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Identification of stress-related genes by co-expression network analysis based on the improved turbot genome.

ABSTRACT: Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present an improved high-quality chromosome-scale genome assembly of turbot using a combination of PacBio long-read and Illumina short-read sequencing technologies. The genome assembly spans 538.22 Mb comprising 27 contigs with a contig N50 size of 25.76 Mb. Annotation of the genome assembly identified 104.45 Mb repetitive sequences, 22,442 protein-coding genes and 3,345 ncRNAs. Moreover, a total of 345 stress responsive candidate genes were identified by gene co-expression network analysis based on 14 published stress-related RNA-seq datasets consisting of 165 samples. Significantly improved genome assembly and stress-related candidate gene pool will provide valuable resources for further research on turbot functional genome and stress response mechanism, as well as theoretical support for the development of molecular breeding technology for resistant turbot varieties.

SUBMITTER: Xu XW

PROVIDER: S-EPMC9243025 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Identification of stress-related genes by co-expression network analysis based on the improved turbot genome.

Xu Xi-Wen XW Zheng Weiwei W Meng Zhen Z Xu Wenteng W Liu Yingjie Y Chen Songlin S

Scientific data 20220629 1

Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present an improved high-quality chromosome-scale genome assembly of turbot using a combination of PacBio long-read and Illumina short-read sequencing technologies. The genome assembly spans 538.22 Mb comprisi ...[more]

PMID: 35768602

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Project description:Background: The tumor microenvironment (TME) of human glioblastoma (GBM) exhibits considerable immune cell infiltration, and such cell types have been shown to be widely involved in the development of GBM. Here, weighted correlation network analysis (WGCNA) was performed on publicly available datasets to identify immune-related molecules that may contribute to the progression of GBM and thus be exploited as potential therapeutic targets. Methods: WGCNA was used to identify highly correlated gene clusters in Chinese Glioma Genome Atlas glioma dataset. Immune-related genes in significant modules were subsequently validated in the Cancer Genome Atlas (TCGA) and Rembrandt databases, and impact on GBM development was examined in migration and vascular mimicry assays in vitro and in an orthotopic xenograft model (GL261 luciferase-GFP cells) in mice. Results: WGCNA yielded 14 significant modules, one of which (black) contained genes involved in immune response and extracellular matrix formation. The intersection of these genes with a GO immune-related gene set yielded 47 immune-related genes, five of which exhibited increased expression and association with worse prognosis in GBM. One of these genes, TREM1, was highly expressed in areas of pseudopalisading cells around necrosis and associated with other proteins induced in angiogenesis/hypoxia. In macrophages induced from THP1 cells, TREM1 expression levels were increased under hypoxic conditions and associated with markers of macrophage M2 polarization. TREM1 siRNA knockdown in induced macrophages reduced their ability to promote migration and vascular mimicry in GBM cells in vitro, and treatment of mice with LP-17 peptide, which blocks TREM1, inhibited growth of GL261 orthotopic xenografts. Finally, blocking the cytokine receptor for CSF1 in induced macrophages also impeded their potential to promote tumor migration and vascular mimicry in GBM cells. Conclusions: Our results demonstrated that TREM1 could be used as a novel immunotherapy target for glioma patients.

Dataset Information

Identification of stress-related genes by co-expression network analysis based on the improved turbot genome.

Publications

Identification of stress-related genes by co-expression network analysis based on the improved turbot genome.

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