Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromosome-level assembly of A. arenosa using PacBio sequencing

ABSTRACT: Chromosome-level assembly of Arabidopsis arenosa from Strečno, Slovakia using PacBio sequencing

PROVIDER: PRJEB42625 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	AARE701A_fixed.embl.gz	Other
	chromosome.txt.gz	Txt
	ERR5170146_1.fastq.gz	Fastqsanger.gz
	ERR5170146_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Tetraploid Arabidopsis Arenosa contig assembly

Project description:Contig assembly for tetraploid A. arenosa (ssp arenosa) from south Sweden

| PRJEB42276 | ENA

Mnemiopsis leidyi chromosome-level genome assembly

Project description:Exploration of Immune repertoire in the chromosome-level genome of the ctenophore Mnemiopsis Leidyi

| PRJEB71361 | ENA

Chromosome-level genome of Ginkgo biloba

Project description:Chromosome-level genome of Ginkgo biloba

| PRJEB28734 | ENA

RNA-seq (Illumina and PacBio) of hESC

Project description:We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data. PacBio long reads and Illumina short reads were generated from the same hESC cell line H1. PacBio reads were error-corrected by Illumina reads to identify transcripts. rSeq is used to estimate gene/transcript abundance of the identified transcriptome.

2013-10-30 | E-GEOD-51861 | biostudies-arrayexpress

Haplotype resolved chromosome level assembly of Apricot.

Project description:Haplotype resolved chromosome level assembly of Apricot generated by application of gamete binning on single cell sequencing data of gametes.

| PRJEB37669 | ENA

Chromosome-level genome assembly of Acrossocheilus fasciatus using PacBio sequencing and Hi-C technology.

Project description:Acrossocheilus fasciatus (Cypriniformes, Cyprinidae) is emerged as a newly commercial stream fish in the south of China with high economic and ornamental value. In this study, a chromosome-level reference genome of A. fasciatus was assembled using PacBio, Illumina and Hi-C sequencing technologies. As a result, a high-quality genome was generated with a size of 879.52 Mb (accession number: JAVLVS000000000), scaffold N50 of 32.7 Mb, and contig N50 of 32.7 Mb. The largest and smallest scafford was 60.57 Mb and 16 kb, respectively. BUSCO analysis showed a completeness score of 98.3%. Meanwhile, the assembled sequences were anchored to 25 pseudo-chromosomes with an integration efficiency of 96.95%. Additionally, we found approximately 390.91 Mb of repetitive sequences that accounting for 44.45% of the assembled genome, and predicted 24,900 protein-coding genes. The available genome reported in the present study provided a crucial resource to further investigate the regulation mechanism of genetic diversity, sexual dimorphism and evolutionary histories.

| S-EPMC10838343 | biostudies-literature

Fasciola hepatica PacBio assembly

Project description:PacBio assembly of Fasciola hepatica

| PRJEB58756 | ENA

Chromosome-Level Genome Assembly of <i>Cerasus humilis</i> Using PacBio and Hi-C Technologies.

Project description: Not available

| S-EPMC7573120 | biostudies-literature

Chromosome-level genome assembly of Plagiognathops microlepis based on PacBio HiFi and Hi-C sequencing.

Project description:Plagiognathops microlepis is an economic freshwater fish in the subfamily Xenocyprinae of Cyprinidae. It is widely distributed in the freshwater ecosystem of China, with moderate economic value and broad development prospects. However, the lack of genomic resources has limited our understanding on the genetic basis, phylogenetic status and adaptive evolution strategies of this fish. Here, we assembled a chromosome-level reference genome of P. microlepis by integrating Pacbio HiFi long-reads, Illumina short-reads and Hi-C sequencing data. The size of this genome is 1004.34 Mb with a contig N50 of 38.80 Mb. Using Hi-C sequencing data, 99.59% of the assembled sequences were further anchored to 24 chromosomes. A total of 578.91 Mb repeat sequences and 28,337 protein-coding genes were predicted in the current genome, of which, 26,929 genes were functionally annotated. This genome provides valuable information for investigating the phylogeny and evolutionary history of cyprinid fishes, as well as the genetic basis of adaptive strategies and special traits in P. microlepis.

| S-EPMC11271555 | biostudies-literature

Chromosome-level genome assembly of Nibea coibor using PacBio HiFi reads and Hi-C technologies.

Project description:Nibea coibor belongs to Sciaenidae and is distributed in the South China Sea, East China Sea, India and the Philippines. In this study, we sequenced the DNA of a male Nibea coibor using PacBio long-read sequencing and generated chromatin interaction data. The genome size of Nibea coibor was estimated to be 611.85~633.88 Mb based on k-mer counts generated with Jellyfish. PacBio sequencing produced 29.26 Gb of HiFi reads, and Hifiasm was used to assemble a 627.60 Mb genome with a contig N50 of 10.66 Mb. We further found the canonical telomeric repeats "TTAGGG" to be present at the telomeres of all 24 chromosomes. The completeness of the assembly was estimated to be 98.9% and 97.8% using BUSCO and Merqury, respectively. Using the combination of ab initio prediction, protein homology and RNAseq annotation, we identified a total of 21,433 protein-coding genes. Phylogenetic analyses showed that Nibea coibor and Nibea albiflora are closely related. The results provide an important basis for research on the genetic breeding and genome evolution of Nibea coibor.

| S-EPMC9633807 | biostudies-literature

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