数字农科院2.0

Unveiling the complexity of red clover (Trifolium pratense l.) transcriptome and transcriptional regulation of isoflavonoid biosynthesis using integrated long-and short-read rnaseq

文献类型： 外文期刊

作者： Kun Shi;Xiqiang Liu;Xinyi Pan;Jia Liu;Wenlong Gong;Pan Gong;Mingshu Cao;Shangang Jia;Zan Wang

作者机构：

关键词： Isoflavonoid biosynthesis;Red clover;Transcription factor;Transcriptome

期刊名称： International Journal of Molecular Sciences

ISSN： 1661-6596

年卷期： 2021 年 22 卷 23 期

页码：

收录情况： JCR（2021版）

摘要： Red clover (Trifolium pratense L.) is used as forage and contains a high level of isoflavonoids. Although isoflavonoids in red clover were discovered a long time ago, the transcriptional regulation of isoflavonoid biosynthesis is virtually unknown because of the lack of accurate and comprehensive characterization of the transcriptome. Here, we used a combination of long-read (PacBio Iso-Seq) and short-read (Illumina) RNAseq sequencing to develop a more comprehensive full-length transcriptome in four tissues (root, stem, leaf, and flower) and to identify transcription factors possibly involved in isoflavonoid biosynthesis in red clover. Overall, we obtained 50,922 isoforms, including 19,860 known genes and 2817 novel isoforms based on the annotation of RefGen Tp_v2.0. We also found 1843 long non-coding RNAs, 1625 fusion genes, and 34,612 alternatively spliced events, with some transcript isoforms validated experimentally. A total of 16,734 differentially expressed genes were identified in the four tissues, including 43 isoflavonoid-biosynthesis-related genes, such as stem-specific expressed TpPAL, TpC4H, and Tp4CL and root-specific expressed TpCHS, TpCHI1, and TpIFS. Further, weighted gene co-expression network analysis and a targeted compound assay were combined to investigate the association between the isoflavonoid content and the transcription factors expression in the four tissues. Twelve transcription factors were identified as key genes for isoflavonoid biosynthesis. Among these transcription factors, the overexpression of TpMYB30 or TpRSM1-2 significantly increased the isoflavonoid content in tobacco. In particular, the glycitin was increased by 50–100 times in the plants overexpressing TpRSM1-2, in comparison to that in the WT plants. Our study provides a comprehensive and accurate annotation of the red clover transcriptome and candidate genes to improve isoflavonoid biosynthesis and accelerate research into molecular breeding in red clover or other crops.

分类号：

  • 相关文献

[1]Analysis of global gene expression profiles to identify differentially expressed genes critical for embryo development in Brassica rapa. Zhang, Yu,Peng, Lifang,Wu, Ya,Shen, Yanyue,Wang, Jianbo,Wu, Xiaoming.

[2]Identification of candidate thermotolerance genes during early seedling stage in upland cotton (Gossypium hirsutum L.) revealed by comparative transcriptome analysis. Cao, Moju,Xu, Jie,Lu, Yanli,Peng, Zhen,He, Shoupu,Gong, Wenfang,Sun, Junling,Pan, Zhaoe,Du, Xiongming,Sun, Gaofei.

[3]Characterization of the global transcriptome for cotton (Gossypium hirsutum L.) anther and development of SSR marker. Xianwen Zhang ,Zhenwei Ye,TiankangWang,Hairong Xiong,Xiaoling Yuan,Zhigang Zhang,Youlu Yuan,Zhi Liu.

[4]Transcription Factor VdCf2 Regulates Growth, Pathogenicity, and the Expression of a Putative Secondary Metabolism Gene Cluster in Verticillium dahliae. Liu, Tao,Qin, Jun,Cao, Yonghong,Subbarao, Krishna, V,Chen, Jieyin,Mandal, Mihir K.,Xu, Xiangming,Shang, Wenjing,Hu, Xiaoping. 2022

[5]Iris lactea var. chinensis plant drought tolerance depends on the response of proline metabolism, transcription factors, transporters and the ROS-scavenging system. Yue Zhang,Ruihai Zhang,Zhen Song,Weidong Fu,Lingling Yun,Jinhui Gao,Guang Hu,Zhonghui Wang,Hanwen Wu,Guoliang Zhang,Jiahe Wu. 2023

