Abstract
BackgroundSimilar to common buckwheat (Fagopyrum esculentum), tartary buckwheat (Fagopyrum tataricum) shows a high level of aluminum (Al) tolerance and accumulation. However, the molecular mechanisms for Al detoxification and accumulation are still poorly understood. To begin to elucidate the molecular basis of Al tolerance and accumulation, we used the Illumina high-throughput mRNA sequencing (RNA-seq) technology to conduct a genome-wide transcriptome analysis on both tip and basal segments of the roots exposed to Al.ResultsBy using the Trinity method for the de novo assembly and cap3 software to reduce the redundancy and chimeras of the transcripts, we constructed 39,815 transcripts with an average length of 1184 bp, among which 20,605 transcripts were annotated by BLAST searches in the NCBI non-redundant protein database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that expression of genes involved in the defense of cell wall toxicity and oxidative stress was preferentially induced by Al stress. Our RNA-seq data also revealed that organic acid metabolism was unlikely to be a rate-limiting step for the Al-induced secretion of organic acids in buckwheat. We identified two citrate transporter genes that were highly induced by Al and potentially involved in the release of citrate into the xylem. In addition, three of four conserved Al-tolerance genes were found to be duplicated in tartary buckwheat and display diverse expression patterns.ConclusionsNearly 40,000 high quality transcript contigs were de novo assembled for tartary buckwheat, providing a reference platform for future research work in this plant species. Our differential expression and phylogenetic analysis revealed novel aspects of Al-tolerant mechanisms in buckwheat.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0395-z) contains supplementary material, which is available to authorized users.
Highlights
Similar to common buckwheat (Fagopyrum esculentum), tartary buckwheat (Fagopyrum tataricum) shows a high level of aluminum (Al) tolerance and accumulation
Tartary buckwheat accumulated higher concentrations of Al in the shoots than common buckwheat in the 10 μM Al treatment, whereas shoot Al concentrations were similar between the two species in the higher Al treatments (20 and 50 μM) (Figure 1B)
The results showed that the expression of genes putatively involved in the tricarboxylic acid cycle, including key enzymes such as malate dehydrogenase and citrate synthase, was not induced by Al stress (Additional file 5: Figure S1), which is consistent with evidence that organic acid metabolism is not a ratelimiting step for Al-induced release of organic acids [38,39,40]
Summary
Similar to common buckwheat (Fagopyrum esculentum), tartary buckwheat (Fagopyrum tataricum) shows a high level of aluminum (Al) tolerance and accumulation. To begin to elucidate the molecular basis of Al tolerance and accumulation, we used the Illumina high-throughput mRNA sequencing (RNA-seq) technology to conduct a genome-wide transcriptome analysis on both tip and basal segments of the roots exposed to Al. Aluminum (Al) toxicity is a major limiting factor for crop production on acid soils, which make up over 30% of the world’s arable soils and up to 70% of the potential arable land [1]. Al-activated organic acid release from roots is a well-documented mechanism of Al detoxification [3,4]. Organic acids such as malate, citrate and oxalate are able to chelate Al and thereby attenuate Al toxicity. Genes involved in oxalate release have not been identified
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