Hongmei Yuan1, Wendong Guo2, Lijuan Zhao3, Ying Yu4, Si Chen3, Lei Tao5, Lili Cheng3, Qinghua Kang3, Xixia Song3, Jianzhong Wu3, Yubo Yao3, Wengong Huang3, Ying Wu5, Yan Liu3, Xue Yang3, Guangwen Wu3. 1. Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China. yuanhm1979@163.com. 2. Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin, 150040, China. 3. Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China. 4. School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China. 5. College of Life Science, Northeast Forestry University, Harbin, 150040, China.
Abstract
BACKGROUND: Members of the WRKY protein family, one of the largest transcription factor families in plants, are involved in plant growth and development, signal transduction, senescence, and stress resistance. However, little information is available about WRKY transcription factors in flax (Linum usitatissimum L.). RESULTS: In this study, comprehensive genome-wide characterization of the flax WRKY gene family was conducted that led to prediction of 102 LuWRKY genes. Based on bioinformatics-based predictions of structural and phylogenetic features of encoded LuWRKY proteins, 95 LuWRKYs were classified into three main groups (Group I, II, and III); Group II LuWRKYs were further assigned to five subgroups (IIa-e), while seven unique LuWRKYs (LuWRKYs 96-102) could not be assigned to any group. Most LuWRKY proteins within a given subgroup shared similar motif compositions, while a high degree of motif composition variability was apparent between subgroups. Using RNA-seq data, expression patterns of the 102 predicted LuWRKY genes were also investigated. Expression profiling data demonstrated that most genes associated with cellulose, hemicellulose, or lignin content were predominantly expressed in stems, roots, and less in leaves. However, most genes associated with stress responses were predominantly expressed in leaves and exhibited distinctly higher expression levels in developmental stages 1 and 8 than during other stages. CONCLUSIONS: Ultimately, the present study provides a comprehensive analysis of predicted flax WRKY family genes to guide future investigations to reveal functions of LuWRKY proteins during plant growth, development, and stress responses.
BACKGROUND: Members of the WRKY protein family, one of the largest transcription factor families in plants, are involved in plant growth and development, signal transduction, senescence, and stress resistance. However, little information is available about WRKY transcription factors in flax (Linum usitatissimum L.). RESULTS: In this study, comprehensive genome-wide characterization of the flax WRKY gene family was conducted that led to prediction of 102 LuWRKY genes. Based on bioinformatics-based predictions of structural and phylogenetic features of encoded LuWRKY proteins, 95 LuWRKYs were classified into three main groups (Group I, II, and III); Group II LuWRKYs were further assigned to five subgroups (IIa-e), while seven unique LuWRKYs (LuWRKYs 96-102) could not be assigned to any group. Most LuWRKY proteins within a given subgroup shared similar motif compositions, while a high degree of motif composition variability was apparent between subgroups. Using RNA-seq data, expression patterns of the 102 predicted LuWRKY genes were also investigated. Expression profiling data demonstrated that most genes associated with cellulose, hemicellulose, or lignin content were predominantly expressed in stems, roots, and less in leaves. However, most genes associated with stress responses were predominantly expressed in leaves and exhibited distinctly higher expression levels in developmental stages 1 and 8 than during other stages. CONCLUSIONS: Ultimately, the present study provides a comprehensive analysis of predicted flax WRKY family genes to guide future investigations to reveal functions of LuWRKY proteins during plant growth, development, and stress responses.
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