Dataset Information

Transcriptome analysis of Drosophila melanogaster laboratory strains of different geographical origin after long-term laboratory maintenance.

ABSTRACT: Positive selection may be the main factor of the between-population divergence in gene expression. Expression profiles of two Drosophila melanogaster laboratory strains of different geographical origin and long-term laboratory maintenance were analyzed using microchip arrays encompassing probes for 18,500 transcripts. The Russian strain D18 and the North American strain Canton-S were compared. A set of 223 known or putative genes demonstrated significant changes in expression levels between these strains. Differentially expressed genes (DEG) were enriched in response to DDT (p = .0014), proteolysis (p = 2.285E-5), transmembrane transport (p = 1.03E-4), carbohydrate metabolic process (p = .0317), protein homotetramerization (p = .0444), and antibacterial humoral response (p = 425E-4). The expression in subset of genes from different categories was verified by qRT-PCR. Analysis of transcript abundance between Canton-S and D18 strains allowed to select several genes to estimate their participation in latitude adaptation. Expression of selected genes was analyzed in five D. melanogaster lines of different geographic origins by qRT-PCR, and we found two candidate genes that may be associated with latitude adaptation in adult flies-smp-30 and Cda9. Quite possible that several alleles of these genes may be important for insect survival in the environments of global warming. It is interesting that the number of genes involved in local adaptation demonstrates expression level appropriate to their geographical origin even after decades of laboratory maintenance.

SUBMITTER: Zarubin M

PROVIDER: S-EPMC7391317 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Transcriptome analysis of <i>Drosophila melanogaster</i> laboratory strains of different geographical origin after long-term laboratory maintenance.

Zarubin Mikhail M Yakhnenko Alena A Kravchenko Elena E

Ecology and evolution 20200608 14

Positive selection may be the main factor of the between-population divergence in gene expression. Expression profiles of two <i>Drosophila melanogaster</i> laboratory strains of different geographical origin and long-term laboratory maintenance were analyzed using microchip arrays encompassing probes for 18,500 transcripts. The Russian strain D18 and the North American strain Canton-S were compared. A set of 223 known or putative genes demonstrated significant changes in expression levels betwe ...[more]

PMID: 32760513

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Project description:During recent decades, model organisms such as Drosophila melanogaster have made it possible to study the effects of different environmental oxygen conditions on lifespan and oxidative stress. However, many studies have often yielded controversial results usually assigned to variations in Drosophila genetic background and differences in study design. In this study, we compared longevity and ROS levels in young, unmated males of three laboratory wild-type lines (Canton-S, Oregon-R and Berlin-K) and one mutant line (Sod1n1) as a positive control of redox imbalance, under both normoxic and hypoxic (2% oxygen for 24 h) conditions. Lifespan was used to detect the effects of hypoxic treatment and differences were analysed by means of Kaplan-Meier survival curves and log-rank tests. Electron paramagnetic resonance spectroscopy was used to measure ROS levels and analysis of variance was used to estimate the effects of hypoxic treatment and to assess ROS differences between strains. We observed that the genetic background is a relevant factor involved in D. melanogaster longevity and ROS levels. Indeed, as expected, in normoxia Sod1n1 are the shortest-lived, while the wild-type strains, despite a longer lifespan, show some differences, with the Canton-S line displaying the lowest mortality rate. After hypoxic stress these variances are amplified, with Berlin-K flies showing the highest mortality rate and most evident reduction of lifespan. Moreover, our analysis highlighted differential effects of hypoxia on redox balance/unbalance. Canton-S flies had the lowest increase of ROS level compared to all the other strains, confirming it to be the less sensitive to hypoxic stress. Sod1n1 flies displayed the highest ROS levels in normoxia and after hypoxia. These results should be used to further standardize future Drosophila research models designed to investigate genes and pathways that may be involved in lifespan and/or ROS, as well as comparative studies on specific mutant strains.

Project description:BackgroundThe formation of matured and individual sperm involves a series of molecular and spectacular morphological changes of the developing cysts in Drosophila melanogaster testis. Recent advances in RNA Sequencing (RNA-Seq) technology help us to understand the complexity of eukaryotic transcriptomes by dissecting different tissues and developmental stages of organisms. To gain a better understanding of cellular differentiation of spermatogenesis, we applied RNA-Seq to analyse the testis-specific transcriptome, including coding and non-coding genes.ResultsWe isolated three different parts of the wild-type testis by dissecting and cutting the different regions: 1.) the apical region, which contains stem cells and developing spermatocytes 2.) the middle region, with enrichment of meiotic cysts 3.) the basal region, which contains elongated post-meiotic cysts with spermatids. Total RNA was isolated from each region and analysed by next-generation sequencing. We collected data from the annotated 17412 Drosophila genes and identified 5381 genes with significant transcript accumulation differences between the regions, representing the main stages of spermatogenesis. We demonstrated for the first time the presence and region specific distribution of 2061 lncRNAs in testis, with 203 significant differences. Using the available modENCODE RNA-Seq data, we determined the tissue specificity indices of Drosophila genes. Combining the indices with our results, we identified genes with region-specific enrichment in testis.ConclusionBy multiple analyses of our results and integrating existing knowledge about Drosophila melanogaster spermatogenesis to our dataset, we were able to describe transcript composition of different regions of Drosophila testis, including several stage-specific transcripts. We present searchable visualizations that can facilitate the identification of new components that play role in the organisation and composition of different stages of spermatogenesis, including the less known, but complex regulation of post-meiotic stages.

Dataset Information

Transcriptome analysis of Drosophila melanogaster laboratory strains of different geographical origin after long-term laboratory maintenance.

Publications

Transcriptome analysis of <i>Drosophila melanogaster</i> laboratory strains of different geographical origin after long-term laboratory maintenance.

Similar Datasets

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