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Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens

ABSTRACT: Gene expression was analyzed with digital gene expression tag profiling (DGEP) with samples taken from P. patens protonema at 3, 14 and 24 days, and also from or leafy shoot tissues l at 30 days after protoplastes isolated, and from 14-day-old caulonemal and chloronemal tissues. Totally, 4333 genes were identified as differentially displayed. Among them, 4129 were developmental-stage specific and 423 were preferentially expressed in either chloronemal or caulonemal tissues. Most of the differentially displayed genes could be assigned to functions in organic substance and energy metabolism or macromolecule biosynthetic and catabolic process based on gene ontology (GO) description. In addition, some regulatory genes were identified as candidates that might be involved in controlling the developmental stage transition and cell differentiation, namely: MYB-like, HB-8, AL3, zinc finger family proteins, bHLH superfamily, GATA superfamily, GATA and bZIP transcription factors, protein kinases, the genes related to protein/amino acid methylation, and auxin, ethylene, and cytokinin signaling pathways.

ORGANISM(S): Physcomitrium patens

PROVIDER: GSE33279 | GEO | 2011/12/20

SECONDARY ACCESSION(S): PRJNA149079

REPOSITORIES: GEO

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Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens

Project description:Gene expression was analyzed with digital gene expression tag profiling (DGEP) with samples taken from P. patens protonema at 3, 14 and 24 days, and also from or leafy shoot tissues l at 30 days after protoplastes isolated, and from 14-day-old caulonemal and chloronemal tissues. Totally, 4333 genes were identified as differentially displayed. Among them, 4129 were developmental-stage specific and 423 were preferentially expressed in either chloronemal or caulonemal tissues. Most of the differentially displayed genes could be assigned to functions in organic substance and energy metabolism or macromolecule biosynthetic and catabolic process based on gene ontology (GO) description. In addition, some regulatory genes were identified as candidates that might be involved in controlling the developmental stage transition and cell differentiation, namely: MYB-like, HB-8, AL3, zinc finger family proteins, bHLH superfamily, GATA superfamily, GATA and bZIP transcription factors, protein kinases, the genes related to protein/amino acid methylation, and auxin, ethylene, and cytokinin signaling pathways. Examination of 4 different sampling times and 2 different organelles.

2011-12-20 | E-GEOD-33279 | 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

2006-08-15 | GSE5103 | GEO

small RNA-seq of Physcomitrella patens rdr mutants

Project description:To investigate the effects of rdr2 and rdr6 mutations upon small RNAs in Physcomitrella patens , small RNA-seq was performed.

2015-06-30 | GSE51416 | GEO

dsRNA-seq of Physcomitrella patens rdr mutants

Project description:To investigate the effects of rdr2 and rdr6 mutations upon the strucutred component of the Physcomitrella patens transcriptome, dsRNAseq performed. The accumulation of dsRNAseq reads within known small RNA (microRNA and siRNA) loci was quantified and compared between wild-type and the two mutants.

2015-06-30 | GSE51418 | GEO

Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens.

Project description: Not available

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The DNA damage response transcriptome of the moss Physcomitrella patens

Project description:The moss Physcomitrella patens is remarkable for the ease with which mutant alleles of any gene can be generated by highly efficient homologous recombination-mediated gene targeting. Targeted transgene integration is believed to be mediated through the capture of transforming DNA by the homologous recombination DNA repair pathway. To identify components of this pathway in P. patens we have undertaken a transcriptomic analysis of the response to the sublethal induction of bleomycin-induced DNA double-strand breaks using massively parallel (Illumina) cDNA sequencing. Transcripts significantly increased in bleomycin-treated tissue include a number encoding conserved DNA-DSB components in both the homology-dependent pathway (including Rad51, CTiP, DNA ligase 1, Replication protein A, ATR) and the non-homologous end-joining pathway (including Xrcc4, DNA ligase 4, Ku70, Ku80, PARP). Differentially regulated cell-cycle components include up-regulated Rad9 and Hus1 DNA-damage-related checkpoint proteins and down-regulated D-type cyclins and B-type CDKs, commensurate with the imposition of a checkpoint in the G2 stage of the cell cycle characteristic of homology-dependent DNA-DSB repair. Comparison of the DNA damage transcriptome of P. patens with that of A. thaliana reveals significant up-regulation of a number of P. patens genes encoding ATP-dependent chromatin remodelling helicases of the SNF-2 class. These represent candidates for investigation of their role in mediating efficient gene targeting in P. patens.

2010-11-10 | GSE25237 | GEO

small RNA-seq of Physcomitrella patens small RNA mutants

Project description:To investigate the effects of dcl3,dcl4,mDCL,rdr2,rdr6,nrpd1b, and nrpd1c mutations upon small RNAs in Physcomitrella patens , small RNA-seq was performed.

2015-06-30 | GSE51419 | GEO

Physcomitrella patens ABA response

Project description:Transcriptome profiling by Combimatrix array of Physcomitrella patens Gransden protonemata treated with ABA

2019-03-11 | E-MTAB-5492 | biostudies-arrayexpress

Physcomitrella patens Reute development

Project description:Transcriptome profiling by Nimblegen array of Physcomitrella patens Reute gametophores, gametophores with gametangia, green sporophytes and brown sporophytes.

2017-05-24 | E-MTAB-4630 | biostudies-arrayexpress

Small RNA genes of Physcomitrella patens

Project description:Small RNA-seq from 10 day-old wild-type Physcomitrella patens was performed using 5 biological replicates. Replicates were grown in three batches at different times. Batch 1 had one replicate from strain "old WT", Batch 2 had two replicates from strain "old WT", and batch 3 had two replicates from strain "2009 WT". Old WT and 2009 WT were collected from Gransden wood, England; "old" has been in lab cultivation for at least 10 years, while "2009" was more recently collected from the wild (in 2009.)

2015-06-30 | GSE44900 | GEO

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