Abstract
Homeodomain-leucine zipper (HD-Zip) transcription factors are unique to plants and play important roles in plant growth and development. Although the HD-Zip gene family has been studied in many plant species, no comprehensive analysis of gene expression patterns under stress conditions has been reported in moso bamboo (Phyllostachys edulis). In this study, 48 putative HD-Zip genes were identified in the moso bamboo genome, and the predicted proteins clustered into four subfamilies (HD-Zip I–IV) based on phylogenetic analysis. Members of each subfamily shared similar conserved motifs, implying that they may perform similar functions. Our evolutionary analyses revealed that HD-Zip genes underwent a large-scale duplication event approximately 15 million years ago, the duplicated HD-Zip genes in moso bamboo are basically under purifying selection, and that the divergence time of HD-Zip genes between rice and moso bamboo was 15–23 million years ago. Analyses of expression in response to drought and salinity showed that some genes display stress-inducible expression patterns. Our study provides a systematic analysis of the HD-Zip gene family in moso bamboo. Analysis of gene expression patterns under abiotic stress may help in understanding the role of HD-Zip genes in moso bamboo and in overcoming challenges in moso bamboo growth and development.
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Acknowledgements
We thank the members of the Laboratory of Modern Biotechnology for their assistance in this study. This work was supported by the Specialized Research Fund for the Forestry Public Welfare Industry (201404601) and Chinese National Natural Science Foundation (31670672). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Author’s contribution
Conceived and designed the experiments: DMC, ZC, HWY, YX. Performed the experiments: DMC, ZC, MW. Analyzed the data: DMC, ZC, HWY. Contributed reagents/materials/analysis tools: DMC, ZC, MW, YW, YJW. Wrote the paper: DMC, ZC, YX.
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Supplementary material S1 Table
Oligonucleotide primer sequences used in qRT-PCR analysis of the 17 moso bamboo HD-ZIP I genes (XLSX 13 kb)
Supplementary material S2 Table
Genomic location and predicted characteristics of the putative HD-Zip proteins in moso bamboo (DOC 95 kb)
Supplementary material S3 Figure
Amino acid sequence motifs present in 48 moso bamboo HD-Zip proteins. Twenty-five motifs were identified by MEME (http://meme.nbcr.net/meme/) (PNG 51 kb)
Supplementary material S4 Table
Detailed information on conserved amino acid sequences and motif lengths (XLSX 10 kb)
Supplementary material S5 Table
Annotation of putative motifs based on Pfam searches (XLSX 10 kb)
Supplementary material S6 Text
Amino acid sequences of moso bamboo, rice, maize and sorghum HD-Zip proteins used for phylogenetic analysis. (TXT 92 kb)
Supplementary material S7 Table
Paralogous HD-Zip gene pairs identified in the moso bamboo genome (DOC 44 kb)
Supplementary material S8 Table
Orthologous HD-Zip gene pairs between moso bamboo and rice (DOC 75 kb)
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Chen, D., Chen, Z., Wu, M. et al. Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Moso Bamboo (Phyllostachys edulis). J Plant Growth Regul 36, 323–337 (2017). https://doi.org/10.1007/s00344-016-9642-x
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DOI: https://doi.org/10.1007/s00344-016-9642-x