Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in <it>Digitalis purpurea</it>
<p>Abstract</p> <p>Background</p> <p><it>Digitalis purpurea </it>is an important ornamental and medicinal plant. There is considerable interest in exploring its transcriptome.</p> <p>Results</p> <p>Through high-throughput 454 sequenci...
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| Format: | Article |
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BMC
2012-01-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/13/15 |
| _version_ | 1830349426063835136 |
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| author | Wu Bin Li Ying Yan Haixia Ma Yimian Luo Hongmei Yuan Lichai Chen Shilin Lu Shanfa |
| author_facet | Wu Bin Li Ying Yan Haixia Ma Yimian Luo Hongmei Yuan Lichai Chen Shilin Lu Shanfa |
| author_sort | Wu Bin |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Digitalis purpurea </it>is an important ornamental and medicinal plant. There is considerable interest in exploring its transcriptome.</p> <p>Results</p> <p>Through high-throughput 454 sequencing and subsequent assembly, we obtained 23532 genes, of which 15626 encode conserved proteins. We determined 140 unigenes to be candidates involved in cardiac glycoside biosynthesis. It could be grouped into 30 families, of which 29 were identified for the first time in <it>D. purpurea</it>. We identified 2660 mRNA-like npcRNA (mlncRNA) candidates, an emerging class of regulators, using a computational mlncRNA identification pipeline and 13 microRNA-producing unigenes based on sequence conservation and hairpin structure-forming capability. Twenty five protein-coding unigenes were predicted to be targets of these microRNAs. Among the mlncRNA candidates, only 320 could be grouped into 140 families with at least two members in a family. The majority of <it>D. purpurea </it>mlncRNAs were species-specific and many of them showed tissue-specific expression and responded to cold and dehydration stresses. We identified 417 protein-coding genes with regions significantly homologous or complementary to 375 mlncRNAs. It includes five genes involved in secondary metabolism. A positive correlation was found in gene expression between protein-coding genes and the homologous mlncRNAs in response to cold and dehydration stresses, while the correlation was negative when protein-coding genes and mlncRNAs were complementary to each other.</p> <p>Conclusions</p> <p>Through comprehensive transcriptome analysis, we not only identified 29 novel gene families potentially involved in the biosynthesis of cardiac glycosides but also characterized a large number of mlncRNAs. Our results suggest the importance of mlncRNAs in secondary metabolism and stress response in <it>D. purpurea</it>.</p> |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T00:02:48Z |
| publishDate | 2012-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-3bbbd952c020400d96ae25d4bb4981492022-12-21T20:00:45ZengBMCBMC Genomics1471-21642012-01-011311510.1186/1471-2164-13-15Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in <it>Digitalis purpurea</it>Wu BinLi YingYan HaixiaMa YimianLuo HongmeiYuan LichaiChen ShilinLu Shanfa<p>Abstract</p> <p>Background</p> <p><it>Digitalis purpurea </it>is an important ornamental and medicinal plant. There is considerable interest in exploring its transcriptome.</p> <p>Results</p> <p>Through high-throughput 454 sequencing and subsequent assembly, we obtained 23532 genes, of which 15626 encode conserved proteins. We determined 140 unigenes to be candidates involved in cardiac glycoside biosynthesis. It could be grouped into 30 families, of which 29 were identified for the first time in <it>D. purpurea</it>. We identified 2660 mRNA-like npcRNA (mlncRNA) candidates, an emerging class of regulators, using a computational mlncRNA identification pipeline and 13 microRNA-producing unigenes based on sequence conservation and hairpin structure-forming capability. Twenty five protein-coding unigenes were predicted to be targets of these microRNAs. Among the mlncRNA candidates, only 320 could be grouped into 140 families with at least two members in a family. The majority of <it>D. purpurea </it>mlncRNAs were species-specific and many of them showed tissue-specific expression and responded to cold and dehydration stresses. We identified 417 protein-coding genes with regions significantly homologous or complementary to 375 mlncRNAs. It includes five genes involved in secondary metabolism. A positive correlation was found in gene expression between protein-coding genes and the homologous mlncRNAs in response to cold and dehydration stresses, while the correlation was negative when protein-coding genes and mlncRNAs were complementary to each other.</p> <p>Conclusions</p> <p>Through comprehensive transcriptome analysis, we not only identified 29 novel gene families potentially involved in the biosynthesis of cardiac glycosides but also characterized a large number of mlncRNAs. Our results suggest the importance of mlncRNAs in secondary metabolism and stress response in <it>D. purpurea</it>.</p>http://www.biomedcentral.com/1471-2164/13/15 |
| spellingShingle | Wu Bin Li Ying Yan Haixia Ma Yimian Luo Hongmei Yuan Lichai Chen Shilin Lu Shanfa Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in <it>Digitalis purpurea</it> BMC Genomics |
| title | Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in <it>Digitalis purpurea</it> |
| title_full | Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in <it>Digitalis purpurea</it> |
| title_fullStr | Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in <it>Digitalis purpurea</it> |
| title_full_unstemmed | Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in <it>Digitalis purpurea</it> |
| title_short | Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in <it>Digitalis purpurea</it> |
| title_sort | comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncrnas associated with secondary metabolism and stress response in it digitalis purpurea it |
| url | http://www.biomedcentral.com/1471-2164/13/15 |
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