Tian Mei, Zhang Xiang, Zhu Yan, Xie Guoyong, Qin Minjian
Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China.
Key Laboratory of Modern Traditional Chinese Medicines (Ministry of Education), China Pharmaceutical University, Nanjing, China.
Front Plant Sci. 2018 Aug 14;9:1160. doi: 10.3389/fpls.2018.01160. eCollection 2018.
(L.) DC., a perennial herb of the family Iridaceae, is rich in a variety of (iso)flavonoids with significant organ-specific distribution and has a swollen rhizome that is widely used in East Asia as a traditional medicine. In the present study, comprehensive transcriptomes of six organs (root, rhizome, aerial stem, leaf, flower, and young fruit) of were obtained by high-throughput RNA-sequencing and assembly. A total of 423,661 unigenes (mean length = 618 bp, median length = 391 bp) were assembled and annotated in seven databases: Non-redundant protein sequences, Nucleotide sequences, Swiss-Prot, Protein family database, euKaryotic Ortholog Groups, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO). A total of 4995 transcription factors were identified, including 408 MYB, 182 bHLH, 277 AP2/ERF, and 228 WRKY genes. A total of 129 cytochrome P450 unigenes belonging to 10 divergent clans were identified and grouped into clades in a phylogenetic tree that showed their inferred evolutionary relationship. Differentially expressed unigenes among the six organs were subjected to GO and KEGG enrichment analysis to profile the functions of each organ. Unigenes associated with (iso)flavonoid biosynthesis were then profiled by expression level analysis. Additionally, the complete coding sequences of six predicted enzymes essential to the (iso)flavonoid pathway were obtained, based on the annotated unigenes. This work reveals clear differences in expression patterns of genes among the six organs and will provide a sound platform to understand the (iso)flavonoid pathways in
（鸢尾科的一种多年生草本植物），富含多种具有显著器官特异性分布的（异）黄酮类化合物，其根茎膨大，在东亚作为传统药物被广泛使用。在本研究中，通过高通量RNA测序和组装获得了六个器官（根、根茎、地上茎、叶、花和幼果）的综合转录组。总共423,661个单基因（平均长度 = 618 bp，中位数长度 = 391 bp）在七个数据库中进行了组装和注释：非冗余蛋白质序列、核苷酸序列、瑞士蛋白质数据库、蛋白质家族数据库、真核直系同源组、京都基因与基因组百科全书（KEGG）和基因本体论（GO）。共鉴定出4995个转录因子，包括408个MYB、182个bHLH、277个AP2/ERF和228个WRKY基因。共鉴定出129个属于10个不同家族的细胞色素P450单基因，并在系统发育树中分组为进化枝，显示了它们推断的进化关系。对六个器官中差异表达的单基因进行GO和KEGG富集分析，以描述每个器官的功能。然后通过表达水平分析对与（异）黄酮生物合成相关联的单基因进行分析。此外，基于注释的单基因获得了（异）黄酮途径中六种预测酶的完整编码序列。这项工作揭示了六个器官中基因表达模式的明显差异，并将为理解……中的（异）黄酮途径提供一个良好的平台
