Summary
Name
Gleditsia triacanthos - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Gleditsia triacanthos
Data Source
Source Name
: de novo assembly
Source Version
: 082614
Date Performed
Monday, August 25, 2014 - 21:00
Number of transcripts
56845
Average Transcript Length
731
Program, Pipeline, Workflow or Method Name
Trinity; CD-HIT-EST
Program Version
cd-hit-v4.6.1-2012-08-27
Cross Reference
Description and Download
Description: 
MiSeq reads from multiple libraries 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 Transcripts56,845
Transcript N501,082 bp
Transcript Average Length731 bp
Number of Proteins30,372
Protein N50312 aa
Protein Average Length256 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-5 cutoff - 54% of transcripts matched a swiss-prot entry
Blastp, 1e-5 cutoff - 73% of proteins matched a swiss-prot entry
BLAST against the Trembl protein database, only plant entries:
Blastx, 1e-4 cutoff - 79% of transcripts matched a trembl entry
Blastp, 1e-5 cutoff - 95% of proteins matched a trembl entry
SSR Pipeline
Excel file with statistics, SSR motifs and primers (327 high quality markers)

Read Statistics

RNA was isolated and sequenced from a root tissues. Abiotic stress assays (heat, cold, drought) were conducted on seedlings. Over 7 million reads (1.9Gb) of sequence were acquired. Raw data has been uploaded to the NCBI Short Read Archive. An additional 4 MiSeq libraries (HLC0, HL80, HL125, HL225) were not used in the assembly but were used in expression analysis. Links are included below.

Illumina MiSeq Data

Library DescriptionLibrary CodePlatformMiSeq ReadsMiSeq Bases
Honey Locust Root - controlHR-R-ContrIllumina MiSeq1,397,340380,006,867
Honey Locust Root - heatHL-HRIllumina MiSeq1,681,462455,039,059
Honey Locust Root - droughtHL-DRIllumina MiSeq1,334,839369,465,662
Honey Locust Root - cold, 24 hrHL-CR-24Illumina MiSeq1,344,414364,375,010
Honey Locust Root - cold, 0 hrHL-CL-0Illumina MiSeq1,302,128355,836,453
TOTAL7,060,1831,924,723,051
The following libraries were not used in the assembly but were used for expression analysis.
Library DescriptionLibrary CodePlatformMiSeq ReadsMiSeq Bases
Honeylocust -pooled seedling RNAs, control (round 1, round 2)HLC0Illumina MiSeq36869471004816629
Honeylocust -pooled seedling RNAs, 80 ppb ozone (round 1, round 2)HL80Illumina MiSeq2979316684835612
Honeylocust -pooled seedling RNAs, 125 ppb ozone (round 1, round 2)HL125Illumina MiSeq3341566868630840
Honeylocust -pooled seedling RNAs, 225 ppb ozone (round 1, round 2)HL225Illumina MiSeq3396754808971594
TOTAL134045833367254675
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