[6]Transcriptomic profiling of wheat stem during meiosis in response to freezing stress. Yao D.,Wang J.,Peng W.,Zhang B.,Wen X.,Wan X.,Wang X.,Li X.,Ma J.,Liu X.,Fan Y.,Sun G.. 2023

[7]Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton. Zhenzhen Wang,Abdul Rehman,Yinhua Jia,Panhong Dai,Shoupu He,Xiaoyang Wang,Hongge Li,Liru Wang,Abdul Qayyum,Zhen Peng,Xiongming Du. 2023

[8]Comprehensive Evaluation and Transcriptome Analysis Reveal the Salt Tolerance Mechanism in Semi-Wild Cotton (Gossypium purpurascens). Zhen Peng,Abdul Rehman,Xiawen Li,Xuran Jiang,Chunyan Tian,Xiaoyang Wang,Hongge Li,Zhenzhen Wang,Shoupu He,Xiongming Du. 2023

[9]Integration of transcriptome and metabolome reveals regulatory mechanisms of volatile flavor formation during tomato fruit ripening. Liu, Zhiqiang,Wu, Jianxin,Wang, Licai,Lu, Xiaonan,Ahammed, Golam Jalal,Zhang, Xiaolan,Cui, Xia,Wang, Haijing. 2025

[10]Heat shock transcription factors regulate thermotolerance gene networks in tomato ( Solanum lycopersicum) flower buds. Li, Hongwei,Liu, Yun,Li, Yongyao,Yang, Qinqin,Yang, Tailai,Zhou, Zhi,Li, Yafei,Zhang, Na,Lyu, Yaqing,Zhu, Yingfang,Lin, Tao. 2025

[11]Transcriptome Analysis Of Leaf Senescence I.n Red Clover (Trifolium P ratense L.). Chao, Yuehui,Guo, Tao,Han, Liebao,Li, Yinruizhi,Liu, Fengqi,Xie, Lijuan,Yuan, Jianbo. 2018

[12]Identification of Transcription Factor Genes and Functional Characterization of PlMYB1 From Pueraria lobata. Guoan Shen,Ranran Wu,Yaying Xia,Yongzhen Pang. 2021

[13]Development and application of a duplex simple sequence repeat panel for outcrossing fertility evaluation in red clover (Trifolium pratense) under open-pollination conditions. Huang, Fan,Li, Jun,Zhou, Shengyan,Li, Zhiyong. 2022

[14]Protein-DNA interactions in the promoter region of the gene encoding diapause hormone and pheromone biosynthesis activating neuropeptide of the cotton bollworm, Helicoverpa armigera. Hong, B,Zhang, ZF,Tang, SM,Yi, YZ,Zhang, TY,Xu, WH.

[15]A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. Liu, Xiaohui,Lu, Tingting,Yu, Shuliang,Li, Ying,Huang, Yuchen,Huang, Tao,Zhang, Lei,Zhu, Jingjie,Zhao, Qiang,Fan, Danlin,Mu, Jie,Shangguan, Yingying,Feng, Qi,Guan, Jianping,Ying, Kai,Zhang, Yu,Lin, Zhixin,Sun, Zongxiu,Qian, Qian,Lu, Yuping,Han, Bin.

[16]A wheat R2R3-MYB gene, TaMYB30-B, improves drought stress tolerance in transgenic Arabidopsis. Zhang, Lichao,Zhao, Guangyao,Xia, Chuan,Jia, Jizeng,Liu, Xu,Kong, Xiuying. 2012

[17]Jasmonate-responsive transcription factors regulating plant secondary metabolism. Zhou, Meiliang,Zhou, Meiliang,Memelink, Johan.

[18]Characteristic Expression Analysis of Five WRKY Transcriptional Factors in Rice Leaf Growth and Disease Resistance Reaction. Miao Liu-Yang,Li Li-Yun,Liu Zhao,Liu Yu-Meng,Liu Guo-Zhen,Jiang Guang-Huai,Yang Feng-Huan,He Chen-Yang. 2013

[19]Isolation and functional characterization of a R2R3-MYB regulator of the anthocyanin biosynthetic pathway from Epimedium sagittatum. Huang, Wenjun,Khaldun, A. B. M.,Lv, Haiyan,Du, Liuwen,Wang, Ying,Du, Liuwen,Zhang, Chanjuan.

[20]Identification and functional characterization of the NAC gene promoter from Populus euphratica. Wang, Jun-Ying,Wang, Jun-Ping,Yang, Hai-Feng.

作者其他论文 更多>>