Cornus florida - Transcriptome Assembly

Summary

Name	Cornus florida - Transcriptome Assembly
Resource Type	Transcriptome Assembly
Organism	C. Florida (Dogwood)
Ontology Browser	View Gene Ontology browser or KEGG Ontology browser for Cornus florida
Data Source	Source Name : de novo assembly
Date Performed	Monday, December 5, 2016 - 20:00
Number of transcripts	43158
Average Transcript Length	delete_me
Program, Pipeline, Workflow or Method Name	Newbler (Roche)
Program Version	Newbler (Roche) [30-Nov-2016]
Cross Reference	NCBI BioProject:360995

Description and Download

Description:

Assembly Statistics

Number of Transcripts	43,158
Transcript N50	1,206 bp
Transcript Average Length	1,086 bp
Number of Proteins	39,577
Protein N50	265 aa
Protein Average Length	231 aa

Download

Assembled sequence data:

	Putative Transcripts (fasta format) 454Isotigs.fna
	Predicted ORFs (fasta format) 454Isotigs.fna.transdecoder.pep

Functional Annotation

BLASTx analysis against Swiss-prot protein database with an e-value cut-off of 1e-5.

	File (tsv file) sprot_ntd.blastx.tab.best.ANNO

BLASTx analysis against Trembl protein database, only plant entries with an e-value cut-off of 1e-5.

	File (tsv file) trembl_ntd.blastx.tab.best.ANNO

InterProScan searches with GO term annotation:

	File (tsv file) 454Isotigs.hmmer.tsv

SSR Pipeline

	Excel file with statistics, SSR motifs and primers (? high quality markers) Dogwood_Isotigs.fna.ssr_report.xlsx
	Fasta file of transcripts with SSR motifs Dogwood_Isotigs.fna.ssr.fasta

Read Statistics

Two cultivars of C. florida were used for sequencing: ‘Appalachian Spring’ and ‘Cherokee Brave’. RNA was extracted from leaf, fully expanded bract, and flower tissue. RNA was combined and sequenced to yield 580Mbp of sequence data from 1,621,644 reads.