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Transcriptome sequencing and comparative analysis of diploid and autotetraploid Paulownia australis

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Abstract

Paulownia is a fast-growing tree native to China. It can provide high-quality timber and a green environment for humans and has been planted in many countries. Compared with diploid Paulownia australis, autotetraploid P. australis exhibits predominance in terms of yields, qualities, growth, and resistance to stress. However, the molecular and biological mechanisms of its predominant characteristics are still unclear. We performed paired-end sequencing of the transcriptomes of diploid and autotetraploid P. australis plants using the Illumina/Solexa Genome Analyzer platform and compared changes in the expression of genes after chromosome doubling. We obtained a total of 48,445,468 and 46,437,758 high-quality reads from diploid P. australis (PA2) and autotetraploid P. australis (PA4), respectively. After assembly, 90,881 (PA2) and 88,566 (PA4) unigenes were obtained. The unigenes from both transcriptomes were then assembled into 93,300 all-unigenes, which included 50,892 clusters and 42,408 singletons. The all-unigene sequences were searched against public protein databases (Nr, Nt, Swiss-Prot, KOG, and KEGG) using BLASTX with a cutoff E-value of 10−5. Gene expression levels in the two libraries were compared, and a total of 8851 differentially expressed unigenes were identified. A large number of unigenes were found to be related to carbohydrate and energy metabolism, biosynthesis of cell wall, and stress tolerance. Many of the differentially expressed P. australis genes were attributable to chromosome doubling between the PA2 and PA4 plants. Functional analysis revealed variations in the mechanism of growth and stress resistance between PA2 and PA4.

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Abbreviations

GAIIx :

Genome Analyzer IIx

ABA:

Abscisic acid

Nr:

NCBI nonredundant protein sequence database

Nt:

NCBI nucleotide databases

COG:

Clusters of orthologous

GO:

Gene Ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

DEU:

Differentially expressed unigenes

qRT-PCR:

Quantitative real-time PCR

CDS:

Coding sequences

FPKM:

Fragments per kilobyte per million fragments

FDR:

false discovery rate

CAT:

Catalase

SOD:

Superoxide dismutases

MDAR:

Monodehydroascorbate reductase

DHAR:

Dehydroascorbate reductase

GPX:

Glutathione peroxidase

APX:

Ascorbate peroxidase

GR:

Glutathione transferase

PSI:

Photosystem I

Pn:

Net photosynthetic rate

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Acknowledgments

This work was financially supported by the National Natural Science Foundation of China (Grant No. 30271082, 30571496, U1204309), by the Outstanding Talents Project of Henan Province (Grant No. 122101110700), and by the Science and Technology Innovation Team Project of Zhengzhou City (Grant No. 121PCXTD515).

Conflict of interest

The authors declare no conflict of interest.

Data archiving statement

The raw sequence data are available at the NIH Short Read Archive database (http://www.ncbi.nlm.nih.gov/sra) under the accession number SRP032321 (Alias: PRJNA224949).

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Authors and Affiliations

  1. Institute of Paulownia, Henan Agricultural University, 450002, 95 Wenhua Road, Jinshui Area, Zhengzhou, Henan, People’s Republic of China

    Enkai Xu, Guoqiang Fan, Suyan Niu, Zhenli Zhao, Minjie Deng & Yanpeng Dong

  2. College of Forestry, Henan Agricultural University, 450002, 95 Wenhua Road, Jinshui Area, Zhengzhou, Henan, People’s Republic of China

    Enkai Xu, Guoqiang Fan, Suyan Niu, Zhenli Zhao, Minjie Deng & Yanpeng Dong

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  1. Enkai Xu
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Correspondence to Guoqiang Fan.

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Communicated by D. B. Neale

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Xu, E., Fan, G., Niu, S. et al. Transcriptome sequencing and comparative analysis of diploid and autotetraploid Paulownia australis . Tree Genetics & Genomes 11, 5 (2015). https://doi.org/10.1007/s11295-014-0828-8

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