Research article
A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa
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* Corresponding author: Jorge M Vivanco j.vivanco@colostate.edu
1 Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523-1173, USA
2 Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523-1173, USA
3 Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523-1173, USA
4 Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
BMC Plant Biology 2007, 7:25 doi:10.1186/1471-2229-7-25
Published: 24 May 2007Additional files
Additional file 1:
Distribution of assembled Centaurea ESTs by cluster size. The data represent clustering of Centaurea ESTs into unique sequence clusters (unigenes) and show distribution by cluster size. The 4969 Centaurea ESTs were assembled into 4423 unique contigs or 'unigenes' using the PLAN database (Noble foundation). In total, 4075 singlet ESTs were unique (not pictured on graph); 348 could be assembled into clusters containing one or more Centaurea unigene, and were plotted relative to their abundance in the EST library.
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Additional file 2:
Title: Distribution of Centaurea unigenes by sequence length. The data represent distribution of Centaurea unigenes by sequence length. The 4423 Centaurea unigenes were plotted by their relative abundance based on sequence length in base pairs.
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Additional file 3:
Taxonomic clades associated with Centaurea unigene top BLAST hits. The data represent taxonomic clades associated with the top similarities of known sequences to Centaurea unigenes. Centaurea unigenes were used to query BLASTX nr database, and the top hit for each unigene was deposited in the PLAN database (3392 unigenes had significant top BLAST hits, others were unable to be annotated). These top hits were assembled by taxonomic group. Approximately 35% of the unigenes had top hits to Arabidopsis, which is part of the Rosid clade.
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Additional file 4:
Evolution/Plasticity-related sequences in Centaurea cDNA library. The table lists sequences identified in the Centaurea cDNA library that may be related to evolution and plasticity, based on similarity to known sequences. Evolution-plasticity related sequences from the Centaurea cDNA library are represented by Centaurea unigene identification number (from the PLAN database). Accession number, organism, functional description, and E value of the top BLAST hit for each unigene is listed.
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Additional file 5:
Alignment of Centaurea unigene (CENT_UG_03500) and related sequences. The data represent predicted amino acid sequence alignment of Centaurea unigene 03500 with related sequences involved in sesquiterpene lactone synthesis. Sesquiterpene lactone synthesis proteins from Artemisia obtusifolia and A. annua were aligned with Centaurea unigene 03500 using (Clustal W). Stars (*) indicate complete sequence conservation;(:) represents amino acids of a similar nature.
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Additional file 6:
Flavanoid Pathway- related sequences in Centaurea cDNA library. The table lists sequences identified in the Centaurea cDNA library that may be involved in the flavanoid pathway, based on similarity to known sequences. Proposed function (Func) of flavanoid pathway related sequences in the Centaurea cDNA library; PAL (phenylalanine ammonia lyase), C4H(cinnamate 4-hydroxylase), C4L (4-coumaryl-CoA ligase), CHS (chalcone synthase), CHI (chalcone isomerase), F3'H (flavanoid 3'-hydroxylase), GT (glycosyl transferase), OMT (O-methyltransferase). The number of unigenes and their identification numbers (PLAN database) are listed for each functional group.
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Additional file 7:
Defense-response-related sequences in Centuarea cDNA library. The table lists sequences identified in the Centaurea cDNA library that may be involved in defense response, based on similarity to known sequences. Defense-response-related sequences from the Centaurea cDNA library are represented by Centaurea unigene identification number (PLAN database). Accession number, organism, functional description, and E value of the top BLAST hit for each unigene is listed.
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