Transcriptome profiling of Arabidopsis embryogenesis in vitro
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Anushka Wickramasuriya
PROVIDER: E-MTAB-2403 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:MicroRNAs (miRNAs) are emerging as essential regulators of biological processes. Somatic embryogenesis is one of the most important techniques for gymnosperm breeding programs, but there is little understanding of its underlying mechanism. To investigate the roles of miRNAs during somatic embryogenesis in larch, we constructed a small RNA library from somatic embryos. High-throughput sequencing of the library identified 83 conserved miRNAs from 35 families, 16 novel miRNAs, and 14 plausible miRNA candidates, with a high proportion specific to larch or gymnosperms. qRT-PCR analysis demonstrated that both the conserved and novel or candidate miRNAs were expressed in larch. Several miRNA precursor sequences were obtained via RACE. We predicted 110 target genes using bioinformatics, and validated nine of them by 5M-bM-^@M-^Y RACE. Eleven conserved miRNA families including 17 miRNAs with critical functions in plant development and six target mRNAs were detected by qRT-PCR in the larch SE. Stage-specific expression of miRNAs and their targets indicate their possible modulation on SE of larch: miR171a/b might exert function on PEMs, while miR171c acts in the induction process of larch SE; miR397 and miR398 mainly involved in modulation of PEM propagation and transition to single embryo; miR162 and miR168 exert their regulatory function during total SE process, especially during stage 5 to stage 8; miR156, miR159, miR160, miR166, miR167, and miR390 might play regulatory roles during cytoledonary embryo development. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving specific and common miRNAs operating post-transcriptionally during embryogenesis. Examination of small RNA expression profilings in Larix somatic embryos over seven developmental stages: 1) after 2 and 15 days on sub-culture; 2) 2, 6, and 11 days post-differentiation culture; and 3) somatic embryos at days 33 and 39.
2012-09-04 | E-GEOD-27898 | biostudies-arrayexpress
Project description:Small non-coding RNAs (sncRNAs) are emerging as key regulators of embryogenesis. To investigate the roles of sRNAs in regulating synchronism of somatic embryogenesis in Larix leptolepis, we deciphered the endogenous "sRNAome" in synchronous and desynchronous embryos. The 24-nt class sRNAs were overrepresented in both synchronous embryos and desynchronous embryos, accounting for 85.29% and 44.79%. A total of 29 miRNAs were upregulated in synchronous embryos, whereas 59 miRNAs were upregulated in desynchronous embryos. We describe the emerging theme for sncRNAs function: inhibiting the precocious expression, thus regulating the synchronism of somatic embryogenesis. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving sRNAs and miRNAs operating transcriptionally and post-transcriptionally during the regulation of synchronism. One embryogenic cell line of Japanese larch (Larix leptolepis), designated as D878, with a high embryo maturation capacity was used in this study. Embryogenic callus was induced from immature embryos of Japanese larch on induction medium followed by sub-culture. Calli at the proembryogenic mass III stage were cultured on maturation medium in a dark environment at 25 M-BM-1 2M-BM-0C. Samples were cultured on ABA-plus or ABA-minus maturation medium for 45 days. All samples were snap-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.
2014-07-19 | E-GEOD-49055 | biostudies-arrayexpress
Project description:Somatic embryogenesis is an important biotechnological technique for large-scale propagation of elite genotypes. Correlations of stage-specific compounds associated with somatic embryo development can help elucidate the ontogenesis of Carica papaya L. somatic embryos and improve tissue culture protocols. To identify the stage-specific proteins that are present during the differentiation of C. papaya somatic embryos, proteomic analyses of embryos at the globular, heart, torpedo and cotyledonary stages were performed. Comparative proteomic analysis revealed a total of 801 proteins, 392 of which were classified as differentially accumulated proteins in at least one of the developmental stages. The globular stage presented a higher number of unique proteins (16), 7 of which were isoforms of 60S ribosomal proteins, suggesting high translational activity at the beginning of somatic embryogenesis. Proteins related to mitochondrial metabolism accumulated to a high degree at the early developmental stages, after which they decreased with increasing development, contributing to cell homeostasis in early somatic embryos. On the other hand, a progressive increase in the accumulation of vicilin, late embryogenesis abundant proteins and chloroplastic proteins leading to somatic embryo maturation was observed. Additionally, the differential accumulation of acetylornithine deacetylase and S-adenosylmethionine synthase 2 proteins correlated with increased contents of putrescine and spermidine, suggesting that polyamine metabolism is important to somatic embryo development. Taken together, the results showed that somatic embryo development in C. papaya is regulated by the differential accumulation of proteins, with ribosomal and mitochondrial proteins being more abundant during the early somatic embryo stages, while proteins involved in seed maturation are more abundant during the late stages.
