Overview
Analysis Namede novo Honey Locust (Gleditsia triacanthos)
Transcriptome NameGleditsia triacanthos 082614
MethodTrinity; CD-HIT-EST (cd-hit-v4.6.1-2012-08-27)
Source (082614)
Date performed2014-08-26
Number of Contigs56,845
OrganismsGleditsia triacanthos

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 Transcripts 56,845
Transcript N50 1,082 bp
Transcript Average Length 731 bp
Number of Proteins 30,372
Protein N50 312 aa
Protein Average Length 256 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 Description Library Code Platform MiSeq Reads MiSeq Bases
Honey Locust Root - control HR-R-Contr Illumina MiSeq 1,397,340 380,006,867
Honey Locust Root - heat HL-HR Illumina MiSeq 1,681,462 455,039,059
Honey Locust Root - drought HL-DR Illumina MiSeq 1,334,839 369,465,662
Honey Locust Root - cold, 24 hr HL-CR-24 Illumina MiSeq 1,344,414 364,375,010
Honey Locust Root - cold, 0 hr HL-CL-0 Illumina MiSeq 1,302,128 355,836,453
TOTAL 7,060,183 1,924,723,051

The following libraries were not used in the assembly but were used for expression analysis.

Library Description Library Code Platform MiSeq Reads MiSeq Bases
Honeylocust -pooled seedling RNAs, control (round 1, round 2) HLC0 Illumina MiSeq 3686947 1004816629
Honeylocust -pooled seedling RNAs, 80 ppb ozone (round 1, round 2) HL80 Illumina MiSeq 2979316 684835612
Honeylocust -pooled seedling RNAs, 125 ppb ozone (round 1, round 2) HL125 Illumina MiSeq 3341566 868630840
Honeylocust -pooled seedling RNAs, 225 ppb ozone (round 1, round 2) HL225 Illumina MiSeq 3396754 808971594
TOTAL 13404583 3367254675
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