title: Genome-wide transcriptomic and phylogenetic analyses reveal distinct aluminum-tolerance mechanisms in the aluminum-accumulating species buckwheat (Fagopyrum tataricum).
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.
authors.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.
authors.forename: Haifeng
authors.initials: H
authors.lastname: Zhu
authors.affiliation: 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. wanghua74@189.cn.
authors.forename: Hua
authors.initials: H
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China. 10110204@njau.edu.cn.
authors.forename: Yifang
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China. jwzou21@njau.edu.cn.
authors.forename: Jianwen
authors.initials: J
authors.lastname: Zou
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China. fangjie.zhao@njau.edu.cn.
authors.forename: Fang-Jie
authors.initials: FJ
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China. chaofeng.huang@njau.edu.cn.
authors.forename: Chao-Feng
authors.initials: CF
authors.lastname: Huang
mesh_terms: D000222:Adaptation, Physiological / Q000187:drug effects / Q000235:genetics*; D000535:Aluminum / Q000633:toxicity*; D002264:Carboxylic Acids / Q000378:metabolism; D015536:Down-Regulation / Q000187:drug effects / Q000235:genetics; D019612:Fagopyrum / Q000187:drug effects / Q000235:genetics* / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D063990:Gene Ontology; D017343:Genes, Plant; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D018517:Plant Roots / Q000187:drug effects / Q000378:metabolism; D018520:Plant Shoots / Q000187:drug effects / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics; D015854:Up-Regulation / Q000187:drug effects / Q000235:genetics
chemical_list: D002264:Carboxylic Acids; D012333:RNA, Messenger; D000535:Aluminum