Transcriptome Exploration in Leymus chinensis under Saline-Alkaline Treatment Using 454 Pyrosequencing

Abstract

Background Leymus chinensis (Trin.) Tzvel. is a high saline-alkaline tolerant forage grass genus of the tribe Gramineae family, which also plays an important role in protection of natural environment. To date, little is known about the saline-alkaline tolerance of L. chinensis on the molecular level. To better understand the molecular mechanism of saline-alkaline tolerance in L. chinensis, 454 pyrosequencing was used for the transcriptome study.ResultsWe used Roche-454 massive parallel pyrosequencing technology to sequence two different cDNA libraries that were built from the two samples of control and under saline-alkaline treatment (optimal stress concentration-Hoagland solution with 100 mM NaCl and 200 mM NaHCO3). A total of 363,734 reads in control group and 526,267 reads in treatment group with an average length of 489 bp and 493 bp were obtained, respectively. The reads were assembled into 104,105 unigenes with MIRA sequence assemable software, among which, 73,665 unigenes were in control group, 88,016 unigenes in treatment group and 57,576 unigenes in both groups. According to the comparative expression analysis between the two groups with the threshold of “log2 Ratio ≥1”, there were 36,497 up-regulated unegenes and 18,218 down-regulated unigenes predicted to be the differentially expressed genes. After gene annotation and pathway enrichment analysis, most of them were involved in stress and tolerant function, signal transduction, energy production and conversion, and inorganic ion transport. Furthermore, 16 of these differentially expressed genes were selected for real-time PCR validation, and they were successfully confirmed with the results of 454 pyrosequencing.ConclusionsThis work is the first time to study the transcriptome of L. chinensis under saline-alkaline treatment based on the 454-FLX massively parallel DNA sequencing platform. It also deepened studies on molecular mechanisms of saline-alkaline in L. chinensis, and constituted a database for future studies.

Transcriptome Analysis in Sheepgrass (Leymus chinensis): A Dominant Perennial Grass of the Eurasian Steppe

“…This method helps to increase the number of sheepgrass-expressed transcripts included in the analysis, especially those related to freezing resistance. Although a saline-alkaline treatment transcriptome has been reported in sheepgrass using Roche-454 massive parallel pyrosequencing technology [31], the significant contributions in this study are that a lot of freezing-response related genes in sheepgrass were identified, as well as many EST-SSRs, including some SSRs related to sheepgrass freezing-responsive genes, were also identified for potential gene-phenotype study in future.…”

“…NGS technologies have been effectively used to generate large-scale transcriptome data in several plant species, such as Medicago [23], Arabidopsis [24], maize [25], barley [26], soybean [27], chickpea [28], [29], and developing oilseeds [30]. Recently, a transcriptome data was generated in sheepgrass ( Leymus chinensis ) under saline-alkaline treatment using Roche-454 massive parallel pyrosequencing technology and a large number of saline-alkaline responsive differentially expressed genes (DEGs) were obtained [31]. In this study, in order to further enrich sheepgrass transcriptome resources, obtain freezing stress resistance genes, accelerate our understanding of the genetic basis of stress tolerance traits, and discover useful genes and molecular marker for the future molecular breeding of sheepgrass and other Poaceae crops, such as wheat and barley, we generate a large collection of ESTs using 454 pyrosequencing technologies and present a comprehensive transcriptome characterization of sheepgrass, including assessments of transcriptome assembly, annotation, gene family and functional representation, useful gene discovery, SSR identification, and a phylogenic analysis of sheepgrass compared to other Poaceae species.…”

Bovine serum albumin in saliva mediates grazing response in Leymus chinensis revealed by RNA sequencing

“…Gene-expression profiling or transcriptome analysis can provide new insights to understand the molecular mechanism of grazing responses in plants. High-throughput next-generation sequencing (NGS) technologies, such as 454 (ROCHE), Solexa (Illumina), and SOLiD (ABI), have been widely and effectively used to generate large-scale transcriptome data in many plant species [ 21 – 28 ], including sheepgrass ( Leymus chinensis ) [ 29 , 30 ]. Sheepgrass is an important forage species in the genus of Leymus , with good quality, high nutrition value, and various stress resistance [ 31 – 34 ].…”

“…One copy of the haploid genome of sheepgrass contains 9.65-Gb, and high-throughput NGS technologies make it possible to generate genome resources at relatively low cost. So far, sheepgrass transcriptome databases have been generated under saline-alkaline treatment [ 29 ] and freezing treatment [ 30 ] using Roche-454 massive pyrosequencing technology. These databases provide numerous DEGs for two stresses.…”

A MYB-related Transcription Factor from Sheepgrass, LcMYB2, Promotes Seed Germination and Root Growth under Drought Stress

“…Sheepgrass, which is widely distributed in Eurasia, adapts well to drought, cold, saline and alkaline conditions [32,33]. To explore the mechanism that underlies the abiotic stress tolerance of sheepgrass, several transcriptome analyses have been performed in the past few years [32][33][34][35], and several genes identified by transcriptome analyses have actually enhanced the abiotic stress tolerance of transgenic plants [36][37][38][39][40][41][42]. Although MYB transcription factors play pivotal roles in drought responses, there is still no report on MYB proteins from sheepgrass that elucidates their contributions to sheepgrass drought tolerance.…”