Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of <i>Dryopteris fragrans</i> (L.) Schott
Background: <i>Dryopteris fragrans</i>, which is densely covered with glandular trichomes, is considered to be one of the ferns with the most medicinal potential. The transcriptomes from selected tissues of <i>D. fragrans</i> were collected and analyzed for functional and com...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/19/7296 |
| _version_ | 1797551967374934016 |
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| author | Lingling Chen Dongrui Zhang Chunhua Song Hemeng Wang Xun Tang Ying Chang |
| author_facet | Lingling Chen Dongrui Zhang Chunhua Song Hemeng Wang Xun Tang Ying Chang |
| author_sort | Lingling Chen |
| collection | DOAJ |
| description | Background: <i>Dryopteris fragrans</i>, which is densely covered with glandular trichomes, is considered to be one of the ferns with the most medicinal potential. The transcriptomes from selected tissues of <i>D. fragrans</i> were collected and analyzed for functional and comparative genomic studies. The aim of this study was to determine the transcriptomic characteristics of wild <i>D. fragrans</i> sporangium in tissues from the SR (root), SL (sporophyll), and TRL (sporophyll with glandular trichomes removed). Results: Cluster analysis identified genes that were highly expressed in an organ-specific manner according to read mapping, feature counting, and normalization. The functional map identified gene clusters that can uniquely describe the function of each tissue. We identified a group of three tissue-specific transcription factors targeting the SL, SR, and TRL. In addition, highly expressed transcription factors (TFs) were found in each tissue-specific gene cluster, where ERF and bHLH transcription factors were the two types showing the most distinct expression patterns between the three different tissues. The specific expression of transcription factor genes varied between the different types of tissues. The numbers of transcription factors specifically expressed in the roots and sporophylls were 60 and 30, respectively, while only seven were found for the sporophylls with glandular trichomes removed. The expression of genes known to be associated with the development of glandular trichomes in flowering plants, including MIXTA, ATML1, and MYB106, were also validated and are discussed. In particular, a unigene encoding MIXTA was identified and exhibited the highest expression level in SL in <i>D. fragrans.</i> Conclusions: This study is the first report of global transcriptomic analysis in different tissues of <i>D. fragrans</i>, and the first to discuss these findings in the context of the development of homologous glandular trichomes. These results set the stage for further research on the development, stress resistance, and secondary metabolism of <i>D. fragrans</i> glandular trichomes. |
| first_indexed | 2024-03-10T15:52:09Z |
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| language | English |
| last_indexed | 2024-03-10T15:52:09Z |
| publishDate | 2020-10-01 |
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| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-d51113b2b8044d3980765c4102430f582023-11-20T15:57:09ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-10-012119729610.3390/ijms21197296Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of <i>Dryopteris fragrans</i> (L.) SchottLingling Chen0Dongrui Zhang1Chunhua Song2Hemeng Wang3Xun Tang4Ying Chang5College of Life Sciences, Northeast Agricultural University, Harbin 150030, Heilongjiang Province, ChinaCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, Heilongjiang Province, ChinaCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, Heilongjiang Province, ChinaCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, Heilongjiang Province, ChinaCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, Heilongjiang Province, ChinaCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, Heilongjiang Province, ChinaBackground: <i>Dryopteris fragrans</i>, which is densely covered with glandular trichomes, is considered to be one of the ferns with the most medicinal potential. The transcriptomes from selected tissues of <i>D. fragrans</i> were collected and analyzed for functional and comparative genomic studies. The aim of this study was to determine the transcriptomic characteristics of wild <i>D. fragrans</i> sporangium in tissues from the SR (root), SL (sporophyll), and TRL (sporophyll with glandular trichomes removed). Results: Cluster analysis identified genes that were highly expressed in an organ-specific manner according to read mapping, feature counting, and normalization. The functional map identified gene clusters that can uniquely describe the function of each tissue. We identified a group of three tissue-specific transcription factors targeting the SL, SR, and TRL. In addition, highly expressed transcription factors (TFs) were found in each tissue-specific gene cluster, where ERF and bHLH transcription factors were the two types showing the most distinct expression patterns between the three different tissues. The specific expression of transcription factor genes varied between the different types of tissues. The numbers of transcription factors specifically expressed in the roots and sporophylls were 60 and 30, respectively, while only seven were found for the sporophylls with glandular trichomes removed. The expression of genes known to be associated with the development of glandular trichomes in flowering plants, including MIXTA, ATML1, and MYB106, were also validated and are discussed. In particular, a unigene encoding MIXTA was identified and exhibited the highest expression level in SL in <i>D. fragrans.</i> Conclusions: This study is the first report of global transcriptomic analysis in different tissues of <i>D. fragrans</i>, and the first to discuss these findings in the context of the development of homologous glandular trichomes. These results set the stage for further research on the development, stress resistance, and secondary metabolism of <i>D. fragrans</i> glandular trichomes.https://www.mdpi.com/1422-0067/21/19/7296transcriptome<i>Dryopteris fragrans</i>transcription factorsgene expression |
| spellingShingle | Lingling Chen Dongrui Zhang Chunhua Song Hemeng Wang Xun Tang Ying Chang Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of <i>Dryopteris fragrans</i> (L.) Schott International Journal of Molecular Sciences transcriptome <i>Dryopteris fragrans</i> transcription factors gene expression |
| title | Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of <i>Dryopteris fragrans</i> (L.) Schott |
| title_full | Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of <i>Dryopteris fragrans</i> (L.) Schott |
| title_fullStr | Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of <i>Dryopteris fragrans</i> (L.) Schott |
| title_full_unstemmed | Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of <i>Dryopteris fragrans</i> (L.) Schott |
| title_short | Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of <i>Dryopteris fragrans</i> (L.) Schott |
| title_sort | transcriptomic analysis and specific expression of transcription factor genes in the root and sporophyll of i dryopteris fragrans i l schott |
| topic | transcriptome <i>Dryopteris fragrans</i> transcription factors gene expression |
| url | https://www.mdpi.com/1422-0067/21/19/7296 |
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