Comparative transcriptome analysis to reveal putative genes responsible for high theacrine content in Kucha (Camellia kucha (Chang et Wang) Chang)

Abstract Background: The purine alkaloid theacrine, synthesized in a high amount in Kucha (Camellia kucha (Chang et Wang) Chang), has shown multiple pharmacological effects such as anti-depression, dehydration and hypnotic activities. It is critical to better understand the theacrine metabolism at the molecular level for future breeding programs. Results: In this study, we carried out comparative transcriptome analysis of Kucha (Kucha-6 and Kucha-11) and conventional varieties (Yinghong 9 and Qingxin 1). HPLC showed that Kucha synthesized more than 27-fold theacrine in comparison to conventional varieties. A total of ~ 671.61 million high quality clean reads were yield, and 71.42 ~ 76.87% of these were aligned to the reference genome for each library. Among the 19,095 differentially expressed genes (DEGs) identified by a pairwise comparison approach, a pool of 1,142 common DEGs between Kucha and conventional varieties were screened. Functional annotation allowed the identified of 20 oxidoreductase (OR) genes and seven methyltransferase (MT) genes with enhanced expression in Kucha, which might be associated with theacrine diversity in the examined materials. Particularly, two N-methyltransferase-encoding genes (TEA010054 and TEA022559) may catalyze the final methylation step during theacrine synthesis in Kucha. Conclusion: The current study focused on screening genes of theacrine formation in tea plant, which contributes to the elucidation of candidate genes and breeding tea plant with high theacrine content.

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Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

Genes ◽

10.3390/genes12030341 ◽

2021 ◽

Vol 12 (3) ◽

pp. 341

Author(s):

Lei Zhang ◽

Haoyun Sun ◽

Tao Xu ◽

Tianye Shi ◽

Zongyun Li ◽

...

Keyword(s):

Transcriptome Analysis ◽

Morphological Analysis ◽

Molecular Mechanisms ◽

Flavonoid Biosynthesis ◽

Phenotypic Characterization ◽

Comparative Transcriptome ◽

Hub Genes ◽

Breeding Programs ◽

Comparative Transcriptome Analysis ◽

Key Pathways

Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis has hindered the genetic improvement of eggplant. In this study, we performed the phenotypic characterization and transcriptome analysis on prickly and prickleless eggplant genotypes to understand prickle development at the morphological and molecular levels. Morphological analysis revealed that eggplant prickles were multicellular, lignified and layered organs. Comparative transcriptome analysis identified key pathways and hub genes involved in the cell cycle as well as flavonoid biosynthetic, photosynthetic, and hormone metabolic processes during prickle development. Interestingly, genes associated with flavonoid biosynthesis were up-regulated in developing prickles, and genes associated with photosynthesis were down-regulated in developing and matured prickles. It was also noteworthy that several development-related transcription factors such as bHLH, C2H2, MYB, TCP and WRKY were specifically down- or up-regulated in developing prickles. Furthermore, four genes were found to be differentially expressed within the Pl locus interval. This study provides new insights into the regulatory molecular mechanisms underlying prickle morphogenesis in eggplant, and the genes identified might be exploited in breeding programs to develop prickleless eggplant cultivars.

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Comparative Transcriptome Analysis of Preterm Placental Tissue with Maternal Diabetes, Obesity and Periodontitis Diseases Using Integrated Bioinformatics Approach

10.21203/rs.3.rs-853009/v1 ◽

2021 ◽

Author(s):

Humaira Amin ◽

Syed Habib Bokhari ◽

Khuram Shahzad

Keyword(s):

Type 1 Diabetes ◽

Preterm Birth ◽

Chronic Diseases ◽

Transcriptome Analysis ◽

Strong Association ◽

Pairwise Comparison ◽

Placental Tissue ◽

Comparative Transcriptome ◽

Comparative Transcriptome Analysis

Abstract Preterm birth (PTB) is one of the major reasons of infant mortalities and morbidities worldwide. Exact mechanism of this disease has not been elucidated yet but studies have shown several factors which have been found associated with the disease. Through several studies, it has been discovered that different chronic diseases like obesity, type 1 diabetes and periodontitis are also associated with PTB but no omics studies have yet been performed to discover their association. In the current study, comparative transcriptome analysis of the preterm birth with type 1 diabetes, obesity and periodontitis using integrated bioinformatics approach was performed to validate their association with preterm birth. Four different datasets retrieved from Gene expression omnibus (GEO) were processed through Bioconductor packages in R. Pairwise comparison of preterm was performed with all three diseases. Several bioinformatics tools were used such as DAVID for Gene ontology (GO) terms and pathway analysis, DIA for impact and direction of KEGG pathways and Cytoscape along with its different plugins for construction of networks, identification of hub genes and modules. Significant number of common differentially expressed genes between datasets and their roles in different pathways were identified. Most of the significant genes and pathways found in these comparisons were involved in initiating different inflammatory processes, degradation of proteins leading to preterm premature rupture of membranes (PPROM), preeclampsia, and cancer which are the known risk factors of PTB. According to our results, all these three chronic diseases were found to have a strong association with PTB.

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