Limits...
Genome-wide transcriptomic and phylogenetic analyses reveal distinct aluminum-tolerance mechanisms in the aluminum-accumulating species buckwheat (Fagopyrum tataricum).

Zhu H, Wang H, Zhu Y, Zou J, Zhao FJ, Huang CF - BMC Plant Biol. (2015)

Bottom Line: In addition, three of four conserved Al-tolerance genes were found to be duplicated in tartary buckwheat and display diverse expression patterns.Nearly 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China. 2012203031@njau.edu.cn.

ABSTRACT

Background: Similar 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.

Results: By 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.

Conclusions: Nearly 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.

No MeSH data available.


Related in: MedlinePlus

Al accumulation in roots and shoots ofFagopyrum tataricumandFagopyrum esculentum. Two-week-old seedlings were exposed to a series of Al concentrations (0, 10, 20, 50 μM Al) for 8 d intermittently. The Al concentrations in roots (A) and shoots (B) and the ratio of shoot to root Al concentrations (C) were analyzed, respectively. Data are means ± SD (n = 4). Means with different letters are significantly different (P < 0.05, Tukey test).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4307214&req=5

Fig1: Al accumulation in roots and shoots ofFagopyrum tataricumandFagopyrum esculentum. Two-week-old seedlings were exposed to a series of Al concentrations (0, 10, 20, 50 μM Al) for 8 d intermittently. The Al concentrations in roots (A) and shoots (B) and the ratio of shoot to root Al concentrations (C) were analyzed, respectively. Data are means ± SD (n = 4). Means with different letters are significantly different (P < 0.05, Tukey test).

Mentions: To compare Al accumulation by tartary buckwheat and common buckwheat, we exposed plants of both species to different Al concentrations for 8 d intermittently in a hydroponic experiment. Both species accumulated appreciable amounts of Al in the roots and shoots in the control treatment (Figure 1A and B), suggesting that both buckwheat species efficiently took up the background level of Al in the nutrient solution. In the treatments with 10–50 μM Al, tartary buckwheat accumulated significantly more Al in the roots than common buckwheat (Figure 1A). 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).Figure 1


Genome-wide transcriptomic and phylogenetic analyses reveal distinct aluminum-tolerance mechanisms in the aluminum-accumulating species buckwheat (Fagopyrum tataricum).

Zhu H, Wang H, Zhu Y, Zou J, Zhao FJ, Huang CF - BMC Plant Biol. (2015)

Al accumulation in roots and shoots ofFagopyrum tataricumandFagopyrum esculentum. Two-week-old seedlings were exposed to a series of Al concentrations (0, 10, 20, 50 μM Al) for 8 d intermittently. The Al concentrations in roots (A) and shoots (B) and the ratio of shoot to root Al concentrations (C) were analyzed, respectively. Data are means ± SD (n = 4). Means with different letters are significantly different (P < 0.05, Tukey test).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4307214&req=5

Fig1: Al accumulation in roots and shoots ofFagopyrum tataricumandFagopyrum esculentum. Two-week-old seedlings were exposed to a series of Al concentrations (0, 10, 20, 50 μM Al) for 8 d intermittently. The Al concentrations in roots (A) and shoots (B) and the ratio of shoot to root Al concentrations (C) were analyzed, respectively. Data are means ± SD (n = 4). Means with different letters are significantly different (P < 0.05, Tukey test).
Mentions: To compare Al accumulation by tartary buckwheat and common buckwheat, we exposed plants of both species to different Al concentrations for 8 d intermittently in a hydroponic experiment. Both species accumulated appreciable amounts of Al in the roots and shoots in the control treatment (Figure 1A and B), suggesting that both buckwheat species efficiently took up the background level of Al in the nutrient solution. In the treatments with 10–50 μM Al, tartary buckwheat accumulated significantly more Al in the roots than common buckwheat (Figure 1A). 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).Figure 1

Bottom Line: In addition, three of four conserved Al-tolerance genes were found to be duplicated in tartary buckwheat and display diverse expression patterns.Nearly 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China. 2012203031@njau.edu.cn.

ABSTRACT

Background: Similar 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.

Results: By 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.

Conclusions: Nearly 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.

No MeSH data available.


Related in: MedlinePlus