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

Frontiers in Plant Science
Qi XieLiebao Han

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 ...Continue Reading

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Citations

May 6, 2016·Frontiers in Plant Science·Xiu HuangYan-Hong Yan
Nov 18, 2018·The Plant Journal : for Cell and Molecular Biology·Maricris L ZaidemMichael D Purugganan
Apr 13, 2017·Frontiers in Plant Science·Maheshi Dassanayake, John C Larkin
Oct 27, 2017·Scientific Reports·Zhizhong RenJian-Kang Zhu

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Datasets Mentioned

BETA
GU290545.1

Methods Mentioned

BETA
reverse transcription PCR
salt treatment
RNA-seq

Software Mentioned

MISA
DEGseq
BLAST
Clustal X
Blastn
BLASTX
MIcroSAtellite
MEGA
Bio
DESeq

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