantitative assessment, 46,412 unigenes were generated with an average length of 998 bp and an N50 of 1,522 bp. A total of 25,644 (55.2%) unigenes were annotated by alignment with public protein databases including NR, SwissProt, KEGG and KOG. Differentially expressed genes (DEGs) were investigated using the RPKM method. A total of 756 DEGs were identified between 0 h and 2 h-cold treatment, with 522 up-regulated and 234 down-regulated; and 5327 DEGs were identified between 0 h and 72 h-cold treatment, with 2453 up-regulated and 2874 down-regulated. The expression profile of 15 DEGs selected randomly was confirmed with qRT-PCR. The results suggest that cold stress can induce desiccation and oxidative stress, inhibit photosynthesis and substance transport. In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated. GA metabolism, ABA and JA stimulus response were affected under cold exposure. This is the first transcriptome sequencing of Z. japonica, providing a large set of sequence data as well as gene expression profiles under cold stress. It will improve our current understanding of the cold response of zoysiagrass and be beneficial in breeding research.

No MeSH data available.


Related in: MedlinePlus

Length distributions of the unigenes.The X-axis lists the length of unigenes, and the Y-axis lists shows the number of unigenes of that size.
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pone.0131153.g002: Length distributions of the unigenes.The X-axis lists the length of unigenes, and the Y-axis lists shows the number of unigenes of that size.

Mentions: A total of 89,868 transcripts with length ≥ 300 nt were generated using Trinity software (Table 1). The mean transcript size was 1262 nt, and N50 is 1854 nt. Clustering analysis was used to assign all transcripts to 46,412 unigene clusters. A set of non-redundant unigenes was obtained by keeping the longest transcript in a cluster as representative. Among these unigenes, the mean length was 998 nt, with N50 being 1522 nt. A total of 28103 (60.55%) unigenes were longer than 500 nt, and 5818 (12.53%) unigenes were longer than 2000 nt (Fig 2), implying that a batch of transcripts with complete CDS were obtained. Reads were then mapped back to unigenes, 82.76%, 85.68%, and 83.60% of reads in libraries of CK, CT_2h, and CT_72h respectively, were mapped successfully, indicating that the transcript data was suitable for further analysis.


Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress.

Wei S, Du Z, Gao F, Ke X, Li J, Liu J, Zhou Y - PLoS ONE (2015)

Length distributions of the unigenes.The X-axis lists the length of unigenes, and the Y-axis lists shows the number of unigenes of that size.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482698&req=5

pone.0131153.g002: Length distributions of the unigenes.The X-axis lists the length of unigenes, and the Y-axis lists shows the number of unigenes of that size.
Mentions: A total of 89,868 transcripts with length ≥ 300 nt were generated using Trinity software (Table 1). The mean transcript size was 1262 nt, and N50 is 1854 nt. Clustering analysis was used to assign all transcripts to 46,412 unigene clusters. A set of non-redundant unigenes was obtained by keeping the longest transcript in a cluster as representative. Among these unigenes, the mean length was 998 nt, with N50 being 1522 nt. A total of 28103 (60.55%) unigenes were longer than 500 nt, and 5818 (12.53%) unigenes were longer than 2000 nt (Fig 2), implying that a batch of transcripts with complete CDS were obtained. Reads were then mapped back to unigenes, 82.76%, 85.68%, and 83.60% of reads in libraries of CK, CT_2h, and CT_72h respectively, were mapped successfully, indicating that the transcript data was suitable for further analysis.

Bottom Line: Zoysiagrasses (Zoysia spp.In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated.GA metabolism, ABA and JA stimulus response were affected under cold exposure.

View Article: PubMed Central - PubMed

Affiliation: College of Life & Environmental Sciences, Minzu University of China, Beijing, PR China.

ABSTRACT
A long green period is essential for a turfgrass species with high ornamental value and a wide area of use. Zoysiagrasses (Zoysia spp. Willd.) are perennial turfgrass species popular in tropical, subtropical and temperate zones, possessing many properties necessary to be economically useful turfgrass. They do not have a long green period because of cold sensitivity. A main focus in zoysiagrass research is to develop cold tolerant cultivars. Understanding the cold response in zoysiagrass is a fundamental area of research. In the present study, 'Meyer' zoysiagrass (Zoysia japonica), a widely cultivated variety in the genus, is used. We employed RNA-Seq to investigate genome-wide gene expression profiles in leaves under cold stress (4°C). Using the Illumina sequencing platform, we obtained approximately 206 million high-quality paired-end reads from three libraries (0 h, 2 h, and 72 h cold treatment at 4°C). After de novo assembly and quantitative assessment, 46,412 unigenes were generated with an average length of 998 bp and an N50 of 1,522 bp. A total of 25,644 (55.2%) unigenes were annotated by alignment with public protein databases including NR, SwissProt, KEGG and KOG. Differentially expressed genes (DEGs) were investigated using the RPKM method. A total of 756 DEGs were identified between 0 h and 2 h-cold treatment, with 522 up-regulated and 234 down-regulated; and 5327 DEGs were identified between 0 h and 72 h-cold treatment, with 2453 up-regulated and 2874 down-regulated. The expression profile of 15 DEGs selected randomly was confirmed with qRT-PCR. The results suggest that cold stress can induce desiccation and oxidative stress, inhibit photosynthesis and substance transport. In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated. GA metabolism, ABA and JA stimulus response were affected under cold exposure. This is the first transcriptome sequencing of Z. japonica, providing a large set of sequence data as well as gene expression profiles under cold stress. It will improve our current understanding of the cold response of zoysiagrass and be beneficial in breeding research.

No MeSH data available.


Related in: MedlinePlus