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Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens

ABSTRACT: Bryophytes are the most basal of the extant land plants. A major feature of these plants is the biphasic alteration of generations between a dominant haploid gametophyte and a minor diploid sporophyte phase. To analyse the differences in the transcriptome of the early gametophyte (protonema) and early and mid-sporophyte phases of the moss Physcomitrella patens, microarray gene expression profiles were performed using dissected sporophyte tissue. Through further analysis the early and mid-sporophyte phases were compared.

ORGANISM(S): Physcomitrium patens

PROVIDER: GSE32928 | GEO | 2013/07/29

SECONDARY ACCESSION(S): PRJNA146495

REPOSITORIES: GEO

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Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens

Project description:Bryophytes are the most basal of the extant land plants. A major feature of these plants is the biphasic alteration of generations between a dominant haploid gametophyte and a minor diploid sporophyte phase. To analyse the differences in the transcriptome of the early gametophyte (protonema) and early and mid-sporophyte phases of the moss Physcomitrella patens, microarray gene expression profiles were performed using dissected sporophyte tissue. Through further analysis the early and mid-sporophyte phases were compared. RNA isolated from the Gametophytic protonemal tissue was hybridised to six microarrays. Each microarray was hybridised with RNA from a separate biological replicate. Three of these microarrays were co-hybridised with RNA isolated from early sporophytes. With the third gametophyte biological replicate and early sporophyte replicate a dye swap was carried out. The remaining three microarrays hybridised with RNA from the gametophytes were co-hybridised with RNA from mid-sporophytic tissue. A dye swap was carried out on the sixth gametophyte replicate and third mid-sporophyte replicate.To meet the quality requirements for the microarray experiment, at least 400 sporophytes were used per extraction. Three or four RNA extracts were then pooled for further precipitation to maximise purity and concentration. Up to 1600 sporophytes were harvested to prepare sufficient RNA for each microarray replicate. In bioinformatic analysis the channels were split into individual channels and the early and mid-sporophyte were compared.

2013-07-29 | E-GEOD-32928 | biostudies-arrayexpress

Small RNAs from the moss Physcomitrella patens

Project description:High-throughput sequencing of endogenous small RNAs from the moss Physcomitrella patens. This dataset encompasses microRNAs and other small RNAs of ~20-24 nucleotides expressed in the moss P. patens. SAMPLES UPDATED JULY 9, 2007 TO INCLUDE DATA ON SEQUENCED SMALL RNAS THAT DO NOT MATCH THE P. PATENS GENOME Keywords: High throughput small RNA sequencing

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Transcription profiling by high throughput sequencing of Funaria hygrometrica sporophyte and gametophyte tissue

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A Physcomitrella protein acts in spermatogenesis and sporophyte abortion

Project description:Functional targeting of PpPINC gene in Physcomitrella, researching it's role during gametangia and sporophyte development.

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Transcription profiling of Ectocarpus strain Esil32 porophyte and gametophyte stages in normal and mutant strains to analyse expression of two sets of genes previously identified as being putatively sporophyte-specific or gametophyte-specific

Project description:The aim of this experiment was to analyse the expression of two sets of genes identified as being putatively sporophyte-specific or gametophyte-specific by a suppressive subtraction hybridisation using cDNA from immature sporophytes and immature gametophytes of the Ectocarpus strain Esil32. The expression of these genes was analysed in the sporophyte and gametophyte generations of the life cycle (again using immature algae that had not yet produces zoidangia) and in the sporophyte generation of a mutant strain, immediate upright, that exhibits gametophyte-like characteristics during the sporophyte generation.

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Transcription profiling of Physcomitrella patens Reute strain

Project description:Transcription profiling of Physcomitrella patens Reute strain gametophore, mature sporophyte and spore stage. These samples are part of an large-scale expression data set for the model moss Physcomitrella patens.

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Funaria hygrometrica sporophyte/gametophyte gene expression

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Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens.

Project description: Not available

| S-EPMC3745722 | biostudies-literature

Dynamics of the transcriptome response to heat in the moss, Physcomitrella Patens

Project description:The moss Physcomitrella patens was employed to study abiotic stress responses in order to understand the effects of mild (30°C) and strong (37°C) continuous heat stresses from 1h to 24h at a transcriptomic level.

2020-04-17 | GSE138467 | GEO

Analysis of transcript abundances in Ectocarpus life cycle mutants

Project description:The aim of this experiment was to compare transcript abundances in parthenotes (i.e. organisms derived by parthenogenetic development of gametes) of two life cycle mutants of the brown alga Ectocarpus siliculosus with transcript abundances in the wild type sporophyte and gametophyte generations. This is of interest because the two mutations, immediate upright (imm) and ouroboros (oro), cause partial and almost complete hometic conversion, respectively, of the sporophyte into the gametophyte. imm parthenotes exhibit gametophyte-like morphology during early development but remain sporophytes in functional terms (they do not produce gametes) whereas oro parthenotes behave as functional gametophytes and are morphologically indistinguishable from gametophytes apart from the appearance some minor sporophyte-like features very early in development in some individuals. To minimise genetic background effects the samples for this experiment were derived from a segregating population derived from an imm/IMM oro/ORO sporophyte. Four classes of gametophyte were derived from this sporophyte were IMM/ORO (wild type), imm/ORO, IMM/oro and imm/oro. Parthenomes were bulked to provide a wild type sporophyte sample, samples corresponding to the two individual mutants, plus the double mutant. A wild type gametophyte sample was also compared for comparison. Hybridisations with cDNA derived from these five samples were carried out using a NimbleGen expressed-sequence-tag-(EST-)based microarray carrying probes corresponding to 10,600 of the 16,256 genes identified in the Ectocarpus genome.

2012-01-14 | E-MTAB-485 | biostudies-arrayexpress

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