Zhu Haifeng, Wang Hua, Zhu Yifang, Zou Jianwen, Zhao Fang-Jie, Huang Chao-Feng
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China.
State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
BMC Plant Biol. 2015 Jan 21;15:16. doi: 10.1186/s12870-014-0395-z.
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.
与普通荞麦（苦荞麦）相似，苦荞（鞑靼荞麦）表现出对铝（Al）的高度耐受性和积累能力。然而，铝解毒和积累的分子机制仍知之甚少。为了开始阐明铝耐受性和积累的分子基础，我们使用Illumina高通量mRNA测序（RNA-seq）技术对暴露于铝的根的顶端和基部片段进行全基因组转录组分析。
通过使用Trinity方法进行从头组装，并使用cap3软件减少转录本的冗余和嵌合体，我们构建了39,815个转录本，平均长度为1184 bp，其中20,605个转录本通过在NCBI非冗余蛋白质数据库中的BLAST搜索进行了注释。基因本体论（GO）和京都基因与基因组百科全书（KEGG）富集分析表明，参与细胞壁毒性防御和氧化应激的基因表达优先受到铝胁迫的诱导。我们的RNA-seq数据还表明，有机酸代谢不太可能是苦荞中铝诱导的有机酸分泌的限速步骤。我们鉴定了两个柠檬酸转运蛋白基因，它们被铝高度诱导，并可能参与柠檬酸向木质部的释放。此外，发现四个保守的耐铝基因中的三个在苦荞中被复制，并表现出不同的表达模式。
为苦荞从头组装了近40,000个高质量的转录本重叠群，为该植物物种的未来研究工作提供了参考平台。我们的差异表达和系统发育分析揭示了苦荞耐铝机制的新方面。
