Expression analysis of genes related to cold tolerance in Dendroctonus valens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA656966 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12446930_1.fastq.gz | Fastqsanger.gz | |||
| SRR12446930_2.fastq.gz | Fastqsanger.gz | |||
| SRR12446931_1.fastq.gz | Fastqsanger.gz | |||
| SRR12446931_2.fastq.gz | Fastqsanger.gz | |||
| SRR12446932_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:To identify genes relevant to cold tolerance and the process of overwintering, we sequenced the transcriptomes of wintering and non-wintering adult and larval D. valens using the Illumina HiSeq platform. Differential expression analysis methods for other non-model organisms were used to compare transcript abundances in adults and larvae at two time periods, followed by the identification of functions and metabolic pathways related to genes associated with cold tolerance. We detected 4387 and 6091 differentially expressed genes (DEGs) between sampling dates in larvae and adults, respectively, and 1140 common DEGs, including genes encoding protein phosphatase, very long-chain fatty acids protein, cytochrome P450, and putative leucine-rich repeat-containing proteins. In a GO enrichment analysis, 1,140 genes were assigned to 44 terms, with significant enrichment for cellulase activity, hydrolase activity, and carbohydrate metabolism. KEGG classification and enrichment analyses showed that the lysosomal and purine metabolism pathways involved the most DEGs, the highly enriched terms included autophagy - animal, pentose and glucuronate interconversions and lysosomal processes. We identified 138 candidate genes associated with cold tolerance, including genes with established roles in this trait (e.g., genes encoding trehalose transporter, fructose-1,6-bisphosphatase, and trehalase). Our comparative transcriptome analysis of adult and larval D. valens in different conditions provides basic data for the discovery of key genes and molecular mechanisms underlying cold tolerance.
2021-01-19 | GSE156139 | GEO
Project description:Dendroctonus valens Genome sequencing and assembly
| PRJNA765904 | ENA
Project description:Dendroctonus valens Genome sequencing and assembly
| PRJNA780393 | ENA
Project description:Raw sequence reads of Dendroctonus valens gut microbiota
| PRJNA379332 | ENA
Project description:Dendroctonus valens gut microbiota Raw sequence reads
| PRJNA431132 | ENA
Project description:Pine beetles are well known in North America for their widespread devastation of pine forests. However, Dendroctonus valens LeConte is an important invasive forest pest in China also. Adults and larvae of this bark beetle mainly winter at the trunks and roots of Pinus tabuliformis and Pinus sylvestris; larvae, in particular, result in pine weakness or even death. Since the species was introduced from the United States to Shanxi in 1998, its distribution has spread northward. In 2017, it invaded a large area at the junction of Liaoning, Inner Mongolia and Hebei provinces, showing strong cold tolerance. To identify genes relevant to cold tolerance and the process of overwintering, we sequenced the transcriptomes of wintering and non-wintering adult and larval D. valens using the Illumina HiSeq platform. Differential expression analysis methods for other non-model organisms were used to compare transcript abundances in adults and larvae at two time periods, followed by the identification of functions and metabolic pathways related to genes associated with cold tolerance. We detected 4,387 and 6,091 differentially expressed genes (DEGs) between sampling dates in larvae and adults, respectively, and 1,140 common DEGs, including genes encoding protein phosphatase, very long-chain fatty acids protein, cytochrome P450, and putative leucine-rich repeat-containing proteins. In a Gene Ontology (GO) enrichment analysis, 1,140 genes were assigned to 44 terms, with significant enrichment for cellulase activity, hydrolase activity, and carbohydrate metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) classification and enrichment analyses showed that the lysosomal and purine metabolism pathways involved the most DEGs, the highly enriched terms included autophagy-animal, pentose and glucuronate interconversions and lysosomal processes. We identified 140 candidate genes associated with cold tolerance, including genes with established roles in this trait (e.g., genes encoding trehalose transporter, fructose-1,6-bisphosphatase, and trehalase). Our comparative transcriptome analysis of adult and larval D. valens in different conditions provides basic data for the discovery of key genes and molecular mechanisms underlying cold tolerance.
| S-EPMC7953874 | biostudies-literature
Project description:Saccharum spontaneum L., the main source of tolerance gene in sugarcane variety, is one of the most valuable germplasms for sugarcane breeding. In this study, 22 clones of S.spontaneum L. were selected from more than 690 collections in our preliminary experiment, and the cold tolerance of these clones were evaluated by physiological and biochemical indicators. Then 2 clones which were designated as lines 1027 and 3217,with contrasting cold tolerance ability were selected for further proteome analysis using DIA and PRM technology.
2023-03-11 | PXD038181 | Pride
Project description:Recently, intensive global climate change has become a major factor impacting plant survival during the winter. Freezing cold temperatures during the winter and abnormal temperature fluctuations during the winter and early spring are the most harmful ambient factors threatening tea plant winter survival and currently cause marked economic losses in tea production. In this study, by simulating natural climate change, we established cold acclimation (CA) and rapid cold stress (after CA) conditions to comprehensively investigate the transcriptome changes involved in CA and rapid cold stress. Electrolyte leakage (EL) rate and expression profile clustering analyses confirmed that the experimental design was valid. Comparative transcription analysis identified many differentially expressed genes (DEGs) involved in both processes. Time course and pathway enrichment analyses further revealed the physiological changes that occur during the initial period of CA and the cell wall changes that occur throughout the entire CA process; these changes play crucial roles in increasing freezing tolerance during this process. Compared with CA, different cold response mechanisms were rapidly activated under cold stress; however, the subsequent accumulation of reactive oxygen species, which affect multiple aspects, caused by freezing cold could be the harshest factor impairing tea leaves. Moreover, we investigated 60 DEGs shared by both processes and highlighted the importance of KCSs, HXXXD-type acyl-transferase family proteins, NAC080, SWEETs and ENOs in the responses to various cold conditions. These results greatly improve our knowledge of cold response mechanisms in tea plants and provide meaningful information for functional studies investigating cold tolerance-related genes.
2017-09-29 | GSE104390 | GEO