Next-generation sequencing-based transcriptome profiling analysis of Pohlia nutans reveals insight into the stress-relevant genes in Antarctic moss

Abstract

Genome-wide characterization of the Pohlia nutans transcriptome is essential for clarifying the role of stress-relevant genes in Antarctic moss adapting to the extreme polar environment. High-throughput Illumina sequencing was used to analyze the gene expression profile of P. nutans after cold treatment. A total of 93,488 unigenes, with an average length of 405 bp, were obtained. Gene annotation showed that 16,781 unigenes had significant similarity to known functional protein-coding genes, most of which were annotated using the GO, KOG and KEGG pathway databases. Global profiling of the differentially expressed genes revealed that 3,796 unigenes were significantly upregulated after cold treatment, while 1,405 unigenes were significantly downregulated. In addition, 816 receptor-like kinases and 1,309 transcription factors were identified from P. nutans. This overall survey of transcripts and stress-relevant genes can contribute to understanding the stress-resistance mechanism of Antarctic moss and will accelerate the practical exploitation of the genetic resources for this organism.

De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis

“…However, 38,115 unigenes (41.3%) have no significant match with any deposited sequence and are considered unknowns. Transcriptome annotation in other bryophyte species have obtained similar results with the percentage of unknown sequences greater than 40%: T. ruralis (40.3%) [36], P. patens (42%) [47], Marchantia polymorpha (43%) [34] and Pohlia nutans (82%) [35]. 14, 057  S. caninervis transcripts had significant similarity to deduced polypeptides in each of the five databases.…”

“…Transcriptome sequencing is one of the most important tools for gene discovery and the identification of expression patterns [30-33]. Bryophyte transcriptomes has been generated and characterized from a number of species including Marchantia polymorpha [34], Pohlia nutans [35], T. ruralis [36,37] and P. patens [32,33]. Next generation high throughput sequencing technologies offer an efficient and economic choice for characterizing non-model organism transcriptomes with little or no prior molecular information available.…”

Dependence on epiphytic bacteria for freezing protection in an Antarctic moss, Bryum argenteum

“…In Ceratodon purpureus , frost hardiness was associated with an increase in unsaturated membrane lipids (Aro and Karunen, ). In the Antarctic Pohlia nutans , cold treatment was found to upregulate over 40 genes by a factor of at least 4 (Liu et al ., ).…”

“…Only one other cold-tolerant moss has been subjected to large-scale sequencing. The Antarctic Pohlia nutans was grown at 16.5 o C in the laboratory and then acclimated to 4 o C for 6 h (Liu et al, 2013). A search of the transcriptome of this sample (acc.…”

Comparative Transcriptomic Analysis of the Response to Cold Acclimation in Eucalyptus dunnii

“…Compared to the traditional sequencing techniques, NGS is more robust and demonstrates greater resolution and inter-lab portability compared to several microarray platforms. NGS could detect millions of transcripts and is beneficial to explore new genes and their expression profiling independent of a reference genome [6] , [20] , [21] . For example, cDNA libraries for E. gunnii have been constructed to identify genes involved in cell protection (such as PCP, Lti6b and metallothionein), LEA/dehydrin accumulation, and cryoprotection [22] , [23] .…”