Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

A Whole Transcriptional Linkage Analysis of Gene Co-Regulation in Insecticide Resistant House Flies, Musca domestica

ABSTRACT: Illumina HiSeq 2000 RNASeq was conducted on the mRNA fraction of three adult female Musca domestica strains. Two strains were the insecticide susceptible strains CS and aabys, which has five distinct recessive morphological markers, one on each of the five autosomes in M. domestica. The third strain was ALHF, which is a highly insecticide resistant strain obtained in Alabama. The reference transcriptome was generated de novo using Trinity. The coding trimmed sequences from Augustus were then used as the mapping reference for the individual FASTQ files from each strain. trace reads were mapped using RSEM to generate FPKM estimates. Gene expression levels were compared to the ALHF strain using EdgeR to identify genes that were downregulated in both aabys and CS. RNA Seq profiling of the mRNA of adult Musca domestica with different autosomal contributions from insecticide resistant and susceptible strains (whole insect pooled samples)

ORGANISM(S): Musca domestica

SUBMITTER: Nannan Liu

PROVIDER: E-GEOD-39327 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A whole transcriptomal linkage analysis of gene co-regulation in insecticide resistant house flies, Musca domestica.

Li Ming M Reid William R WR Zhang Lee L Scott Jeffery G JG Gao Xiwu X Kristensen Michael M Liu Nannan N

BMC genomics 20131119

<h4>Background</h4>Studies suggest that not only is insecticide resistance conferred via multiple gene up-regulation, but it is mediated through the interaction of regulatory factors. However, no regulatory factors in insecticide resistance have yet been identified, and there has been no examination of the regulatory interaction of resistance genes. Our current study generated the first reference transcriptome from the adult house fly and conducted a whole transcriptome analysis for the multiple ...[more]

PMID: 24252181

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Project description:Escherichia coliÂ spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) andÂ E. coliÂ core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species. Four E.coli strains, laboratory strain K12 (MG1655), a commensal model strain (IAI1), a soil-isolated strain (TW11588-Clade IV), and a freshwater-isolated strain (TW09308âClade V) were used. Each strain was grown on a minimal growth medium (Ihssen and Egli, 2004) in three treatment modes: chemostat, batch, and starvation. Cells from batch culture were collected when reaching steady-state. For starvation, the medium flow was stopped during steady-state and bacteria were collected after 4âh.

Dataset Information

A Whole Transcriptional Linkage Analysis of Gene Co-Regulation in Insecticide Resistant House Flies, Musca domestica

Publications

A whole transcriptomal linkage analysis of gene co-regulation in insecticide resistant house flies, Musca domestica.

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