Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1001804 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25549378_1.fastq.gz | Fastqsanger.gz | |||
| SRR25549378_2.fastq.gz | Fastqsanger.gz | |||
| SRR25549379_1.fastq.gz | Fastqsanger.gz | |||
| SRR25549379_2.fastq.gz | Fastqsanger.gz | |||
| SRR25549380_1.fastq.gz | Fastqsanger.gz |
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Project description:Pea (Pisum sativum L.) cultivar Arka Chaitra (AC) is considered heat tolerant variety, whereas cultivar Matar Ageta (MA) the heat sensitive variety. In this study, we initially report the repertoire of morpho-physiological traits namely pod number (PNP), weight of pods (PW), seed number/pod (SNP) and weight of seed/pod (SW) during high temperature environment in AC and MA. Subsequently, we conducted pollen viability assay to further examine the pollen behaviour under heat stress (HS). Morpho-physiological analysis revealed that cultivar AC exhibited greater number of pods and seeds, as well as higher pod and seed weights, compared to MA under HS. Furthermore, pollen viability in cultivar AC was reduced by 23%, whereas in cultivar MA, it was reduced by 41%, indicating that AC possess robust tolerance mechanisms under high temperature conditions. Based on these observations, we delve deeper to investigate the regulatory mechanisms by profiling the transcriptomes of cultivars AC and MA using RNA Sequencing under HS. We identified 1922 DEGs in the ACCON-ACHS cluster, 411 DEGs in the MACON-MAHS cluster, and 11,129 DEGs in the ACHS-MAHS cluster indicating substantial transcriptional reprogramming induced by HS. Further, the identified DEGs were annotated through gene ontology (GO) analysis, revealing a significant GO term associated with pollen and flower development, heat stress proteins, and plastid development in tolerant variety, in contrast, the sensitive variety was enriched with GO terms related to cell morphogenesis, cell growth, and cell wall biogenesis. These findings provide in-depth analysis of genes and pathways involved in imparting thermotolerance across pea cultivars AC and MA.
2025-03-31 | GSE286400 | GEO
Project description:Utilization of in vitro (cellular) techniques, like Cell Painting and transcriptomics-based methods could provide powerful tools for risk assessment and regulatory decision-making. However, using these models generates challenges translating in vitro concentrations to corresponding in vivo internal exposures. We tested whether in vivo (rat liver) transcriptional and apical points of departure (PODs) could be accurately predicted from in vitro (rat hepatocyte or human HepaRG) transcriptional PODs or HepaRG Cell Painting PODs using PBPK modeling. We compared two PBPK models, ADMET predictor and the httk R package, and found httk to predict the rat hepatocyte no observed transcriptional effect level (NOTEL)-derived PODs more accurately. Our findings suggest that a rat liver apical and transcriptome POD can be estimated utilizing a combination of in vitro transcriptome-based PODs coupled with PBPK modeling for IVIVE.
2025-06-28 | GSE269501 | GEO
Project description:Bioinformatic prediction, deep sequencing of microRNA and expression analysis during phenotypic plasticity in the pea aphid acyrthosiphon pisum We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 155 miRNAs including 56 conserved and 99 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode.
2010-03-01 | GSE20107 | GEO
Project description:Inflorescence architecture contributes to essential plant traits. It determines plant shape, contributing to morphological diversity, also determines position and number of the flowers and fruits produced by the plant, influencing seed yield. Most legumes have compound inflorescences, where flowers are produced in secondary inflorescences (I2), formed at the flanks of the main primary inflorescence (I1), in contrast to simple inflorescences of plants like Arabidopsis, in which flowers are directly formed on the I1. The pea VEGETATIVE1/ FULc (VEG1) gene, and its homologues in other legumes, specify the formation of the I2 meristem, a function apparently restricted to legumes. To understand the control of I2 development it is important to identify the genes working downstream of VEG1. In this study, we adopted a novel strategy to identify genes expressed in the I2 meristem, as potential regulatory targets of VEG1. To identify pea I2-meristem genes we compared the transcriptomes of inflorescence apices from wild type and mutants affected in I2 development, proliferating inflorescence meristems (pim - with more I2 meristems), veg1 and vegetative2 (both without I2 meristems). Analysis of the differentially expressed genes using Arabidopsis genome databases combined with RT-qPCR expression analysis in pea, allowed the selection of genes expressed in the pea inflorescence apex. In situ hybridization of four of these genes showed that all four genes are expressed in the I2 meristem, proving our approach to identify I2-meristem genes successful. Finally, analysis by VIGS in pea identified one gene, PsDAO1, whose silencing lead to small plants and another gene, PsHUP54, whose silencing leads to plants with very large stubs, meaning that this gene controls activity of the I2 meristem. PsHUP54-VIGS plants also are large and, more importantly, produce large pods with almost double of seeds than the control. Our study shows a new useful strategy to isolate I2-meristem genes and identifies a novel gene, PsHUP54, which seems a promising tool to improve yield in pea and another legumes.
