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Root transcriptome sequencing and differentially expressed drought-responsive genes in the Platycladus orientalis (L.)

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Abstract

Platycladus orientalis (L.) is used extensively for afforestation and is a common medicinal ingredient. Because of its drought tolerance, P. orientalis is widely used for afforestation in arid and semi-arid areas. To better understand the mechanisms involved in drought-stress tolerance in this important tree, the transcriptome profiles of drought-treated P. orientalis seedlings were analyzed using Illumina technology, and differentially expressed genes (DEGs) between drought-treated and well-watered trees were identified. We performed transcriptome sequencing of P. orientalis roots using the Illumina 4000 paired-end sequencing technique. More than 53 million 151-bp paired-end clean reads were obtained from each of the cDNA libraries and biological replicates, and de novo assembly generated 148,392 unigenes with an average length of 927.77 bp. After removing contaminating sequences, we found that 29.9 % (34,845) of the unigenes exhibited significant similarity to known sequences in the GenBank non-redundant protein database. A total of 3930 unigenes were found to be significantly differentially expressed between drought-treated and well-watered trees. Among them, 881 (22.42 %) were up-regulated and 3049 (77.58 %) were down-regulated in roots. Several DEGs had known functions in categories related to the biosynthesis of secondary metabolites, phenylalanine metabolism, starch and sucrose metabolism, and arginine and proline metabolism. A total of 194 genes that were found to be differentially regulated in response to drought stress were categorized as transcription factors. The transcriptome profiles obtained provide a valuable resource for future research to understand the molecular adaptation of Cupressaceae plants under drought condition and facilitate the exploration of drought-tolerant candidate genes.

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Acknowledgments

This work was financially supported by the National Forestry Industry Research Special Funds for Public Welfare Projects (China) (201404302).

Authors’ contributions

ZZ developed and supervised the work. The preparation of plant material, library construction, gene-expression analyses and data analysis were conducted by SZ and LLZ. YML, KKZ, LS, and QYZ helped the sample collection and quantitative reverse transcription PCR experiment. All authors read and approved the final manuscript.

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Authors and Affiliations

  1. College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People’s Republic of China

    Sheng Zhang, Lingling Zhang, Zhong Zhao, Yiming Li, Kaikai Zhou, Li Su & Qianyi Zhou

  2. Key Comprehensive Laboratory of Forestry, Shaanxi Provice, Yangling, Shaanxi, People’s Republic of China

    Sheng Zhang, Zhong Zhao, Yiming Li, Kaikai Zhou, Li Su & Qianyi Zhou

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  1. Sheng Zhang
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  2. Lingling Zhang
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Correspondence to Zhong Zhao.

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Communicated by C. Chen

Data archiving statement

All of the raw data from the Illumina sequencing have been deposited in NCBI Sequence Read Archive (SRA) under accession number (SRX1717972, SRX1717973, SRX1717974, SRX1717969, SRX1717970 and SRX1717971).

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Additional file 1

Summary of sequences analysis and length distribution of assembled unigenes PO1_1, PO1_1 and PO1_3: Well-watered sample (three independent biological replicates) PO3_1, PO3_2 and PO3_3: Drought-treated sample (three independent biological replicates) Q20: The percentage of base with a phred value > 20 Q30: The percentage of base with a phred value > 30 (DOC 51 kb)

Additional file 2

Summary of Gene Ontology (GO) classification of assembled unigenes (XLS 3491 kb)

Additional table 2

Statistics of annotation results of unigene sequences (DOC 36 kb)

Additional file 3

Eukaryotic Orthologous Groups (KOG) annotation of putative proteins (XLS 16 kb)

Additional file 4

Pathway assignment based on Kyoto Encyclopedia of Gene and Genomes (KEGG) (XLS 31 kb)

Additional file 5

Summary of Simple Sequence Repeats (SSRs) detected from transcriptome data (DOC 54 kb)

Additional file 6

Gene Ontology (GO) analyses of the differentially expressed genes (DEGs) (XLS 188 kb)

Additional file 7

Differentially expressed genes (DEGs) subjected to Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway analysis (XLS 110 kb)

Additional file 8

List of Gene Ontology (GO) enrichment analysis (XLS 229 kb)

Additional file 9

Transcription factors associated with drought response (XLS 303 kb)

Additional file 10

Transcription factors differentially expressed in drought stress (up- or down-regulated) (XLS 26 kb)

Additional file 11

Changes in gene expression levels confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) (DOC 56 kb)

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Zhang, S., Zhang, L., Zhao, Z. et al. Root transcriptome sequencing and differentially expressed drought-responsive genes in the Platycladus orientalis (L.). Tree Genetics & Genomes 12, 79 (2016). https://doi.org/10.1007/s11295-016-1042-7

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