Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

De novo assembly and characterization of the Hucho taimen transcriptome

ABSTRACT: De novo assembly and characterization of the Hucho taimen transcriptome

PROVIDER: PRJEB19675 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1857180_1.fastq.gz	Fastqsanger.gz
	ERR1857180_2.fastq.gz	Fastqsanger.gz
	ERR1857179_1.fastq.gz	Fastqsanger.gz
	ERR1857179_2.fastq.gz	Fastqsanger.gz
	ERR2029723.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 7

Similar Datasets

Hucho taimen

Project description:Hucho taimen overview

| PRJNA78737 | ENA

Hucho taimen

Project description:Hucho taimen Genome sequencing

| PRJNA545580 | ENA

Hucho taimen

Project description:Hucho taimen Raw sequence reads

| PRJNA549105 | ENA

Hucho hucho

Project description:Hucho hucho overview

| PRJNA475170 | ENA

De novo assembly of siRNA immunity in wild plants

Project description:We describe an application of deep sequencing and de novo assembly of short RNA reads to investigate small interfering (si)RNAs mediated immunity in leaf samples from eight tree taxa naturally occurring in Wytham Woods, Oxfordshire, UK. BLAST search for homologues of contigs in the GenBank identified siRNA populations against a number of RNA viruses and a Ty1-copia retrotransposons in these tree species. Small RNA sequencing and de novo assembly

2012-06-01 | E-GEOD-22079 | biostudies-arrayexpress

<i>De novo</i> assembly and characterization of the <i>Hucho taimen</i> transcriptome.

Project description:Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA-Seq is a useful tool for obtaining genetic information and developing genetic markers for nonmodel species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA-Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high-quality transcriptome with a N50 size of 1,060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein-coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including eight salmonids and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: It possesses more immune-related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids, and selective breeding for threatened taimen.

| S-EPMC5773338 | biostudies-literature

Aspergillus fumigatus de novo genome assembly

Project description:Aspergillus fumigatus de novo genome assembly

| PRJEB59410 | ENA

De novo assembly of macaque gene models

Project description:We reported an atlas of de novo-defined, full-length macaque gene models on the basis of single molecule long-read transcriptome sequencing (Iso-seq).

2021-04-17 | GSE158668 | GEO

Hucho hucho

Project description:Hucho Hucho raw RNA sequence reads

| PRJNA480959 | ENA

Calcareous Sponge Sycon Ciliatum De-Novo Transcriptome Assembly

Project description:S.ciliatum de-novo transcriptome assembly

| PRJEB49276 | ENA