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Comprehensive transcriptome analysis reveals genes potentially involved in isoflavone biosynthesis in Pueraria thomsonii Benth

文献类型： 外文期刊

作者： He, Meijun 1 ; Yao, Yiwei 3 ; Li, Yanni 3 ; Yang, Meng 3 ; Li, Yu 2 ; Wu, Bin 3 ; Yu, Dazhao 1 ;

作者机构： 1.Wuhan Univ, Coll Life Sci, Wuhan, Hubei, Peoples R China

2.Hubei Acad Agr Sci, Inst Chinese Med Mat, Enshi, Peoples R China

3.Chinese Acad Med Sci, Ctr Bioinformat, Inst Med Plant Dev, Beijing, Peoples R China

4.Peking Union Med Coll, Beijing, Peoples R China

期刊名称：PLOS ONE （ 影响因子：3.24； 五年影响因子：3.788 ）

ISSN： 1932-6203

年卷期： 2019 年 14 卷 6 期

页码：

收录情况： SCI

摘要： Pueraria thomsonii Benth is an important medicinal plant. Transcriptome sequencing, unigene assembly, the annotation of transcripts and the study of gene expression profiles play vital roles in gene function research. However, the full-length transcriptome of P. thomsonii remains unknown. Here, we obtained 44,339 nonredundant transcripts of P. thomsonii by using the PacBio RS II Isoform and Illumina sequencing platforms, of which 43,195 were annotated genes. Compared with the expression levels in the plant roots, those of transcripts with a vertical bar fold change vertical bar >= 4 and FDR < 0.01 in the leaves or stems were assigned as differentially expressed transcripts (DETs). In total, we found 9,225 DETs, 32 of which came from structural genes that were potentially involved in isoflavone biosynthesis. The expression profiles of 8 structural genes from the RNA-Seq data were validated by qRT-PCR. We identified 437 transcription factors (TFs) that were positively or negatively correlated with at least 1 of the structural genes involved in isoflavone biosynthesis using Pearson correlation coefficients (r) (r > 0.8 or r < -0.8). We also identified a total of 32 microRNAs (miRNAs), which targeted 805 transcripts. These miRNAs caused enriched function in 'ATP binding', 'defense response', 'ADP binding', and 'signal transduction'. Interestingly, MIR156a potentially promoted isoflavone biosynthesis by repressing SBP, and MIR319 promoted isoflavone biosynthesis by repressing TCP and HB-HD-ZIP. Finally, we identified 2,690 alternative splicing events, including that of the structural genes of trans-cinnamate 4-mono-oxygenase and pullulanase, which are potentially involved in the biosynthesis of isoflavone and starch, respectively, and of three TFs potentially involved in isoflavone biosynthesis. Together, these results provide us with comprehensive insight into the gene expression and regulation of P. thomsonii.

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