2020-11-12 | PXD021107 | Pride
Project description:Sour passion fruit (Passiflora edulis Sims) has economic and social relevance and is an alternative crop mainly for family farming agriculture. The use of micropropagation by somatic embryogenesis offers scale-up clonal propagation with high phytosanitary quality. The aim of this work was to evaluate the influence of polyethylene glycol (PEG) on the maturation of somatic embryos associated with differential accumulation of proteins and changes in the endogenous polyamines (PAs) content during somatic embryogenesis of P. edulis ‘UENF Rio Dourado’. Maturation of somatic embryos was performed using embryogenic callus in MS culture medium with PEG 6% or without PEG (control). PEG 6% promoted the maturation of a significantly higher number of somatic embryos at globular and cotyledonary stages when compared to control treatment. The higher somatic embryo formation induced by PEG 6% was associated with an increase in endogenous contents of free spermine, a PA with an important role in the maturation process of somatic embryogenesis cultures. PEG also promoted a significantly higher content of putrescine and total free PAs at the end of maturation, which was relevant for the increase in the number of somatic embryos. Comparative proteomic analyses of PEG 6%/control revealed that PEG 6% treatment induced the up-accumulation of proteins related to the glycolytic process, generation of precursor metabolites energy, and response to light stimulus, we can highlight the enolase ENO1, triosephosphate isomerase (TPI), ribulose bisphophate carboxylase/oxygenase activase chloroplastic (RCA), glyceraldehyde-3-phosphate dehydrogenase GAPCP-1, chloroplastic (GAPCP-1), succinate dehydrogenase [ubiquinone] flavoprotein subunit1, mitochondrial (SDH1-1), pyruvate dehydrogenase E1 component subunit alpha, mitochondrial (IAR4), ATP synthase CF1 beta subunit (PB), malate dehydrogenase [NADP], chloroplastic (AT5G58330) and chlorophyll a-b binding protein 21, chloroplastic (LHB1B1), and the down-accumulated proteins related mainly to the cellular metabolic process with proteins such as NADP-dependent malic enzyme (NADP-ME4), phosphoenolpyruvate carboxylase 2 (PPC1), UDP-glucose 6-dehydrogenase 1 and 4 (UGD2) and sucrose synthase 2 isoform X2 (SSA) and cell division cycle protein 48 homolog (ATCDC48B). The use of PEG induced thematuration and development of somatic embryos of P. edulis Sims ‘UENF Rio Dourado’ by the differential accumulation of proteins and modulation of endogenous contents of PAs
2024-02-21 | PXD031175 | Pride
Project description:The goal of the experiment was to investigate impact of the apoplast on somatic embryogenesis in Cyclamen persicum
2010-04-20 | E-TABM-837 | biostudies-arrayexpress
Project description:The goal is to examine the molecular aspects underpinning somatic embryogenesis (SE) within shoot tissues of adult white spruce trees by conducting transcriptome-wide expression profiling of shoot explants taken from responsive and nonresponsive genotypes. One-color analysis of vegetative buds in somatic embryogenesis responsive and nonresponsive genotypes, before and after 7 days of SE induction. There are 5 biological replicates for each of the 4 combinations of genotype/time of induction for a total of 20 slides. Each replicate is comprised of a pool of 6 buds.
2013-10-17 | E-GEOD-46977 | biostudies-arrayexpress
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:Somatic embryogenesis is an important biological process in several plant species, including sugarcane. Proteomics approaches have shown that H+ pumps are differentially regulated during somatic embryogenesis; however, the relationship between H+ flux and embryogenic competence is still unclear. This work aimed to elucidate the association between extracellular H+ flux and somatic embryo maturation in sugarcane. We performed a microsomal proteomics analysis and analyzed changes in extracellular H+ flux and H+ pump (P-H+-ATPase, V-H+-ATPase and H+-PPase) activity in embryogenic and non-embryogenic callus. A total of 657 proteins were identified, 16 of which were H+ pumps. We observed that P-H+-ATPase and H+-PPase were more abundant in embryogenic callus. Compared with non-embryogenic callus, embryogenic callus showed high H+ influx, especially at maturation day 14 as well as higher H+ pump activity, mainly P-H+-ATPase and H+-PPase activity. The H+-PPase appears to be the major H+ pump in embryogenic callus during somatic embryo formation, functioning in both vacuole acidification and PPi homeostasis. These results provide evidence for an association between higher H+ pump protein abundance and, consequently, higher H+ flux and embryogenic competence acquisition in the callus of sugarcane.
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Project description:To investigate the roles of sRNAs in keeping embryo dormancy or germination in Larix leptolepis, we deciphered the endogenous "sRNAome" in dormant and germinated embryos. High-throughput sequencing of the sRNA libraries showed that dormant embryos exhibited a length bias towards 24-nt, while germinated embryos showed a bias towards a 21-nt and/or 22-nt length. Both of proportions for miRNAs to the non-redundant and redundant sRNAs were higher in germinated embryos than those in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. The proportion of 21-nt and 22-nt sRNAs increased in germinated embryos, which might attribute to the higher expression level of miRNAs. We identified a total of 160 conserved miRNAs from 39 families, 16 novel miRNAs, and 14 plausible miRNA candidates, of which novel and non-conserved known miRNAs might be the main contributors. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving sRNAs and miRNAs operating transcriptionally and post-transcriptionally during embryo dormancy and germination. One embryogenic cell line of Japanese larch (Larix leptolepis), designated as D878, with a high embryo maturation capacity was used in this study. Embryogenic callus were induced from immature embryos of larch on induction medium, followed by sub-culture, and culture on ABA-containing mature medium in a dark environment at 25 2 C. After cultured 45 days in mature medium, embryogenic calli developed into mature somatic embryos. In our study, the samples were harvested at day 57, one sample was collected after mature embryos continued to stay for 12 days on ABA-containing medium, and the other one was harvested after cultured for 12 days on ABA-removing medium. All samples were snap-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.
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Project description:Four cDNA libraries from immature embryos, mature embryos, microspore derived embryos and mature leaves were constructed. cDNA were sequenced by the Roche-454 GS-FLX.
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