Summary
Name
[Archived] Castanea dentata - Transcriptome Assembly AC454_v3
Resource Type
Transcriptome Assembly
Organism
Data Source
Source Name
: de novo assembly
Source Version
: 081508
Date Performed
Thursday, August 14, 2008 - 21:00
Number of transcripts
45288
Average Transcript Length
449
Program, Pipeline, Workflow or Method Name
SeqManPro
Program Version
8.0. 2
Description and Download
Description: 
This transcriptome assembly was originally hosted on the Fagaceae Genomics Web (FGW), which has now been archived. Sequence information is maintained here in downloadable format only. Publications: Barakat A, Staton M, Cheng CH, Park J, Yassin NB, Ficklin S, Yeh CC, Hebard F, Baier K, Powell W, Schuster SC. Chestnut resistance to the blight disease: insights from transcriptome analysis. BMC Plant Biology. 2012 Mar 19;12(1):1. Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell WA, Wheeler N, Sederoff R, Carlson JE. Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biology. 2009 May 9;9(1):1. Transcriptome Information
FGW NameAC454 Unigene V3
Date2008-08-15
SoftwareSeqManPro
Number of Contigs 45,288
Libraries Included in Assembly5 ( ACCanker, ACHS1n, ACHS2n, ACWP1, ACWP2)

Assembly Statistics

Number of Transcripts45,288
Transcript N50470 bp
Transcript Average Length449 bp
Number of Proteins18,981
Protein N50173 aa
Protein Average Length174 aa
Download assembled data:
Contigs (fasta format)
Predicted ORFs (fasta format)
Ace file

Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-4 cutoff - 50% of transcripts matched a swiss-prot entry
Blastp, 1e-4 cutoff - 72% of proteins matched a swiss-prot entry
BLAST against the Trembl protein database, only plant entries:
Blastx, 1e-4 cutoff - 72% of transcripts matched a Trembl plant entry
Blastp, 1e-4 cutoff - 94% of proteins matched a Trembl plant entry
SSR Pipeline
Excel file with statistics, SSR motifs and primers

Read Statistics

Raw data may be downloaded from NCBI SRA, linked below.

454 Data

Library DescriptionLibrary CodePlatform454 Reads454 Bases
American Chestnut blight canker tissueACCanker454 GS FLX129,50814.6M
American Chestnut healthy stem 1ACHS1n454 GS FLX222,93966.6M
American Chestnut healthy stem 2ACHS2n454 GS FLX254,810126.4M
American Chestnut whole plant tissues 1ACWP1454 GS FLX47,65312.6M
American Chestnut whole plant tissues 2ACWP2454 GS FLX33,2888.5M
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