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Project description:A total of 18 samples were selected from 4 periods during the growth of phaseolus vulgaris pods and grains, and total RNA was extracted respectively for transcriptome sequencing and functional detection of the corresponding genes, which laid a certain data foundation for subsequent studies.
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Project description:transcriptome changes in pea leaves with sulfur deficency/sufficiency during reproductive phase.-Characterization of transcriptome changes in leaves of wild-type and PsSultr4 mutant lines (for a sulfur transporter) subjected or not to sulfur deficiency during the reproductive phase 4plex_pea_2014_01 - transcriptome changes in pea leaves with sulfur deficency/sufficiency during reproductive phase. - Role of sulfur and of the sulfate store in leaf metabolism. - Comparison of: 1- The leaf transcriptome of pea subjected or not to sulfur deficiency during the reproductive phase (S+ versus S –) 2- The leaf transcriptome of wild-type and mutant lines for a sulfur transporter (two TILLING alleles) grown under sulfur sufficient conditions : WT1/Mut1 S+ et WT2/Mut2 S+ 3- The leaf transcriptome of wild-type and mutant lines for a sulfur transporter (two TILLING alleles) grown under sulfur deficient conditions : WT1/Mut1 S+ et WT2/Mut2 S+
2021-01-01 | GSE121967 | GEO
Project description:We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 155 miRNAs including 56 conserved and 99 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode.
2010-03-01 | GSE20106 | GEO
Project description:Pea (Pisum. sativum L.) is a traditional and important edible legume that can be sorted into grain pea and vegetable pea according to their harvested maturely or not. Vegetable pea by eating the fresh seed is becoming more and more popular in recent years. These two type peas display huge variations of the taste and nutrition, but how seed development and nutrition accumulation of grain pea and vegetable pea and their differences at the molecular level remains poorly understood. To understand the genes and gene networks regulate seed development in grain pea and vegetable pea, high throughput RNA-Seq and bioinformatics analysis were used to compare the transcriptomes of vegetable pea and grain pea developing seed. RNA-Seq generated 18.7 G raw data, which was then de novo assembled into 77,273 unigenes with a mean length of 930 bp. Functional annotation of the unigenes was carried out using the nr, Swiss-Prot, COG, GO and KEGG databases. There were 459 and 801 genes showing differentially expressed between vegetable pea and grain pea at early and late seed maturation phases, respectively. Sugar and starch metabolism related genes were dramatically activated during pea seed development. The up-regulated of starch biosynthesis genes could explain the increment of starch content in grain pea then vegetable pea; while up-regulation of sugar metabolism related genes in vegetable pea then grain pea should participate in sugar accumulation and associated with the increase in sweetness of vegetable pea then grain pea. Furthermore, transcription factors were implicated in the seed development regulation in grain pea and vegetable pea. Thus, our results constitute a foundation in support of future efforts for understanding the underlying mechanism that control pea seed development and also serve as a valuable resource for improved pea breeding.
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Project description:Bioinformatic prediction, deep sequencing of microRNA and expression analysis during phenotypic plasticity in the pea aphid acyrthosiphon pisum We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 155 miRNAs including 56 conserved and 99 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode. deep sequencing of small RNAs from parthenogenetic Acyrthosiphon pisum
2010-03-01 | E-GEOD-20107 | biostudies-arrayexpress