Identification of key gene networks controlling vernalization development characteristics of Isatis indigotica by full-length transcriptomes and gene expression profiles

Abstract

Isatis indigotica Fort., as a common Chinese medicinal raw material, will lose its medicinal value if it blooms early, so it is highly valuable to clarify the induction mechanism of the vernalization of I. indigotica at low temperature. In this study, the concentrations of soluble sugar, proline, glutathione and zeatin in two germplasms of I. indigotica with different degrees of low temperature tolerance (Y1 and Y2) were determined at 10 days, 20 days and 30 days of low-temperature treatment, and the full-length transcriptome of 24 samples was sequenced by Nanopore sequencing with Oxford Nanopore Technologies (ONT). After that, the data of transcripts involved in the vernalization of I. indigotica at low temperature were obtained, and these transcripts were identified using weighted gene co-expression network analysis (WGCNA). The results revealed the massive accumulation of soluble sugar and proline in Y1 and Y2 after low temperature induction. A total of 18,385 new transcripts, 6168 transcription factors and 470 lncRNAs were obtained. Differential expression analysis showed that gibberellin, flavonoids, fatty acids and some processes related to low temperature response were significantly enriched. Eight key transcripts were identified by WGCNA, among which ONT.14640.1, ONT.9119.1, ONT.13080.2 and ONT.16007.1 encodes a flavonoid transporter, 9-cis-epoxycarotenoid dioxygenase 3 (NCED3), growth factor gene and L-aspartate oxidase in plants, respectively. It indicated that secondary metabolites such as hormones and flavonoids play an important role in the vernalization of I. indigotica. qRT-PCR proved the reliability of transcriptome results. These results provide important insights on the low-temperature vernalization of I. indigotica, and provide a research basis for analyzing the vernalization mechanism of I. indigotica.

Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis

“…This approach effectively clusters genes exhibiting similar expression patterns into distinct modules, which are characterized by shared functions or pathways [40]. By leveraging plant life activities and high-throughput sequencing technology, WGCNA enables the acquisition of multiple expression traits and facilitates the construction of a scale-free network topology centered around pivotal regulatory genes [41]. Hou et al combined WGCNA and transcriptomic analyses revealed a coexpression gene network associated with rutin synthesis [42].…”

Transcriptomic Determination of the Core Genes Regulating the Growth and Physiological Traits of Quercus mongolica Fisch. ex Ledeb

“…In WGCNA, genes with similar expression patterns are assigned to the same module, and specific modules that are strongly associated with the target trait and their core genes are identified. As an efficient data mining method, WGCNA enables the analysis of multi-sample big data [49], pointing to new lines of research and providing clues for further mining of the functional genes of the target trait.…”