Overview
Analysis Namede novo American Chestnut (Castanea dentata) - AC454_v3
Transcriptome NameCastanea dentata 081508
MethodSeqManPro (8.0. 2)
Source (081508)
Date performed2008-08-15
Number of Contigs45,288
OrganismsCastanea dentata
An assembly of 398,783 American Chestnut 454 sequences by the SeqManPro assembly software.

This transcriptome assembly was originally hosted on the Fagaceae Genomics Web (FGW), which has now been archived.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 Name AC454 Unigene V3
Date 2008-08-15
Software SeqManPro
Number of Contigs 45,288
Libraries Included in Assembly 5 ( ACCanker, ACHS1n, ACHS2n, ACWP1, ACWP2)

Assembly Statistics

Number of Transcripts 45,288
Transcript N50 470 bp
Transcript Average Length 449 bp
Number of Proteins 18,981
Protein N50 173 aa
Protein Average Length 174 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 Description Library Code Platform 454 Reads 454 Bases
American Chestnut blight canker tissue ACCanker 454 GS FLX 129,508 14.6M
American Chestnut healthy stem 1 ACHS1n 454 GS FLX 222,939 66.6M
American Chestnut healthy stem 2 ACHS2n 454 GS FLX 254,810 126.4M
American Chestnut whole plant tissues 1 ACWP1 454 GS FLX 47,653 12.6M
American Chestnut whole plant tissues 2 ACWP2 454 GS FLX 33,288 8.5M