Metabolomics technology has enabled an important method for the identification and quality control of Traditional Chinese Medical materials. In this study, we isolated metabolites from cultivated Dendrobium officinale and Dendrobium huoshanense stems of different growth years in the methanol/water phase and identified them using gas chromatography coupled with mass spectrometry (GC-MS). First, a metabolomics technology platform for Dendrobium was constructed. The metabolites in the Dendrobium methanol/water phase were mainly sugars and glycosides, amino acids, organic acids, alcohols. D. officinale and D. huoshanense and their growth years were distinguished by cluster analysis in combination with multivariate statistical analysis, including principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA). Eleven metabolites that contributed significantly to this differentiation were subjected to t-tests (P<0.05) to identify biomarkers that discriminate between D. officinale and D. huoshanense, including sucrose, glucose, galactose, succinate, fructose, hexadecanoate, oleanitrile, myo-inositol, and glycerol. Metabolic profiling of the chemical compositions of Dendrobium species revealed that the polysaccharide content of D. huoshanense was higher than that of D. officinale, indicating that the D. huoshanense was of higher quality. Based on the accumulation of Dendrobium metabolites, the optimal harvest time for Dendrobium was in the third year. This initial metabolic profiling platform for Dendrobium provides an important foundation for the further study of secondary metabolites (pharmaceutical active ingredients) and metabolic pathways.

Brown cotton is a kind of naturally colored cotton. Because of less processing and little dying, it is more friendlier to environment than white cotton. For brown cotton, pigment accumulation in fiber is one of the most important characteristics. In this study, we selected a brown fiber line and a white fiber cultivar to determine the factor that affects the pigmentation in brown fiber. Accordingly, fibers were collected to verify the presence of PAs by p-dimethylaminocinnamaldehyde (DMACA) and toluidine blue O (TBO) staining. The PAs content and related genes expressions were determined. As a result, there were obvious differences on the aspect of PAs synthesis in fiber between white cotton and brown cotton. For white fiber, the PAs content reached maximum at 5 DPA, and then gradually decreased to zero. But for brown fiber, the PAs content was increased from 5 to 15 DPA stage, and reached the maximum at the 15 DPA stage, then gradually decreased from 15 to 40 DPA stage. On the contrary, in white cotton, PAs were synthesized in the whole developmental stage from 5 to 40 DPA. And PAs content in brown fiber were far more than that in white fiber, which may be the reason why the brown pigment accumulated in brown fiber.

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Purple corn is a rich source of anthocyanins. In the experiment, two anthocyanins-enriched purple corn lines Ha0414 and Ha6130 were identified. The anthocyanins were respectively accumulated in the pericarp of Ha0414 and the aleurone layer of Ha6130 with different composition and content. Transcriptome analysis of the two tissues in both lines identified 16 and 14 differentially expressed genes belonging to anthocyanin metabolism pathway in pericarp and the aleurone layer, individually. Of these genes, two genes encoding 2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase superfamily proteins, and one gene annotated as UDP-glycosyltransferase superfamily protein exhibited increased transcript abundance in both the colored pericarp and aleurone layer. Otherwise, one gene annotated as flavonoid 3′, 5′-hydroxylase, and another gene encoding flavonoid 3′-monooxygenase displayed increased transcript abundance in the aleurone layer of Ha6130. Moreover, 36 transcription factors were identified with increased transcript abundance in the pericarp of Ha0414, such as bHLH transcription factors, WRKY transcription factors, and HB transcription factors. And 79 transcription factors were isolated with an increased expression level in the aleurone layer of Ha6130, including MYB transcription factors, MYB-related transcription factors, and bHLH transcription factors. These genes expression may result in the tissue-specific accumulation of anthocyanins in pericarp and aleurone layer.

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MYB transcription factors play important roles in different plant biological processes during plant growth, development and stress response. In this study, 101 (DoMYB1-101) and 99 (PaMYB1-99) R2R3-MYB genes were identified in the genomes of Dendrobium officinale and Phalaenopsis aphrodite, respectively. To classify the isolated candidate genes, the R2R3-MYB genes from A. thaliana were selected as references. As a result, all identified DoMYB and PaMYB genes were classified into 22 subfamilies. Phylogenetic analysis revealed that S21 had the largest number of members of all the subfamilies. The numbers of introns, exons and conserved sequences in all of the identified genes are different. In addition, 20 DoMYB genes from six subfamilies were selected for further analysis of tissue-specific expression and responses to various abiotic stresses treatments. The results showed that all of the DoMYB genes in S4 and S19 subfamilies exhibited the highest relative expression levels in flowers. And five DoMYB genes including DoMYB31, DoMYB40, DoMYB49, DoMYB52 and DoMYB54, responded to the stress response. These results may provide useful information for further studies of the R2R3-MYB gene family.

Dendrobium officinale is a kind of traditional Chinese herbal medicine. Its flowers could be used as health care tea for its aroma flavor and medicinal value. Most recent studies demonstrated that terpenoids are the main components of the aromatic compounds in the flowers, but the biosynthesis of terpenoids is poorly understood in D. officinale. In the experiment, the flowers from two cultivars of D. officinale with different smells were collected. The transcriptome analysis and combined volatile terpenoids determination were performed to identify the genes related to the biosynthesis of the terpenoids. The results showed that the different products of volatile terpenoids are α-thujene, linalool, α-terpineol, α-phellandrene, γ-muurolene, α-patchoulene, and δ-elemene in two cultivar flowers. The transcriptome analysis detected 25,484 genes in the flowers. And 18,650 differentially expressed genes were identified between the two cultivars. Of these genes, 253 genes were mapped to the terpenoid metabolism pathway. Among these genes, 13 terpene synthase (TPS) genes may have correlations with AP2/ERF, WRKY, MYB, bHLH, and bZIP transcription factors by weighted gene co-expression network analysis (WGCNA). The transcription factors have regulatory effects on TPS genes. These results may provide ideas for the terpenoid biosynthesis and regulatory network of D. officinale flowers.

MADS-box transcription factors widely regulate all aspects of plant growth including development and reproduction. Although the MADS-box gene family genes have been extensively characterized in many plants, they have not been studied in closely related species. In this study, 73 and 74 MADS-box genes were identified in European pear (Pyrus communis) and Chinese pear (Pyrus bretschneideri), respectively. Based on the phylogenetic relationship, these genes could be clustered into five groups (Mα, Mβ, Mr, MIKCC, MIKC*) and the MIKCC group was further categorized into 10 subfamilies. The distribution of MADS-box genes on each chromosome was significantly nonrandom. Thirty-seven orthologs, twenty-five PcpMADS (P. communis MADS-box) paralogs and nineteen PbrMADS (P. bretschneideri MADS-box) paralogs were predicted. Among these paralogous genes, two pairs arose from tandem duplications (TD), nineteen from segmental duplication (SD) events and twenty-three from whole genome duplication (WGD) events, indicating SD/WGD events led to the expansion of MADS-box gene family. The MADS-box genes expression profiles in pear fruits indicated functional divergence and neo-functionalization or sub-functionalization of some orthologous genes originated from a common ancestor. This study provided a useful reference for further analysis the mechanisms of species differentiation and biodiversity formation among closely related species.