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Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea
- Source :
- BMC Genomics, Vol 13, Iss 1, p 15 (2012), BMC Genomics
- Publisher :
- Springer Nature
-
Abstract
- Background Digitalis purpurea is an important ornamental and medicinal plant. There is considerable interest in exploring its transcriptome. Results 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 D. purpurea. 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 D. purpurea 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. Conclusions 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 D. purpurea.
- Subjects :
- lcsh:QH426-470
lcsh:Biotechnology
Molecular Sequence Data
Cardiac Glycosides
Transcriptome
Gene Expression Regulation, Plant
lcsh:TP248.13-248.65
Gene expression
Genetics
RNA, Messenger
Secondary metabolism
Gene
Plant Proteins
Regulation of gene expression
Digitalis
Base Sequence
Dehydration
biology
Cold-Shock Response
Digitalis purpurea
biology.organism_classification
Cold shock response
MicroRNAs
lcsh:Genetics
Nucleic Acid Conformation
DNA microarray
Research Article
Biotechnology
Subjects
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 13
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....9c3a6f48ff2e2e5030a752adb6869439
- Full Text :
- https://doi.org/10.1186/1471-2164-13-15