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Open AccessArticle

De Novo Transcriptome Sequencing Analysis of cDNA Library and Large-Scale Unigene Assembly in Japanese Red Pine (Pinus densiflora)

Asian Natural Environmental Science Center, The University of Tokyo, Midori-cho 1-1-8, Nishi Tokyo, Tokyo 188-0002, Japan
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Author to whom correspondence should be addressed.
Academic Editor: Jianhua Zhu
Int. J. Mol. Sci. 2015, 16(12), 29047-29059; https://doi.org/10.3390/ijms161226139
Received: 29 September 2015 / Revised: 13 November 2015 / Accepted: 26 November 2015 / Published: 4 December 2015
(This article belongs to the Special Issue Plant Molecular Biology)
Japanese red pine (Pinus densiflora) is extensively cultivated in Japan, Korea, China, and Russia and is harvested for timber, pulpwood, garden, and paper markets. However, genetic information and molecular markers were very scarce for this species. In this study, over 51 million sequencing clean reads from P. densiflora mRNA were produced using Illumina paired-end sequencing technology. It yielded 83,913 unigenes with a mean length of 751 bp, of which 54,530 (64.98%) unigenes showed similarity to sequences in the NCBI database. Among which the best matches in the NCBI Nr database were Picea sitchensis (41.60%), Amborella trichopoda (9.83%), and Pinus taeda (4.15%). A total of 1953 putative microsatellites were identified in 1784 unigenes using MISA (MicroSAtellite) software, of which the tri-nucleotide repeats were most abundant (50.18%) and 629 EST-SSR (expressed sequence tag- simple sequence repeats) primer pairs were successfully designed. Among 20 EST-SSR primer pairs randomly chosen, 17 markers yielded amplification products of the expected size in P. densiflora. Our results will provide a valuable resource for gene-function analysis, germplasm identification, molecular marker-assisted breeding and resistance-related gene(s) mapping for pine for P. densiflora. View Full-Text
Keywords: Pinus densiflora; transcriptome sequencing; unigene assembly; simple sequence repeats; EST-SSR marker discovery Pinus densiflora; transcriptome sequencing; unigene assembly; simple sequence repeats; EST-SSR marker discovery
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Liu, L.; Zhang, S.; Lian, C. De Novo Transcriptome Sequencing Analysis of cDNA Library and Large-Scale Unigene Assembly in Japanese Red Pine (Pinus densiflora). Int. J. Mol. Sci. 2015, 16, 29047-29059.

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