Preisanfragen ApexBio

Transcriptome sequencing is high-throughput sequencing of total RNA produced by a specific species or cell in a specific functional state, but now we mainly use it to detect mRNA.

APExBIO’s services not only detect differences in gene expression levels, but also provide structural analysis. Our work aims to help you discover unknown transcripts and rare transcripts, and accurately identify differentially variable splice sites, gene fusions, SNPs and InDel mutations, etc.  The results can be applied to research into growth and development regulation mechanisms and the pathogenesis of important human diseases.

 Metabolome and transcriptome sequence analysis reveals anthocyanin metabolism in pink flowers of anthocyanin-rich tea (Camellia sinensis)

Almost all flowers of the tea plant (Camellia sinensis) are white, which has led to few researchers paying attention to the accumulation of anthocyanins and color changes in tea flowers. A new purple leaf variety, Baitang Purple Tea (BTP), has been discovered in the Baitang Mountains of Guangdong, whose flowers are naturally pink, and may provide an opportunity to understand anthocyanin metabolic networks and the evolution of flower color in tea flowers. In the present study, twelve anthocyanin components were identified in the pink tea flowers, namely cyanidin-O-syringic acid, petunidin-3-O-glucoside, pelargonidin-3-O-beta-D-glucoside, which is the first time that these Compounds found were found in tea flowers. The presence of these anthocyanins seems most likely to be the reason for the pink coloring of the buds. Twenty-one differentially expressed genes (DEGs) involved in anthocyanin signaling were identified using functional enrichment of the KEGG signaling pathway,Specifically, during the period of peak anthocyanin synthesis, 17 structural genes were upregulated and only four structural genes were downregulated. Ultimately, eight critical genes were identified using weighted gene coexpression network analysis (WGCNA), which were found to have a direct impact on the biosynthesis and accumulation of three flavonoid compounds, namely cyanidin-3-O-glucoside, petunidin-3-O-glucoside and epicatechin gallate. These results provide useful information on the molecular mechanisms of coloration in rare pink tea flowers of anthocyanin-rich tea, enriching the gene resource and guiding further research on anthocyanin enrichment in violet tea.

The OPLS-DA results showed that the main biological components were significantly altered along with changing developmental stages.An OPLS-DA plot showing the significance of the change in metabolic profile from one developmental stage to the next. The composition between the first stage and the second stage (BTP1 vs. BTP2), the second stage and the third stage (BTP2 vs. BTP3), the third stage and the fourth stage (BTP3 vs. BTP4) and the fourth stage and the fifth stage (BTP4 vs. BTP5) each clustered together in the OPLS score plots. The R2Y of this OPLS-DA model was 1.0, 1.0, 0.999 and 1.0 in metabolomic differences of different flower development, respectively. While the model’s Q2Y was 0.992, 0.959, 0.938 and 0.975 (from BTP1 to BTP5) respectively. These data show highly significant differences in metabolite profiles based on developmental stage.

To reveal the gene expression levels involved in anthocyanins and flavonoid pathways, anthocyanin-associated modules were obtained from WGCNA. A module can be viewed as a cluster of closely related genes. The connectivity of two genes is a combination of the proximity between them and the strength of the connections they share with other “third party” genes. This measure of proximity used by WGCNA is known as the topological overlap measure (TOM). Using TOM, WGCNA groups data into dendrogram “tree” type. Individual branches of the tree represent clusters of interconnected genes, which are then defined as “modules”. Each module is measured for co-expression with the trait phenotype, in this case flavonoids, to see

The transcriptome response of cardiac and skeletal muscle to heat stress in low- and high-altitude-adapted Kenyan chicken ecotypes reveal differences in thermal tolerance and stress response

Heat stress (HS) has a negative impact on chicken performance. Agricultural expansion will take place in regions with high ambient temperatures where fast-growing commercial chickens are vulnerable. Indigenous chickens of such regions might have higher heat tolerance due to exposure to environmental issues over generations. In this study, two native chicken ecotypes,from the hot and humid Mombasa region (lowlands) and the colder Naivasha region (highlands) were used to assess the effects of acute (5 h, 35 °C) and chronic (3 days at 35 °C for 8 h/day) HS to be examined in heart and skeletal muscle by RNA sequencing. Rectal temperature rise and the number of differentially expressed genes (DEGs) [false discovery rate (FDR) < 0.05] were twice as high in the acute stage in both ecotypes as in the chronic stage, suggesting that cycling exposure to HS contributes may lead to adjustment. A tissue- and stage-specific difference in response to HS was observed, with peroxisome proliferator-activated receptor (PPAR) and mitogen-activated protein kinase (MAPK) signaling pathways in the heart and heart, respectively. Skeletal muscle and p53 enriched in both tissues only in the acute stage. The acute and chronic stage DEGs were integrated by a region-specific gene coexpression network (GCN), and genes with the highest number of connections (hub genes) were identified. The lowland network hub genes were CCNB2, Crb2, CHST9, SESN1, and NR4A3, while the highland network hub genes were COMMD4, TTC32, H1F0, ACYP1, and RPS28. Pathway analysis of genes in the GCN showed that p53 and PPAR signaling pathways were enriched in both Low and Highland networks, while MAPK signaling and protein processing in the endoplasmic reticulum were only enriched in the gene network of Highland chickens .

This shows that the ecotypes activated or repressed different genes, to dissipate accumulated heat, reduce heat-induced apoptosis, and promote DNA damage repair. indicating the differences in thermal tolerance and HS response mechanisms between the ecotypes. This study provides information on the HS response of chickens adapted to two different agroclimatic environments and advances our understanding of the mechanisms of the HS response and the impact of adaptation in controlling HS.

Rectal temperature rise during HS treatment and sample relationship derived from principal component analysis. (A) Box plot showing increase in rectal temperature due to HS treatment. AHL, acute highland; CHL, chronic highland; ALL, acute lowland; CLL, chronic lowland. (B) Principal component analysis showing that the maximum variation is due to differences between ecotypes. Only a small percentage of the variation is due to the HS effect.

Gene Coexpression Network (GCN) and pathway enrichment analysis integrated for the skeletal and cardiac muscle DEGs. (A) Degree sorted network of DEGs in at least one contrast in the highland chickens. The nodes are genes and the edges are based on correlation coefficients. Only partially correlated genes | r | of ≥0.99 were included in the network. The node color denotes the tissue type where gene expression was highest, while the node border denotes the stage where gene expression was highest.

(B) KEGG pathway networks in which all genes in the upland GCN network have been enriched. (c) Degree sorted network of the DEG in at least one contrast in the lowland chickens. The nodes are genes and the edges are based on correlation coefficients. Only partially correlated genes | r | from ≥0, 99 were added to the network. The node color denotes the tissue type where gene expression was highest, while the node border denotes the stage where gene expression was highest. (D) KEGG pathway networks in which all genes in the lowland GCN network have been enriched.