Min Zhang , Wenle Wang , Qian Liu , Erhuan Zang , Lijun Wu , Guofa Hu , Minhui Li
{"title":"三叶草转录组分析及抽苔和开花基因的挖掘","authors":"Min Zhang , Wenle Wang , Qian Liu , Erhuan Zang , Lijun Wu , Guofa Hu , Minhui Li","doi":"10.1016/j.chmed.2022.08.008","DOIUrl":null,"url":null,"abstract":"<div><h3>Objective</h3><p>Early bolting of <em>Saposhnikovia divaricata</em> has seriously hindered its medicinal value and sustainable development of resources. The molecular mechanism of bolting and flowering of <em>S. divaricata</em> is still unclear and worth of research. In our study, we explored the transcriptome of the genes related to the bolting and flowering of <em>S. divaricata.</em></p></div><div><h3>Methods</h3><p>The transcriptome library was constructed, sequenced, assembled and annotated from the bolting and unbolting leaves of <em>S. divaricata</em> by high-throughput sequencing at the bud and flowering stage. Focus on the pathways related to bolting and flowering in plants, and exploring genes. The expression of seven candidate genes was verified by real-time fluorescence quantitative PCR (qRT-PCR).</p></div><div><h3>Results</h3><p>Transcriptome results showed that 249 889 422 high-quality clean reads were obtained. A total of 67 866 unigenes were assembled with an average length of 948.1 bp. Trinity <em>de Novo</em> assembly produced 67 866 unigenes with an average length of 948.1 bp. Among 993 differentially expressed genes, 484 genes were significantly up-regulated and 509 genes were down-regulated in the SdM group. A total of 79 GO terms were significantly enriched for differentially expressed genes. KEGG results showed that 11 154 unigenes were enriched in 89 pathways. And 21 candidate genes related to bolting and flowering of <em>S. divaricata</em> were excavated. The qRT-PCR results showed that expression trends of <em>HDA9</em>, <em>PHYB</em>, <em>AP2</em>, <em>TIR1</em>, <em>Hsp90</em>, <em>CaM</em>, and <em>IAA7</em> were consistent with transcriptomic sequencing results. In addition, RNA-seq had identified 10 740 transcription factors and classified them into 58 families by their conserved domains. Further studies showed that the transcription factors regulating the flowering of <em>S. divaricata</em> were mainly distributed in the NAC, MYB_related, HB-other, ARF, and AP2 families.</p></div><div><h3>Conclusion</h3><p>Based on the results of this study, it was found that the plant hormone signal transduction pathway was one of the decisive factors to control bolting and flowering. Among them, auxin related genes <em>IAA</em> and <em>TIR1</em> are the key genes in the bolting and flowering process of <em>S. divaricata</em>.</p></div>","PeriodicalId":9916,"journal":{"name":"Chinese Herbal Medicines","volume":"15 4","pages":"Pages 574-587"},"PeriodicalIF":4.7000,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1674638423000072/pdfft?md5=703c16c9c5da314be2c5324a1fd320b2&pid=1-s2.0-S1674638423000072-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Transcriptome analysis of Saposhnikovia divaricata and mining of bolting and flowering genes\",\"authors\":\"Min Zhang , Wenle Wang , Qian Liu , Erhuan Zang , Lijun Wu , Guofa Hu , Minhui Li\",\"doi\":\"10.1016/j.chmed.2022.08.008\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Objective</h3><p>Early bolting of <em>Saposhnikovia divaricata</em> has seriously hindered its medicinal value and sustainable development of resources. The molecular mechanism of bolting and flowering of <em>S. divaricata</em> is still unclear and worth of research. In our study, we explored the transcriptome of the genes related to the bolting and flowering of <em>S. divaricata.</em></p></div><div><h3>Methods</h3><p>The transcriptome library was constructed, sequenced, assembled and annotated from the bolting and unbolting leaves of <em>S. divaricata</em> by high-throughput sequencing at the bud and flowering stage. Focus on the pathways related to bolting and flowering in plants, and exploring genes. The expression of seven candidate genes was verified by real-time fluorescence quantitative PCR (qRT-PCR).</p></div><div><h3>Results</h3><p>Transcriptome results showed that 249 889 422 high-quality clean reads were obtained. A total of 67 866 unigenes were assembled with an average length of 948.1 bp. Trinity <em>de Novo</em> assembly produced 67 866 unigenes with an average length of 948.1 bp. Among 993 differentially expressed genes, 484 genes were significantly up-regulated and 509 genes were down-regulated in the SdM group. A total of 79 GO terms were significantly enriched for differentially expressed genes. KEGG results showed that 11 154 unigenes were enriched in 89 pathways. And 21 candidate genes related to bolting and flowering of <em>S. divaricata</em> were excavated. The qRT-PCR results showed that expression trends of <em>HDA9</em>, <em>PHYB</em>, <em>AP2</em>, <em>TIR1</em>, <em>Hsp90</em>, <em>CaM</em>, and <em>IAA7</em> were consistent with transcriptomic sequencing results. In addition, RNA-seq had identified 10 740 transcription factors and classified them into 58 families by their conserved domains. Further studies showed that the transcription factors regulating the flowering of <em>S. divaricata</em> were mainly distributed in the NAC, MYB_related, HB-other, ARF, and AP2 families.