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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

Expression analysis of Al-tolerance gene homologs in different root regions under different Al conditions. (A)ART1 homologs, FtARL1 and FtARL2. (B)ALS1 homologs, FtALOL1 and FtALOL2. (C)STAR1 homologs, FtSTOL1 and FtSTOL2. (D)FtSTAR2. The data were normalized to the expression of gene homolog1 in the root tips without Al treatment. Data shown are means ± SD (n = 3).
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Fig8: Expression analysis of Al-tolerance gene homologs in different root regions under different Al conditions. (A)ART1 homologs, FtARL1 and FtARL2. (B)ALS1 homologs, FtALOL1 and FtALOL2. (C)STAR1 homologs, FtSTOL1 and FtSTOL2. (D)FtSTAR2. The data were normalized to the expression of gene homolog1 in the root tips without Al treatment. Data shown are means ± SD (n = 3).

Mentions: A number of genes required for Al tolerance in rice and Arabidopsis have been cloned and characterized recently. To understand the mechanisms of Al tolerance in the Al hyperaccumulator buckwheat, we performed expression and phylogenetic analysis of homologs of four conserved Al-tolerance genes in rice and Arabidopsis, ART1/STOP1, ALS1, STAR1 and STAR2/ALS3. We identified two homologs of ART1, namely ARL1 and ARL2 (ART1-Like) in buckwheat. Phylogenetic analysis indicated that both ARL1 and ARL2 are closer to Arabidopsis STOP1 than to rice ART1 (Figure 7A), suggesting that the duplication event of ART1 in buckwheat happened after the dicot-monocot split. Real-time RT-PCR analysis showed that both ARL1 and ARL2 were equally expressed in the root tips and basal roots, and their expression was not affected by the Al treatment (Figure 8A).Figure 7


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)

Expression analysis of Al-tolerance gene homologs in different root regions under different Al conditions. (A)ART1 homologs, FtARL1 and FtARL2. (B)ALS1 homologs, FtALOL1 and FtALOL2. (C)STAR1 homologs, FtSTOL1 and FtSTOL2. (D)FtSTAR2. The data were normalized to the expression of gene homolog1 in the root tips without Al treatment. Data shown are means ± SD (n = 3).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig8: Expression analysis of Al-tolerance gene homologs in different root regions under different Al conditions. (A)ART1 homologs, FtARL1 and FtARL2. (B)ALS1 homologs, FtALOL1 and FtALOL2. (C)STAR1 homologs, FtSTOL1 and FtSTOL2. (D)FtSTAR2. The data were normalized to the expression of gene homolog1 in the root tips without Al treatment. Data shown are means ± SD (n = 3).
Mentions: A number of genes required for Al tolerance in rice and Arabidopsis have been cloned and characterized recently. To understand the mechanisms of Al tolerance in the Al hyperaccumulator buckwheat, we performed expression and phylogenetic analysis of homologs of four conserved Al-tolerance genes in rice and Arabidopsis, ART1/STOP1, ALS1, STAR1 and STAR2/ALS3. We identified two homologs of ART1, namely ARL1 and ARL2 (ART1-Like) in buckwheat. Phylogenetic analysis indicated that both ARL1 and ARL2 are closer to Arabidopsis STOP1 than to rice ART1 (Figure 7A), suggesting that the duplication event of ART1 in buckwheat happened after the dicot-monocot split. Real-time RT-PCR analysis showed that both ARL1 and ARL2 were equally expressed in the root tips and basal roots, and their expression was not affected by the Al treatment (Figure 8A).Figure 7

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