Genome-wide transcriptomic and phylogenetic analyses reveal distinct aluminum-tolerance mechanisms in the aluminum-accumulating species buckwheat (Fagopyrum tataricum).
Genome-wide transcriptomic and phylogenetic analyses reveal distinct aluminum-tolerance mechanisms in the aluminum-accumulating species buckwheat (Fagopyrum tataricum).
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DOI：
10.1186/s12870-014-0395-z
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发表时间：
2015-01-21
影响因子：
5.3
通讯作者：
Huang CF
中科院分区：
文献类型：
--
作者：
Zhu H;Wang H;Zhu Y;Zou J;Zhao FJ;Huang CF
苦荞麦(Fagopyrum Esculentum)与普通荞麦(Fagopyrum Esculentum)相似，具有较高的铝耐性和积累能力。然而，铝解毒和积累的分子机制仍然知之甚少。为了阐明铝耐性和积累的分子基础，我们利用Illumina高通量mRNA测序(RNA-seq)技术对铝暴露下的根的顶端和基段进行了全基因组转录组学分析。通过使用三位一体方法进行从头组装，并利用Cap3软件减少转录本的冗余度和嵌合体，我们构建了39,815个转录本，平均长度为1184个碱基对，其中20,605个转录本通过BLAST搜索在NCBI非冗余蛋白质数据库中进行了标注。基因本体论(GO)和京都基因和基因组百科全书(KEGG)的丰富分析表明，铝胁迫优先诱导与细胞壁毒性和氧化胁迫防御相关的基因表达。我们的RNA-seq数据还表明，有机酸代谢不太可能是铝诱导荞麦分泌有机酸的限速步骤。我们鉴定了两个柠檬酸转运蛋白基因，它们被铝高度诱导，并可能参与柠檬酸释放到木质部中。此外，4个保守的耐铝基因中有3个在苦荞麦中复制，并表现出不同的表达模式。构建了近4万个高质量的苦荞麦转录重叠群，为苦荞麦的进一步研究提供了参考平台。我们的差异表达和系统发育分析揭示了荞麦耐铝机制的新方面。本文的在线版本(doi：10.1186/s12870-0140395-z)包含补充材料，授权用户可以使用。
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. 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. 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. The online version of this article (doi:10.1186/s12870-014-0395-z) contains supplementary material, which is available to authorized users.