Overview
Analysis Namede novo Dogwood (Cornus florida)
Transcriptome NameCornus_florida_12062016
MethodNewbler (Roche) (Newbler (Roche) [30-Nov-2016])
Sourcede novo assembly
Date performed2016-12-06
Number of Reads454
Number of Contigs43,158
OrganismsCornus florida
A single custom, normalized library for Roche/454 sequencing was prepared and sequenced for bract (‘Cherokee Brave’) and leaf (‘Appalachian Spring’ and ‘Cherokee Brave’) pooled RNA at Indiana University’s Center for Genomics and Bioinformatics. The 454 sequence reads were assembled into isotigs using Newbler software.

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

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Assembled sequence data:

Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Functional Annotation

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

File (tsv file)

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

File (tsv file)

InterProScan searches with GO term annotation:

File (tsv file)

SSR Pipeline

Excel file with statistics, SSR motifs and primers (? high quality markers)
Fasta file of transcripts with SSR motifs

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.

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