Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genetic selection shaped the gene expression patterns of mRNA and protein in rice subspecies

ABSTRACT: Genetic selection shaped the gene expression patterns of mRNA and protein in rice subspecies

PROVIDER: PRJNA598235 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10806779_1.fastq.gz	Fastqsanger.gz
	SRR10806779_2.fastq.gz	Fastqsanger.gz
	SRR10806780_1.fastq.gz	Fastqsanger.gz
	SRR10806780_2.fastq.gz	Fastqsanger.gz
	SRR10806781_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Genetic selection shaped the gene expression patterns of mRNA and protein in rice subspecies

Project description:Eukaryotes gene expression of mRNA and protein is a basic cellular activity and regulated by multiple process, yet the expression patterns at these two levels and their genetic and evolutionary determinants remain undefined in plants. Here, using RNA-sequencing and TMT labeled LC-MS/MS analysis, we investigated the genome-wide variation of mRNA and protein expression in rice subspecies japonica C92, indica MH63 and their F1 hybrid. Different expression patterns of mRNA and protein between C92 and MH63 were linked to distinct functional categories. Genes with consistent divergence of mRNA and protein expression between subspecies tend to be regulated by cis effect and had higher sequence variation in nonsynonymous sites. Population differentiation (FST) analysis showed that genes with conserved expression of either mRNA or protein in C92 and MH63 were more likely to be under purify selection, while genes with consistent divergence in mRNA or protein expression were more likely to be under positive selection, especially in their nonsynonymous site have high frequency of positive selected genes that changed their protein sequence by nonsynonymous mutation. Furthermore, oxidative stress response genes were enriched in genes with consistent divergence of expression, and showed higher sequence variation in nonsynonymous sites and are more likely to be positive selected in evolution. These results suggested that cis-regulation with high nonsynonymous-variation was evolutionarily important feature to shape divergent expression patterns of mRNA and protein and may contribute to diversity in oxidative stress response between rice subspecies.

2023-12-27 | GSE142770 | GEO

Transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice (Oryza sativa L.)

Project description:Hybrids and allopolyploids typically exhibit radically altered gene expression patterns relative to their parents, a phenomenon termed âtranscriptomic shock.â To distinguish the effects of hybridization from polyploidization on coregulation of divergent alleles, we analyzed expression of parental copies (homoeologs) of 11,608 genes using RNA-seq-based transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice (Oryza sativa L.)

2014-02-18 | E-MTAB-4271 | biostudies-arrayexpress

Brown rat subspecies

Project description:Brown rat subspecies

| PRJEB47576 | ENA

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids.

Project description:The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here we report highly integrated maps of the epigenome, mRNA and small RNA transcriptomes of two rice subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents and more small RNAs were down-regulated than up-regulated in the reciprocal hybrids. Together, our data reveals a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses, and provides a very useful resource for the rice community.

2010-01-20 | GSE19602 | GEO

Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells

Project description:Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells

| PRJNA338193 | ENA

Natural selection shapes genome wide patterns of copy number polymorphism in D. melanogaster

Project description:The role natural selection plays in governing the locations and early evolution of copy number mutations remains largely unexplored. Here we employ high-density full-genome tiling arrays to create a fine-scale genomic map of copy number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2,658 independent CNPs, 56% of which overlap genes. These include CNPs likely to be under positive selection, most notably high frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns and those falling on the X-chromosome seem to be subject to the strongest purifying selection. In order to characterize copy number polymorphisms (CNPs) in Drosophila malanogaster, we applied comparative genome hybridization (CGH) using tiling arrays covering the full euchromatic genome of Drosophila melanogaster. We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates and the reference genome strain. Training data for copy number changes were obtained via hybridization with a line known to contain a ~200kb homozygous duplication and from a set of 52 validated homozygous deletions. The probabilities of mutation were parsed to make CNP calls. Key words: comparative genomic hybridization, CGH, copy number polymorphism, CNP, copy number variation, CNV, duplication, deletion

2008-06-06 | GSE11326 | GEO

Natural selection and repeated patterns of molecular evolution following allopatric divergence

Project description:Natural selection and repeated patterns of molecular evolution following allopatric divergence

| PRJEB35996 | ENA

Global subspecies distribution

Project description:Subspecies in the global human gut microbiome

| PRJEB17632 | ENA

Lactobacillus delbrueckii subspecies characterization by MudPIT analysis

Project description:We have characterized three strains belonging to L. delbrueckii subspecies (bulgaricus, B; lactis, L; L.delbrueckii 23, M) highlighting their divergent origin, different galactose metabolic capabilities and we have demonstrated potential probiotic features.

2017-06-29 | PXD006551 | Pride

Mycobacterium avium subspecies paratuberculosis diversity

Project description:Mycobacterium avium subspecies paratuberculosis diversity

| PRJEB2204 | ENA