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Transcriptome profiling and characterization of gene families with zinc finger and nucleotide binding site (NBS) domains in Larix kaempferi

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Abstract

Larix kaempferi is widely cultivated because of its significant ecological and economic values. However, the molecular mechanism underlying the growth and development of Larix kaempferi remains largely unknown because of its long growth cycle and highly complex genetic background. In this study, global transcriptome sequencing of Larix kaempferi was conducted via Solexa sequencing. In total, 15.49 million clean reads were assembled into 20,395 unigenes and then annotated. The study found hundreds of highly expressed unigenes involved in growth and development (e.g. plant hormone regulation pathways or starch and sucrose metabolic pathways), of which 25 unigenes with full-length coding regions interested us the most. In addition, two gene families containing the zinc finger and nucleotide-binding site (NBS) domains were further explored. A total of 48 C3H-type zinc finger genes, most containing a conversed C-X7–10-C-X5-C-X3-H motif, were identified and divided into eight distinct subfamilies through phylogenetic analysis. Twenty-one genes containing the NBS domain represented four subfamilies. These findings provided new insights into the transcriptome characteristics of Larix kaempferi and abundant sequence information to elucidate the roles of the functional genes in Larix kaempferi.

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Acknowledgments

We thank Dr. Liwang Qi at the Chinese Academy of Forestry, Beijing, China for kindly providing the Larix kaempferi parental lines (Larix13 and Larix82) and their reciprocal hybrids (Larix13 × Larix82-21 and Larix82 × Larix13-6). This work was performed with financial support from the National Natural Science Foundation of China (Nos. 31100234, 31300564 and 31371249) and the Natural Science Foundation of Tianjin (Nos. 14JCQNJC15000, 13JCZDJC29000 and 15JCQNJC15100).

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Authors and Affiliations

  1. College of Life Sciences, Nankai University, Tianjin, 300071, China

    Jing Wang, Chengbin Chen, Wenqin Song & Chunguo Wang

  2. Department of Horticulture, Tianjin Agricultural University, Tianjin, 300384, China

    Ai Li & Hui Li

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  1. Ai Li
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  2. Jing Wang
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  4. Chengbin Chen
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Correspondence to Wenqin Song or Chunguo Wang.

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Li, A., Wang, J., Li, H. et al. Transcriptome profiling and characterization of gene families with zinc finger and nucleotide binding site (NBS) domains in Larix kaempferi . J. Plant Biochem. Biotechnol. 26, 149–159 (2017). https://doi.org/10.1007/s13562-016-0375-5

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