Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq study of sexual reproduction in the diatom Skeletonema marinoi induced by a change in salinity

ABSTRACT: The aim of the experiment was to study the gene expression changes occurring when cells of the diatom Skeletonema marinoi undergo sexual reproduction. In this species, sex can be induced by an environmental trigger, specifically a change in salinity of the cultivation media. In diatoms the unique mode of cell division with unequal inheritance of the rigid cell wall components determines a progressive cell size reduction as cells divide. Large cells above a given size threshold are not competent for sex, on the other hand small cells, under appropriate conditions, can undergo sexual reproduction. RNA-seq included three experimental conditions: a) large cells above the sexualization size threshold, grown at standard salinity (control condition: no sex, no salinity stress); b) large cells above the sexualization size threshold transferred to higher salinity (treatment 1: no sex, salinity stress); c) small cells below the sexualization size threshold transferred to higher salinity (treatment 2: sex, salinity stress).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Skeletonema marinoi

SUBMITTER: Maria Immacolata Ferrante

PROVIDER: E-MTAB-8091 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Pseudo-nitzschia multistriata is a planktonic diatom species with a diplontic life cycle comprising a short sexual phase during which gametes are produced from the encounter of two diploid cells of opposite mating type (MT). Gene expression studies have highlighted the presence of substantial changes occurring at the onset of sexual reproduction. Collectively, there is clear evidence of a chemical cross talk which mediates the mating step.Herein, we have hypothesized that these major transcriptomic changes are associated to variations in the amount and nature of the metabolites produced by the cells. In order to investigate such chemical diversity in an unbiased manner, we undertook an untargeted metabolomics approach. Liquid chromatography – tandem mass spectrometry was applied to investigate the differences in the metabolic profiles between control cells in the vegetative phase (MT+ and MT-) and mixed strains of opposite MTs (cross) undergoing sexual reproduction. Of the 2408 high-quality features obtained, 70 known metabolites could be identified based on in-house libraries and online databases; molecular networking proved valuable to classify additional 47 non-identified features.The present exploratory study provides an overview of the chemical diversity detectable in P. multistriata, presenting a dynamic picture of the changes occurring during sexual reproduction. In particular, the reduction of phytol detected in the cross can be linked to the general downregulation of photosynthesis during sexual reproduction observed elsewhere. The dysregulation of other metabolites stands as a starting point for the understanding of the mechanisms regulating sexual reproduction: a metabolite that was tentatively identified as 7-dehydrodesmosterol exhibited the highest upregulation in the comparison between the two MTs of opposite sex, as well as between MT+ vs cross.The effects of extraction solvents and harvesting times on the ensemble of endo-metabolites were also analyzed.

Project description:Background: Stalk-eyed flies (family Diopsidae) are a model system for studying sexual selection due to the presence of elongated and sexually dimorphic eye-stalks in many species. Recent genomic studies on these flies have revealed a neo-X chromosome and evidence of gene movement onto or off of this X chromosome. To determine if sex linkage and gene movement are related to sexual dimorphism and sexual conflict, we compared gene expression between males and females using oligonucleotide microarrays and RNA from either developing eyestalk tissue or adult heads from a dimorphic species, Teleopsis dalmanni, or from developing eyestalk tissue in a congeneric monomorphic species, T. quinqueguttata. Results: Comparison of gene expression between the sexes for 3,748 genes indicates that dosage compensation is present due to elevated expression of X-linked genes in males. However, sex-biased expression was detected in 26% of the genes present in eye-antennal imaginal discs of larval T. dalmanni. Functional annotation reveals that female-biased genes are associated with transcription, anatomical development and cell communication in the nucleus, while male-biased genes are associated with metabolism and the mitochondria. Comparison of gene expression between experiments identified 140 genes with concordant sex-biased expression in the larval and adult tissues of T. dalmanni and 17 genes with identical sex-biased expression between species. There were only five reversals of sex-biased expression across experiments. In T. dalmanni, male-biased genes are more common on autosomes than on the X while female-biased genes are more common on the X in T. quinqueguttata. Female-biased expression is especially common among genes that moved onto the ancestral X while male-biased expression is more common among genes that moved onto an autosome. Conclusions: Genes with sex-biased expression exhibit different functions in each sex as expected if sexual conflict has influenced their evolution. The strong relationship between sex-biased expression and gene movement found in this study is consistent with resolution of sexual conflict by an RNA- or DNA-mediated process that moves genes between chromosomes. Measurement of gene expression in additional species should provide a more complete picture of how gene expression change occurs over evolutionary time in these extraordinary flies. Two-condition experiment, female vs. male RNA using larval eye discs for two species (Teleopsis dalmanni, Teleopsis quinqueguttata), and adult heads for one species (Teleopsis dalmanni).

Project description:Pseudo-nitzschia multistriata is a planktonic diatom species with a diplontic life cycle comprising a short sexual phase during which gametes are produced from the encounter of two diploid cells of opposite mating type (MT). Gene expression studies have highlighted the presence of substantial changes occurring at the onset of sexual reproduction. Collectively, there is clear evidence of a chemical cross talk which mediates the mating step. Herein, we have hypothesized that these major transcriptomic changes are associated to variations in the amount and nature of the metabolites produced by the cells. In order to investigate such chemical diversity in an unbiased manner, we undertook an untargeted metabolomics approach. Liquid chromatography – tandem mass spectrometry was applied to investigate the differences in the metabolic profiles between control cells in the vegetative phase (MT+ and MT-) and mixed strains of opposite MTs (cross) undergoing sexual reproduction. Of the 2408 high-quality features obtained, 70 known metabolites could be identified based on in-house libraries and online databases; molecular networking proved valuable to classify additional 47 non-identified features. The present exploratory study provides an overview of the chemical diversity detectable in P. multistriata, presenting a dynamic picture of the changes occurring during sexual reproduction. In particular, the reduction of phytol detected in the cross can be linked to the general downregulation of photosynthesis during sexual reproduction observed elsewhere. The dysregulation of other metabolites stands as a starting point for the understanding of the mechanisms regulating sexual reproduction: a metabolite that was tentatively identified as 7-dehydrodesmosterol exhibited the highest upregulation in the comparison between the two MTs of opposite sex, as well as between MT+ vs cross. The effects of extraction solvents and harvesting times on the ensemble of endo-metabolites were also analyzed.

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RNA-seq study of sexual reproduction in the diatom Skeletonema marinoi induced by a change in salinity

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