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

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.

DOI: 10.1007/s13562-016-0375-5

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Cite this paper

@article{Li2016TranscriptomePA, title={Transcriptome profiling and characterization of gene families with zinc finger and nucleotide binding site (NBS) domains in Larix kaempferi}, author={Ai Min Li and Jing Wang and Hui Li and Chengbin Chen and Wenqin Song and Chunguo Wang}, journal={Journal of Plant Biochemistry and Biotechnology}, year={2016}, volume={26}, pages={149-159} }