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De novo transcriptome sequencing of Acer palmatum and comprehensive analysis of differentially expressed genes under salt stress in two contrasting genotypes

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Abstract

Maple (Acer palmatum) is an important species for landscape planting worldwide. Salt stress affects the normal growth of the Maple leaf directly, leading to loss of esthetic value. However, the limited availability of Maple genomic information has hindered research on the mechanisms underlying this tolerance. In this study, we performed comprehensive analyses of the salt tolerance in two genotypes of Maple using RNA-seq. Approximately 146.4 million paired-end reads, representing 181,769 unigenes, were obtained. The N50 length of the unigenes was 738 bp, and their total length over 102.66 Mb. 14,090 simple sequence repeats and over 500,000 single nucleotide polymorphisms were identified, which represent useful resources for marker development. Importantly, 181,769 genes were detected in at least one library, and 303 differentially expressed genes (DEGs) were identified between salt-sensitive and salt-tolerant genotypes. Among these DEGs, 125 were upregulated and 178 were downregulated genes. Two MYB-related proteins and one LEA protein were detected among the first 10 most downregulated genes. Moreover, a methyltransferase-related gene was detected among the first 10 most upregulated genes. The three most significantly enriched pathways were plant hormone signal transduction, arginine and proline metabolism, and photosynthesis. The transcriptome analysis provided a rich genetic resource for gene discovery related to salt tolerance in Maple, and in closely related species. The data will serve as an important public information platform to further our understanding of the molecular mechanisms involved in salt tolerance in Maple.

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Acknowledgments

This study was funded by the National Natural Science Foundation of China (31300584), and the Jiangsu Agricultural Science and Technology Innovation Project [cx (14)5077]. We also thank Genepioneer Biotechnologies for their help with the bioinformatics analyses.

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  1. Institute of Horticulture, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China

    Liping Rong, Qianzhong Li, Shushun Li, Ling Tang & Jing Wen

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  1. Liping Rong
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  2. Qianzhong Li
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  4. Ling Tang
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Correspondence to Qianzhong Li.

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This study was funded by the National Natural Science Foundation of China (31300584), and the Jiangsu Agricultural Science and Technology Innovation Project [cx (14)5077].

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All the authors declare no conflict of interest.

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Communicated by S. Hohmann.

Availability of supporting data: The RNA sequence dataset supporting the results of this article is available in NCBI (http://www.ncbi.nlm.nih.gov/sra/SRX982234).

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Rong, L., Li, Q., Li, S. et al. De novo transcriptome sequencing of Acer palmatum and comprehensive analysis of differentially expressed genes under salt stress in two contrasting genotypes. Mol Genet Genomics 291, 575–586 (2016). https://doi.org/10.1007/s00438-015-1127-2

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