Analysis Namede novo Red Alder (Alnus rubra)
Transcriptome NameAlnus rubra 021816
MethodTrinity, built under bowtie-1.0.1 and samtools-0.1.19; CD-HIT-EST (trinityrnaseq_r20131110, cd-hit-v4.6.1-2012-08-27)
Source (021816)
Date performed2016-02-18
Number of Contigs29,113
OrganismsAlnus rubra

MiSeq reads from a single library were cleaned with Trimmomatic and assembled by Trinity. CD-hit with parameter -c 0.95 was used to collapse highly similar reads into a single sequence. Protein sequences were predicted using Trinity. Data has been uploaded to NCBI ( go to NCBI BioProject page).

Assembly Statistics

Number of Transcripts 29,113
Transcript N50 617 bp
Transcript Average Length 496 bp
Number of Proteins 14,657
Protein N50 209 aa
Protein Average Length 194 aa

Download assembled data:

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


BLAST against the Swiss-prot protein database:

Blastx, 1e-4 cutoff - 59% of transcripts matched a swiss-prot entry
Blastp, 1e-4 cutoff - 74% of proteins matched a swiss-prot entry

BLAST against the Trembl protein database, only plant entries:

Blastx, 1e-4 cutoff - 82% of transcripts matched a trembl entry
Blastp, 1e-4 cutoff - 94% of proteins matched a trembl entry

HMMER search against Pfam database

Excel output of all hits

SSR Pipeline

Excel file with statistics, SSR motifs and primers (239 high quality markers)

Read Statistics

RNA was isolated and sequenced from pooled leaf tissues.

Illumina MiSeq Data

Library Description Library Code Platform MiSeq Reads MiSeq Bases
Red Alder - pooled seedling leaf RNAs from ozone treatments (round 1, round 2) RA1 Illumina MiSeq 3,088,680 783,469,947