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Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis)

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Abstract

Japanese larch (Larix leptolepis) is an ecologically and economically important species mainly grown in northeastern China, Japan and Europe. However, erratic flowering and poor germplasm resources caused by high embryo abortion rates have hampered breeding of Larix species. Somatic embryogenesis (SE) is an effective tool for the production of L. leptolepis with desirable characteristics, such as expression of totipotency, preparation of synthetic seeds, and genetic transformation. However, public genomic resources for this species are limited. We sequenced 591,759 raw expressed sequence tags (ESTs) from a 454 sequencing cDNA library of L. leptolepis somatic embryos, resulting in 572,403 high-quality reads. These reads were assembled into 70,927 unique sequences (UniGenes), including 32,321 contigs and 38,606 singletons. After removal of low-quality sequences, 65,115 UniGenes were annotated using the UniProtKB program. Based on their sequence similarity with known proteins, the matched 30,372 sequences from 664 species were estimated to represent approximately 19,000 unique genes. Gene ontology analysis revealed 21,324 UniGenes assigned to 51 categories. By Kyoto Encyclopedia of Genes and Genomes mapping, 25,773 transcripts were associated with 160 biochemical pathways. Further analysis screened four signal transduction pathways represented by 337 enzymes and 17 secondary metabolites. In silico analysis reveals that 207 UniESTs in Larix are homologous to MAPKs genes identified from other model plants, which may be involved in regulating SE development. This study provides an initial insight into the Larix transcriptomes of the pro-embryogenic mass and is a sound basis for future studies.

Key message We constructed a large, full-length 454 sequencing cDNA library of Larix leptolepis during somatic embryogenesis. More than 590,000 sequences were obtained and a deep-coverage EST database was constructed.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (NSFC) (Grant Nos. 30830086) and the National Basic Research Program of China (973 Program: Grant Nos. 2009CB119100) and National High Technology Research and Development Program of China (Grant Nos. 2011AA100203). The authors thank Dr. Shuigen Li and Long Li for the primary collection of information and Mrs. Ting Li for the processing of data for the paper.

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  1. Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China

    Yuan Zhang, Shougong Zhang, Xinmin Li & Liwang Qi

  2. Key Laboratory of Research Institute of Forest Ecology and Protection, Chinese Academy of Forestry, Beijing, 100091, China

    Suying Han

  3. Department of Pathology and Laboratory Medicine, University of California at Los Angeles, 1000 Veteran Ave, Los Angeles, CA, 90095, USA

    Xinmin Li

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Zhang, Y., Zhang, S., Han, S. et al. Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis). Plant Cell Rep 31, 1637–1657 (2012). https://doi.org/10.1007/s00299-012-1277-1

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