</p></div><div><h3>Conclusion</h3><p>Based on the results of this study, it was found that the plant hormone signal transduction pathway was one of the decisive factors to control bolting and flowering. Among them, auxin related genes <em>IAA</em> and <em>TIR1</em> are the key genes in the bolting and flowering process of <em>S. divaricata</em>.</p></div>\",\"PeriodicalId\":9916,\"journal\":{\"name\":\"Chinese Herbal Medicines\",\"volume\":\"15 4\",\"pages\":\"Pages 574-587\"},\"PeriodicalIF\":4.7000,\"publicationDate\":\"2023-10-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S1674638423000072/pdfft?md5=703c16c9c5da314be2c5324a1fd320b2&pid=1-s2.0-S1674638423000072-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Chinese Herbal Medicines\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1674638423000072\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MEDICINAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Chinese Herbal Medicines","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1674638423000072","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
Transcriptome analysis of Saposhnikovia divaricata and mining of bolting and flowering genes
Objective
Early bolting of Saposhnikovia divaricata has seriously hindered its medicinal value and sustainable development of resources. The molecular mechanism of bolting and flowering of S. divaricata is still unclear and worth of research. In our study, we explored the transcriptome of the genes related to the bolting and flowering of S. divaricata.
Methods
The transcriptome library was constructed, sequenced, assembled and annotated from the bolting and unbolting leaves of S. divaricata by high-throughput sequencing at the bud and flowering stage. Focus on the pathways related to bolting and flowering in plants, and exploring genes. The expression of seven candidate genes was verified by real-time fluorescence quantitative PCR (qRT-PCR).
Results
Transcriptome results showed that 249 889 422 high-quality clean reads were obtained. A total of 67 866 unigenes were assembled with an average length of 948.1 bp. Trinity de Novo assembly produced 67 866 unigenes with an average length of 948.1 bp. Among 993 differentially expressed genes, 484 genes were significantly up-regulated and 509 genes were down-regulated in the SdM group. A total of 79 GO terms were significantly enriched for differentially expressed genes. KEGG results showed that 11 154 unigenes were enriched in 89 pathways. And 21 candidate genes related to bolting and flowering of S. divaricata were excavated. The qRT-PCR results showed that expression trends of HDA9, PHYB, AP2, TIR1, Hsp90, CaM, and IAA7 were consistent with transcriptomic sequencing results. In addition, RNA-seq had identified 10 740 transcription factors and classified them into 58 families by their conserved domains. Further studies showed that the transcription factors regulating the flowering of S. divaricata were mainly distributed in the NAC, MYB_related, HB-other, ARF, and AP2 families.
Conclusion
Based on the results of this study, it was found that the plant hormone signal transduction pathway was one of the decisive factors to control bolting and flowering. Among them, auxin related genes IAA and TIR1 are the key genes in the bolting and flowering process of S. divaricata.
期刊介绍：
Chinese Herbal Medicines is intended to disseminate the latest developments and research progress in traditional and herbal medical sciences to researchers, practitioners, academics and administrators worldwide in the field of traditional and herbal medicines. The journal's international coverage ensures that research and progress from all regions of the world are widely included.
CHM is a core journal of Chinese science and technology. The journal entered into the ESCI database in 2017, and then was included in PMC, Scopus and other important international search systems. In 2019, CHM was successfully selected for the “China Science and Technology Journal Excellence Action Plan” project, which has markedly improved its international influence and industry popularity. CHM obtained the first impact factor of 3.8 in Journal Citation Reports (JCR) in 2023.
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