Identification of metabolic pathways differentially regulated in somatic and zygotic embryos of maritime pine
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ABSTRACT:
PROVIDER: PRJNA798773 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17666300_1.fastq.gz | Fastqsanger.gz | |||
| SRR17666300_2.fastq.gz | Fastqsanger.gz | |||
| SRR17666301_1.fastq.gz | Fastqsanger.gz | |||
| SRR17666301_2.fastq.gz | Fastqsanger.gz | |||
| SRR17666302_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Analysis of the transcriptome of developing somatic and zygotic embryos from maritime pine.
2022-04-24 | GSE194039 | GEO
Project description:The significant morphological differences observed during embryo development in angiosperms and gymnosperms are expected to be the result of a differential control of gene expression. We used a loblolly pine (Pinus taeda) cDNA microarray to analyze global transcriptional changes along zygotic embryogenesis in maritime pine (Pinus pinaster). A time-course analysis of the data obtained from the five embryo developmental groups used in this study led to the identification of 4,645 genes whose expression varied along P. pinaster embryogenesis. These transcripts were clustered into six distinct expression profiles. The grouping of these profiles in early, mid-embryogenesis and embryo maturation, according to the developmental period where most of the sequences were up-regulated, evidenced that characteristic transcriptional changes are associated to each developmental period. The application of a cut-off value of 1.95-fold change led to the identification of 1,838 differentially expressed transcripts that were categorized by biological process. Metabolism, interaction with the environment, oxidation-reduction and transport were some of the most represented categories. During early embryogenesis genes putatively involved in phytohormone-mediated signaling were identified, whereas in middle stages the overrepresented genes could be associated with cotyledon formation and induction of somatic embryogenesis. Genes associated with the synthesis of storage products were up-regulated in the latest stages of pine embryo development. It was also during this developmental period that the largest number of sequences putatively encoding transcription factors was identified. Pine immature zygotic embryos were pooled into five different developmental groups according to the collection date (Day0; Day5; Day11; Day15 and Day25). A common reference design was used. Total RNA was extracted from each sample. Three extractions were prepared per sample (biological replicates). A defined ammount from each RNA sample was pooled to use as reference. Messenger RNA was amplified for both test samples and reference. These were hybridized together in two separate experiments (technical replicates). In total, 30 slides were analyzed.
2012-01-30 | E-GEOD-32551 | biostudies-arrayexpress
Project description:The significant morphological differences observed during embryo development in angiosperms and gymnosperms are expected to be the result of a differential control of gene expression. We used a loblolly pine (Pinus taeda) cDNA microarray to analyze global transcriptional changes along zygotic embryogenesis in maritime pine (Pinus pinaster). A time-course analysis of the data obtained from the five embryo developmental groups used in this study led to the identification of 4,645 genes whose expression varied along P. pinaster embryogenesis. These transcripts were clustered into six distinct expression profiles. The grouping of these profiles in early, mid-embryogenesis and embryo maturation, according to the developmental period where most of the sequences were up-regulated, evidenced that characteristic transcriptional changes are associated to each developmental period. The application of a cut-off value of 1.95-fold change led to the identification of 1,838 differentially expressed transcripts that were categorized by biological process. Metabolism, interaction with the environment, oxidation-reduction and transport were some of the most represented categories. During early embryogenesis genes putatively involved in phytohormone-mediated signaling were identified, whereas in middle stages the overrepresented genes could be associated with cotyledon formation and induction of somatic embryogenesis. Genes associated with the synthesis of storage products were up-regulated in the latest stages of pine embryo development. It was also during this developmental period that the largest number of sequences putatively encoding transcription factors was identified.
2012-01-30 | GSE32551 | GEO
Project description:Embryogenesis is a complex phase of conifer development involving hundreds of genes, and a proper understanding of this process is critical not only to produce embryos with different applied purposes but also for comparative studies with angiosperms. A global view of transcriptome dynamics during pine somatic and zygotic embryogenesis is currently missing. Here, we present a genome-wide transcriptome analysis of somatic and zygotic embryos at three developmental stages to identify conserved biological processes and gene functions during late embryogenesis. Most of the differences became more significant as the developmental process progressed from early to cotyledonary stages, and a higher number of genes were differentially expressed in somatic than in zygotic embryos. Metabolic pathways substantially affected included those involved in amino acid biosynthesis and utilization, and this difference was already observable at early developmental stages. Overall, this effect was found to be independent of the line (genotype) used to produce the somatic embryos. Additionally, transcription factors differentially expressed in somatic versus zygotic embryos were analyzed. Some potential hub regulatory genes were identified that can provide clues as to what transcription factors are controlling the process and to how the observed differences between somatic and zygotic embryogenesis in conifers could be regulated.
