Similar Datasets
Project description:High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.
| PRJNA731856 | ENA
Project description:Pi availability is a significant limiting factor for plant growth in both natural and agricultural systems. To cope with such limiting conditions, plants have adapted developmental and biochemical strategies to enhance Pi acquisition and to avoid starvation. A myriad of genes that are involved in the regulation and display of these strategies have been identified. However, the possible epigenetic components regulating the phosphate starvation responses have not been thoroughly investigated. DNA methylation is a major epigenetic mark involved in diverse biological processes and it may play a critical role in Pi starvation stress adaptation, also changes in DNA methylation can lead to a unique gene expression pattern in response to specific developmental and environmental conditions. Here in we demonstrate that non-CpG DNA methylation is required for proper expression of a number of Pi-limitation responsive genes in Arabidopsis thaliana and results in altered morphologic and physiologic phosphate starvation responses.Our data suggest that DNA methylation is involved in the modulation of Pi starvation responses via the transcriptional regulation of a set of phosphate-starvation responsive genes.
2015-12-31 | GSE72770 | GEO
Project description:The current human reference genome (GRCh38), with its superior quality, has contributed significantly to genome analysis. However, GRCh38 may still underrepresent the ethnic genome, specifically for Asians, though exactly what we are missing is still elusive. Here, we juxtaposed GRCh38 with a high-contiguity genome assembly of one Korean (AK1) to show that a part of AK1 genome is missing in GRCh38 and that the missing regions harbored ~1390 putative coding elements. Furthermore, we found that multiple populations shared some certain parts in the missing genome when we analyzed the "unmapped" (to GRCh38) reads of fourteen individuals (five East-Asians, four Europeans, and five Africans), amounting to ~5.3 Mb (~0.2% of AK1) of the total genomic regions. The recovered AK1 regions from the "unmapped reads", which were the estimated missing regions that did not exist in GRCh38, harbored candidate coding elements. We verified that most of the common (shared by ?7 individuals) missing regions exist in human and chimpanzee DNA. Moreover, we further identified the occurrence mechanism and ethnic heterogeneity as well as the presence of the common missing regions. This study illuminates a potential advantage of using a pangenome reference and brings up the need for further investigations on the various features of regions globally missed in GRCh38.
| S-EPMC7697454 | biostudies-literature
Project description:BackgroundLong-term stored serum is considered challenging for epigenomic analyses: as there are no cells, circulating DNA is scarce, and amplification removes epigenetic signals. Additionally, pre-analytical treatments and storage might introduce biases and fragmentation to the DNA. In particular, starting with low-input DNA can result in low-diversity libraries. However, successful whole-genome bisulphite sequencing (WGBS) of such serum samples has the potential to open biobanks for epigenetic analyses and deliver novel prediagnostic biomarkers. Here, we perform WGBS using the Accel-NGS library preparation kit on ultralow amounts of DNA from long-term archived samples with diverse pretreatments from the Janus Serum Bank.ResultsNinety-four of the 96 samples produced satisfactory methylation calls; an average of 578 M reads per sample generated a mean coverage of 17× and mean duplication level of 35%. Failed samples were related to poor bisulphite conversion rather than to sequencing or library preparation. We demonstrate the feasibility of WGBS on ultralow DNA yields from serum samples stored up to 48 years.ConclusionsOur results show the potential of large serum biobank collections for future epigenomic studies and biomarker discovery.
| S-EPMC8114536 | biostudies-literature
Project description:The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
| S-EPMC9778375 | biostudies-literature
Project description:Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) that was found dead in the mountainous region in Gansu, China. We generate a near-complete genome assembly containing only 18 gaps scattering in 8 out of the 40 assembled chromosomes. We characterize the DNA methylation landscape which is correlated with GC content and gene expression. Our phylogenomic analysis suggests Otidiformes and Musophagiformes are sister groups that diverged from each other 46.3 million years ago. The genetic diversity of great bustard is found the lowest among the four available Otidiformes genomes, possibly due to population declines during past glacial periods. As one of the heaviest migratory birds, great bustard possesses several expanded gene families related to cardiac contraction, actin contraction, calcium ion signaling transduction, as well as positively selected genes enriched for metabolism. Finally, we identify an extremely young evolutionary stratum on the sex chromosome, a rare case among birds. Together, our study provides insights into the conservation genomics, adaption and chromosome evolution of the great bustard.
| S-EPMC10354230 | biostudies-literature
Project description:Reference genome for cabbage obtained with SMRT
| PRJEB36070 | ENA
Project description:Reference genome for cabbage
| PRJEB36072 | ENA
Project description:With development of sequencing technology, dense single nucleotide polymorphisms (SNPs) have been available, enabling uncovering genetic architecture of complex traits by genome-wide association study (GWAS). However, the current GWAS strategy usually ignores epistatic and gene-environment interactions due to absence of appropriate methodology and heavy computational burden. This study proposed a new GWAS strategy by combining the graphics processing unit- (GPU-) based generalized multifactor dimensionality reduction (GMDR) algorithm with mixed linear model approach. The reliability and efficiency of the analytical methods were verified through Monte Carlo simulations, suggesting that a population size of nearly 150 recombinant inbred lines (RILs) had a reasonable resolution for the scenarios considered. Further, a GWAS was conducted with the above two-step strategy to investigate the additive, epistatic, and gene-environment associations between 701,867 SNPs and three important quality traits, gelatinization temperature, amylose content, and gel consistency, in a RIL population with 138 individuals derived from super-hybrid rice Xieyou9308 in two environments. Four significant SNPs were identified with additive, epistatic, and gene-environment interaction effects. Our study showed that the mixed linear model approach combining with the GPU-based GMDR algorithm is a feasible strategy for implementing GWAS to uncover genetic architecture of crop complex traits.
| S-EPMC4539430 | biostudies-literature
Project description:DNA methylation is a key epigenetic modification in mammals, have essential and important roles in muscle development. Here, using cattle as a model, we investigate the systematic association between DNA methylation and muscle development. We sample longissimus thoracis tissues from a famous elite native breed of Chinese Qinchuan cattle living within comparable environments under fetal and adult stages. Using methylated DNA immunoprecipitation sequencing (MeDIP-Seq) , we generate and provide a genome-wide landscapes of DNA methylomes for muscle studies. The analysis shows global similarity and difference among fetal and adult stage and identifies the differentially methylated regions. The differentially methylated regions in promoters are highly associated with muscle development via expression repression of both known muscle-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of muscle growth and development.
2014-11-20 | GSE46504 | GEO