Open Access Research article

De novo characterization of the Chinese fir (Cunninghamia lanceolata) transcriptome and analysis of candidate genes involved in cellulose and lignin biosynthesis

Hua-Hong Huang12, Li-Li Xu2, Zai-Kang Tong2, Er-Pei Lin2*, Qing-Po Liu3, Long-Jun Cheng2 and Mu-Yuan Zhu1*

Author Affiliations

1 State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang, P.R. China

2 Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, Zhejiang, 311300, P.R. China

3 School of Agricultural and Food Science, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, Zhejiang, 311300, P.R. China

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BMC Genomics 2012, 13:648  doi:10.1186/1471-2164-13-648

Published: 21 November 2012

Additional files

Additional file 1:

Gap distribution of assembled scaffolds and Unigenes. (N/size)% is a measure of the gap percentage (N amount/sequence length) distribution where N represents ambiguous bases in the reads.

Format: JPEG Size: 1.4MB Download file

Open Data

Additional file 2:

Quality characteristics of the assembled Unigenes from Chinese fir. (a) Distribution of the high-quality reads used in the assembly on the assembled Unigenes. (b) Distribution of the Illumina sequencing reads in all the assembled Unigenes. The x-axis indicates the relative position of sequencing reads in the assembled Unigenes. The orientation of Unigene is from the 5’ to 3’ end.

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Open Data

Additional file 3:

Top BLAST hits from the NCBI NR database. BLAST results against the NCBI NR database for all the assembled Unigenes with an E-value threshold of 1e-5.

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Additional file 4:

Effects of query sequence length on percentage of significant matches.

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Additional file 5:

List of the most abundant Unigenes in the transcriptome sequencing data. All C. lanceolata Unigenes with RPKM values >500 are included in the list.

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Additional file 6:

List of annotated Unigenes that match genes involved in the cellulose biosynthesis pathway. C. lanceolata Unigenes involved in cellulose biosynthesis are listed.

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Additional file 7:

List of annotated Unigenes that match genes involved in the lignin biosynthesis pathway. C. lanceolata Unigenes involved in lignin biosynthesis are listed.

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Additional file 8:

List of Unigenes that cover 18 selected genes respectively. C. lanceolata Unigenes that cover 18 selected genes involved in cellulose and lignin biosynthesis respectively are listed.

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Additional file 9:

A schematic drawing that illustrates assembly process of Unigene.

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Additional file 10:

Primer sequences for the 18 selected genes involved in cellulose and lignin biosynthesis. Specific primers of eighteen genes involved in cellulose and lignin biosynthesis designed for RACE, full-length RT-PCR and real time qRT-PCR using the Oligo software (version 6.0) are shown.

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