| S-EPMC9159154 | biostudies-literature
Project description:Maritime pine (Pinus pinaster Aiton) is a coniferous native of the Mediterranean basin. Because of its adaptability to a wide range of environmental conditions, the species have become a model for studies in coniferous forest management and functional genomics. Somatic embryogenesis (SE) has been so far, the preferred biotechnological strategy for maritime pine breeding programs initiated at the middle-end of the 20th century. To overcome the limitations of the induction and maturation phases in maritime pine SE, we analyzed the possible maternal influence on the embryogenic capability of megagametophytes from controlled crosses, as well as the effect of the temperature and water availability during SE process on the production of plants. A strong maternal effect on the embryogenic potential of maritime pine megagametophytes was observed in our experiments using half-sib and full-sib progenies, while paternal effect was almost undetectable. Besides, it seems possible to improve somatic embryo production of maritime pine megagametophytes by adjusting optimal temperature throughout the process: 28°C during induction and proliferation, and 23°C during the maturation phase. Using induction and proliferation media with reduced water availability (6 g/L Gelrite) can also increase embryo production. Since other limitation of maritime pine SE is culture decline of embryogenic masses (EMs), that reduces embryo yield and germination, we assessed the profile of ABA and IAA and the expression of two embryogenesis-related genes (LEC1 and WOX2) during maturation of EMs of two morphotypes that differed in their maturation capability. Spiky morphotype (SK), with high maturation capability, had a steady increase in both hormones along the 12 weeks of the maturation, whereas ABA content in smooth morphotype picked at the 4th week and dropped. EMs with this morphotype also had a higher IAA content at the beginning of the maturation. A decrease of LEC1 and WOX2 gene expression over the course of embryo development was found to be characteristic of the SK with high maturation capability.
| S-EPMC6389691 | biostudies-literature
Project description:We used a next-generation sequencing approach, Illumina Digital Gene Expression II (DGEII) technology, to Genome-wide profiling of gene expression during somatic (SE) and zygotic embryo (ZE) development. As a result, 4242 differentially expressed genes (DEGs) were identified between SE and ZE. Expression pattern cluster and functional classification analysis of the differentially expressed genes revealed that large number of genes indicative of response to stress highly expressed in somatic embryos. Combined with KEGG analysis and BLAST annotation, genes related to stress response in DEGs have been comprehensively analyzed, mainly including: ABA biosynthesis, ABA and JA (jasmonic acid) response, LEA (late embryogenesis abundant protein) family members, RD (responsive to dehydration) and ERD (early responsive to dehydration) family members, Hot Shock Proteins, WRKY family members and NAC family members. Semi-quantitative Reverse Transcriptase-PCR (RT-PCR) analysis was performed on 27 selected genes and and the results enhance that genes related to stress response were involved in SE development. Our main goal is to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. This is a systematical expression analysis focusing on somatic embryo development, and also a global comparison between somatic and zygotic embryo at transcript level. Therefore, this study might bring new insights into the regulation of somatic embryo development. An analysis of differentially expressed genes at 3 parallel stages during somatic and zygotic embryo development in cotton by next-generation sequencing, using Illumina Digital Gene Expression II (DGE II) .
2013-09-27 | E-GEOD-45671 | biostudies-arrayexpress
Project description:Transcriptional regulation of arogenate dehydratase genes linked to lignin biosynthesis in maritime pine
| PRJNA595897 | ENA
Project description:There are several issues complicating somatic embryogenesis in conifers, for instance the low initiation frequency, the weak maturation capacity, and the loss of an embryogenic potential after a prolonged cultivation. The aim of our study was to clarify molecular details of the this process in the tree Pinus nigra Arn. We performed comparative proteomic analysis based on the two-dimensional gel electrophoresis in 2 genotypes coded 362 and 366 of: 1) proliferating embryogenic tissues (E) initiated from immature zygotic embryos, 2) non-embryogenic calli (NEC) started from cotyledons of somatic seedlings, 3) embryogenic tissues that lost the maturation capacity (E-L). Pine tissues showed distinct morphologic features: a) E362 and E366 were characterized by the presence of early bipolar structures capable of maturation and plantlet regeneration; b) NEC362 and NEC366 were composed of round shaped cells without any organisation; c) for E-L362 and E-L366 the long-term culture of initially embryogenic tissues resulted in the disorganisation of early bipolar structures. We found 24 differentially accumulated protein spots common for both genotypes after comparison of E versus NEC.
2017-09-06 | PXD004611 | Pride
Project description:Transcriptional regulation of arogenate dehydratase genes linked to lignin biosynthesis in maritime pine [11PP17]
| PRJNA595903 | ENA
Project description:Transcriptional regulation of arogenate dehydratase genes linked to lignin biosynthesis in maritime pine [11PP16A]
| PRJNA595904 | ENA