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Open Access Highly Accessed Research article

De novo assembly and characterization of Camelina sativa transcriptome by paired-end sequencing

Chao Liang1, Xuan Liu2, Siu-Ming Yiu2 and Boon Leong Lim1*

Author Affiliations

1 School of Biological Sciences, the University of Hong Kong, Pokfulam, Hong Kong, China

2 Department of Computer Science, the University of Hong Kong, Pokfulam, Hong Kong, China

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BMC Genomics 2013, 14:146  doi:10.1186/1471-2164-14-146

Published: 5 March 2013

Additional files

Additional file 1:

Supplementary Figures for this study. Figure S1 Overview of assembly by SOAPdenovo. (a) Length frequency distribution of contigs obtained from de novo assembly of high-quality clean “reads”. (b) Length frequency distribution of gap ratios (N/size) in assembled scaffolds. (c) Frequency distribution of assembled scaffold lengths. (d) Length frequency distribution of unigenes produced by contig joining, gap filling, and scaffold clustering. (e) Gap frequency distribution of assembled unigenes. x-axis values are ratios of gap length to length of assembled unigenes. y-axis values are frequencies of unigenes containing gaps. (f) Random frequency distribution of Illumina sequencing reads in assembled unigenes. x-axis values are relative positions of sequencing reads in assembled unigenes. The orientation of unigenes is from the 5’ end to the 3’ end. Figure S2 Venn Diagrams of the three categories of GO. In total, 33,475 unigenes were assigned to at least one GO category. Figure S3 Venn diagram results from diverse databases. (a) Venn diagram showing the number of unigenes matched to sequences in NR, Swiss-Prot and KEGG databases. All annotations were based on best BLASTX hits with E-Values ≤ 1.0E-5. The overlapping regions represent the number of unigenes that matched in different databases. (b) Venn diagram showing the number of unigenes in NR, Swiss-Prot, KEGG and COG databases. All annotations were based on the best BLASTX hits with E-Values ≤ 1.0E-5. Figure S4Camelina sativa transcriptome coding sequence (CDS) predicted by BLASTX and ESTScan software. (a) Number of predicted CDS with gap ratio frequency distribution (N/size). (b) Length frequency distribution of predicted CDS. (c) Length frequency distribution of predicted protein sequences. (d) Gap ratio frequency distribution of CDS predicted by ESTScan software. (e) Length frequency distribution of CDS predicted by ESTScan software. (f) Length frequency distribution of protein sequences predicted by ESTScan software.

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Open Data

Additional file 2:

NR annotations of Camelina sativa with an E-value threshold of 1.0E-5.

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Additional file 3:

722 unigenes annotated to Brassica and 190 annotated to Brassica disease resistance protein coding genes.

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Additional file 4:

119 KEGG pathways with pathway ID and KO information.

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Open Data

Additional file 5:

Number of annotated unigenes involved in fatty acid synthesis in Camelina sativa.

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Open Data

Additional file 6:

Differences in 119 KEGG pathways between Camelina sativa and Arabidopsis thaliana.

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Open Data