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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

Gene ontology (GO) analysis of selected genes. A total of 8110 genes were categorized into three groups: Molecular function (A), Cell component (B) and Biological process (C).
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Fig3: Gene ontology (GO) analysis of selected genes. A total of 8110 genes were categorized into three groups: Molecular function (A), Cell component (B) and Biological process (C).

Mentions: BLAST searches revealed that 20,605 of 39,815 contigs had significant matches in the NCBI non-redundant protein database. Gene Ontology (GO) analysis of the matched contigs identified 8110 genes that were categorized into different GO groups (Figure 3). Some of the gene categories are partially redundant, which led to some genes being categorized into more than one group. In the molecular function category, genes assigned to the “catalytic activity” and “binding (other binding)” groups are highly enriched. In the cellular component category, genes in the “cell” and “intracellular” groups were the most abundant. In the biological process category, the “cellular process” and “macromolecule metabolism” groups contain the highest number of genes (Figure 3).Figure 3


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)

Gene ontology (GO) analysis of selected genes. A total of 8110 genes were categorized into three groups: Molecular function (A), Cell component (B) and Biological process (C).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Gene ontology (GO) analysis of selected genes. A total of 8110 genes were categorized into three groups: Molecular function (A), Cell component (B) and Biological process (C).
Mentions: BLAST searches revealed that 20,605 of 39,815 contigs had significant matches in the NCBI non-redundant protein database. Gene Ontology (GO) analysis of the matched contigs identified 8110 genes that were categorized into different GO groups (Figure 3). Some of the gene categories are partially redundant, which led to some genes being categorized into more than one group. In the molecular function category, genes assigned to the “catalytic activity” and “binding (other binding)” groups are highly enriched. In the cellular component category, genes in the “cell” and “intracellular” groups were the most abundant. In the biological process category, the “cellular process” and “macromolecule metabolism” groups contain the highest number of genes (Figure 3).Figure 3

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