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Int. J. Mol. Sci. 2014, 15(3), 5079-5093; doi:10.3390/ijms15035079
Article

Differential Transcriptome Analysis between Paulownia fortunei and Its Synthesized Autopolyploid

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Received: 13 December 2013; in revised form: 17 February 2014 / Accepted: 18 February 2014 / Published: 21 March 2014
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Abstract: Paulownia fortunei is an ecologically and economically important tree species that is widely used as timber and chemical pulp. Its autotetraploid, which carries a number of valuable traits, was successfully induced with colchicine. To identify differences in gene expression between P. fortunei and its synthesized autotetraploid, we performed transcriptome sequencing using an Illumina Genome Analyzer IIx (GAIIx). About 94.8 million reads were generated and assembled into 383,056 transcripts, including 18,984 transcripts with a complete open reading frame. A conducted Basic Local Alignment Search Tool (BLAST) search indicated that 16,004 complete transcripts had significant hits in the National Center for Biotechnology Information (NCBI) non-redundant database. The complete transcripts were given functional assignments using three public protein databases. One thousand one hundred fifty eight differentially expressed complete transcripts were screened through a digital abundance analysis, including transcripts involved in energy metabolism and epigenetic regulation. Finally, the expression levels of several transcripts were confirmed by quantitative real-time PCR. Our results suggested that polyploidization caused epigenetic-related changes, which subsequently resulted in gene expression variation between diploid and autotetraploid P. fortunei. This might be the main mechanism affected by the polyploidization. Our results represent an extensive survey of the P. fortunei transcriptome and will facilitate subsequent functional genomics research in P. fortunei. Moreover, the gene expression profiles of P. fortunei and its autopolyploid will provide a valuable resource for the study of polyploidization.
Keywords: Paulownia fortunei; transcriptome; polyploidy; de novo assembly; next-generation sequencing Paulownia fortunei; transcriptome; polyploidy; de novo assembly; next-generation sequencing
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Zhang, X.; Deng, M.; Fan, G. Differential Transcriptome Analysis between Paulownia fortunei and Its Synthesized Autopolyploid. Int. J. Mol. Sci. 2014, 15, 5079-5093.

AMA Style

Zhang X, Deng M, Fan G. Differential Transcriptome Analysis between Paulownia fortunei and Its Synthesized Autopolyploid. International Journal of Molecular Sciences. 2014; 15(3):5079-5093.

Chicago/Turabian Style

Zhang, Xiaoshen; Deng, Minjie; Fan, Guoqiang. 2014. "Differential Transcriptome Analysis between Paulownia fortunei and Its Synthesized Autopolyploid." Int. J. Mol. Sci. 15, no. 3: 5079-5093.



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