Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

1500 wild and cultivated soybean genomes

ABSTRACT: 1500 wild and cultivated soybean genomes were sequenced to identify 32 Mil. SNPs. The collection is composed of wild, landraces and elite cultivars of soybean that were grown in East Asia or major soybean cultivating areas around the world. comprehensive analysis of publicly available large-scale genome sequencing data of diverse cultivated accessions and the newly in-house sequenced wild accessions greatly increased the soybean genome-wide variation resolution. This could facilitate a variety of genetic and molecular-level analyses in soybean.

INSTRUMENT(S): -

ORGANISM(S): Glycine Max

SUBMITTER: Donald Danforth Center, St. Louis, MO.

PROVIDER: PRJEB77193 | EVA | 2024-07-07

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SNPdata_01.accessioned.vcf.gz	Vcf
	SNPdata_01.accessioned.vcf.gz.csi	Vcf
	SNPdata_01.vcf.csi	Other
	SNPdata_01.vcf.gz	Vcf

Items per page:

1 - 4 of 4

Similar Datasets

Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans

Project description:Cultivated soybean has domesticated in China for a long history, and there are several significant phenotypic differences between wild and cultivated soybeans. Seed of cultivar is generally larger than wild soybean, therefore here we comprehensively analyzed transcriptomes of thirteen soybean accessions seeds including seven wild soybeans and six landraces through applying strand-specific RNA sequencing. Differential expressed genes related seed weight were identified, some of them were known to be associated with seed development in Arabidopsis. Noncoding RNAs are known to play important roles in plant development, and we profiled the expression pattern of long noncoding RNA (lncRNA) in cultivated and wild soybean seeds. We have identified 1,251 long intergenic noncoding RNA, 243 intronic RNA and 81 antisense lncRNA, transcriptional levels of a number of lncRNAs were significantly different between cultivated and wild soybeans, suggesting that lncRNA may be involved in soybean seed development.

2017-06-13 | GSE94366 | GEO

Genomewide copy number profiles for breast cancer from Taiwanese women

Project description:The incidence of breast cancer has been rapidly increasing in East Asia. This is the first study of genome wide copy number of breast cancer in East Asia. We conducted this study to compare the genetic alterations between East and West.

2021-05-05 | GSE80526 | GEO

RNA-Seq Study Reveals Genetic Responses of Diverse Wild Soybean Accessions to Increased Ozone Levels

Project description:Analysis of gene expression data from four genetically diverse wild soybean accessions helps reveal both sensitive and resistant responses of the plants to increased ozone levels. Results help characterize genetic response of wild soybean to ozone stress and could help provide information on genetic resources for creating ozone-tolerant soybean breeding lines.

2017-07-21 | GSE85146 | GEO

Global analysis of the transcriptional difference between indigenous and invasive whiteflies reveals the possible mechanism of whitefly invasion

Project description:The whitefly Bemisa tabaci is a species complex of more than 31 cryptic species which include some of the most destructive invasive pests of many ornamental and glasshouse crops worldwide. Among them, Middle East-Asia Minor 1 (herein MEAM1) and Mediterranean (herein MED) have invaded many countries around the world and displaced the native whitefly species. However, the molecular differences between invasive and indigenous whiteflies remain largely unknown. The global transcriptional difference between the two invasive whitefly Bemisia tabaci species (MEAM1, MED) and one indigenous whitefly species (Asia II 3) were analyzed using the Illumina sequencing technology.

2013-11-24 | E-GEOD-41864 | biostudies-arrayexpress

Genome-wide Investigation of Population Structure in Myanmar

Project description:Myanmar locates in the crossroads of South Asia, Southeast Asia, and East Asia, and is known for high culture diversity in different ethnic groups. It is considered to be important for understanding human evolutionary history and genetic diversity in East Eurasia. However, relatively few studies have examined the population structure and demographic history in Myanmar to date. In this study, we analyzed more than 220,000 genome-wide SNPs in 175 new samples of five ethnic groups from Myanmar and compared them with the published data. Our results showed that the Myanmar population is intricately substructured, with the main observed clusters corresponding roughly to western/northern highlanders (Chin, Naga, and Jingpo) and central/southern lowlanders (Bamar and Rakhine). The gene flow inferred from South Asia has a substantial influence (~11%) on the gene pool of central/southern lowlanders rather than western/northern highlanders. The genetic admixture is dated around 650 years ago. These findings suggest that the genome-wide variation in Myanmar was likely shaped by the linguistic, cultural, and historical changes.

2019-12-31 | GSE74100 | GEO

Comparison of mid-log transcriptomes of clinical isolates of Mycobacterium tuberculosis

Project description:The global diversity of Mycobacterium tuberculosis comprises at least seven lineages, each with its distinct geographic distribution. The aim of this experiment was to perform a comparative analysis of two of these lineages: Lineage 1 and Lineage 2. The former is found around the rim of the Indian ocean and in south-east Asia, while the latter is widely spread throughout Asia and shows an increasing global spread. We have chosen three fully drug susceptible clincal isolates to represent each of the two lineages. We performed RNAseq analysis on rRNA depleted samples isolated from cultures during mid-log phase. Each strain was measured in triplicate.

2020-12-31 | E-MTAB-8103 | biostudies-arrayexpress

Global analysis of the transcriptional difference between indigenous and invasive whiteflies reveals the possible mechanism of whitefly invasion

2013-11-24 | GSE41864 | GEO

Development of Hypsizygus marmoreus

Project description:Hypsizygus marmoreus is one of the most popular industrialized cultivation mushrooms in East Asia, including China, Korea and Japan. It draws our attention due to its desirable, mildly sweet nutty flavor, unique texture and medicinal properties. As a result, the number of H. marmoreus cultivation factories increased gradually in different regions of the world, especially in China. H. marmoreus is the third wildly cultivated industrialized cultivated mushroom in China now. However, its development process is still not very clear. In this study, we use proteomics analysis to investigate the mechanism involved in development of Hypsizygus marmoreus.

2021-11-02 | PXD028353 | Pride

Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean

Project description:We report total mRNA library using Illumina Nova Seq high-throughput sequencing platform platform for analysis of transcriptome between the two relatives of the soybean ie weedy and cultivar growth types in F7 generation derived from the crossing of wild and cultivated soybean.

2021-11-12 | GSE188519 | GEO

First Comprehensive Proteome Analyses of Lysine Succinylation in Physalis angulata, a medicinal plant with a high pharmaceutical value

Project description:Physalis angulata is a medicinal plant with a high pharmaceutical value that is widely cultivated in East Asia. Lysine succinylation, a newly identified post-translational modification, is associated with various cellular processes. However, the regulatory mechanism underlying the metabolism of P. angulata is largely unknown. Here, liquid chromatography tandem-mass spectrometry combined with a high-efficiency succinyl-lysine antibody was used to identify the succinylated peptides in P. angulata. In total, 422 lysine succinylation sites in 242 proteins were identified.

2019-11-08 | PXD006778 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data