Transcriptome sequencing of the Antarctic vascular plant Deschampsia antarctica Desv. under abiotic stress

Abstract

Antarctic hairgrass (Deschampsia antarctica Desv.) is the only natural grass species in the maritime Antarctic. It has been studied as an extremophile that has successfully adapted to marginal land with the harshest environment for terrestrial plants. However, limited genetic research has focused on this species due to the lack of genomic resources. Here, we present the first de novo assembly of its transcriptome by massive parallel sequencing and its expression profile using D. antarctica grown under various stress conditions. Total sequence reads generated by pyrosequencing were assembled into 60,765 unigenes (28,177 contigs and 32,588 singletons). A total of 29,173 unique protein-coding genes were identified based on sequence similarities to known proteins. The combined results from all three stress conditions indicated differential expression of 3,110 genes. Quantitative reverse transcription polymerase chain reaction showed that several well-known stress-responsive genes encoding late embryogenesis abundant protein, dehydrin 1, and ice recrystallization inhibition protein were induced dramatically and that genes encoding U-box-domain-containing protein, electron transfer flavoprotein-ubiquinone, and F-box-containing protein were induced by abiotic stressors in a manner conserved with other plant species. We identified more than 2,000 simple sequence repeats that can be developed as functional molecular markers. This dataset is the most comprehensive transcriptome resource currently available for D. antarctica and is therefore expected to be an important foundation for future genetic studies of grasses and extremophiles.

Transcriptome Profiling to Discover Putative Genes Associated with Paraquat Resistance in Goosegrass (Eleusine indica L.)

“…29,056 [23], 60,765 [20], 65,340 [21], 79,082 [22]). 35,016 unigenes were annotated by nr database from 100,742 unigenes.…”

“…Next-generation sequencing (NGS) technology has rapidly advanced the analysis of genomes and transcriptomes in model plant and crop species which can now be applied to other species whose genomes have not been sequenced [18]–[19]. NGS has also been widely used for comparative transcriptome analysis to identify genes that are differentially expressed across different cultivars or tissues or treatment conditions [20]–[23].…”

RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants

“…In the fi rst case, the transcriptomes of plants known for their adaptability to cold have been studied. Examples are Ammopiptanthus mongolicus , an evergreen broadleaf legume shrub, distributed in Mid-Asia where the temperature can be as low as −30 °C during winter (Pang et al 2013 ), the sheepgrass Leymus chinensis , an important perennial forage grass across the Eurasian Steppe , or the extremophile Antarctic hairgrass Deschampsia antarctica , the only natural grass species in the maritime Antarctic (Lee et al 2013 ). In the second case, researchers studied the transcriptomes of tropical or other cold-sensitive plants useful in biotechnology or horticulture.…”

“…Standard transcriptome annotation included BLAST alignments against the NCBI nonredundant (NR) database and the COG database as well as GO and KEGG annotations. However, in some works an extensive annotation has been done also by alignments against EST databases (Wang et al 2013b , d ;Lee et al 2013 ), the From Pertea et al ( 2003 ) TAIR10 database (Wang et al 2013d ), or the PlantGDB database ).…”

“…For Leymus chinensis and Deschampsia antarctica , the transcriptome assembly allowed performing phylogenetic analyses Lee et al 2013 ). In each of these studies, thousands of genes were found to be differentially expressed under cold.…”