Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.)
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...
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doaj-730066c217654accaaef17e7b4c1e3202021-05-23T11:24:31ZengBMCBMC Genomics1471-21642021-05-0122111510.1186/s12864-021-07697-wGenome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.)Hongmei Yuan0Wendong Guo1Lijuan Zhao2Ying Yu3Si Chen4Lei Tao5Lili Cheng6Qinghua Kang7Xixia Song8Jianzhong Wu9Yubo Yao10Wengong Huang11Ying Wu12Yan Liu13Xue Yang14Guangwen Wu15Heilongjiang Academy of Agricultural SciencesInstitute of Natural Resources and Ecology, Heilongjiang Academy of SciencesHeilongjiang Academy of Agricultural SciencesSchool of Basic Medicine, Guizhou University of Traditional Chinese MedicineHeilongjiang Academy of Agricultural SciencesCollege of Life Science, Northeast Forestry UniversityHeilongjiang Academy of Agricultural SciencesHeilongjiang Academy of Agricultural SciencesHeilongjiang Academy of Agricultural SciencesHeilongjiang Academy of Agricultural SciencesHeilongjiang Academy of Agricultural SciencesHeilongjiang Academy of Agricultural SciencesCollege of Life Science, Northeast Forestry UniversityHeilongjiang Academy of Agricultural SciencesHeilongjiang Academy of Agricultural SciencesHeilongjiang Academy of Agricultural SciencesAbstract 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.https://doi.org/10.1186/s12864-021-07697-wFlaxTranscription factorWRKYPhylogenetic analysisExpression patterns |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hongmei Yuan Wendong Guo Lijuan Zhao Ying Yu Si Chen Lei Tao Lili Cheng Qinghua Kang Xixia Song Jianzhong Wu Yubo Yao Wengong Huang Ying Wu Yan Liu Xue Yang Guangwen Wu |
spellingShingle |
Hongmei Yuan Wendong Guo Lijuan Zhao Ying Yu Si Chen Lei Tao Lili Cheng Qinghua Kang Xixia Song Jianzhong Wu Yubo Yao Wengong Huang Ying Wu Yan Liu Xue Yang Guangwen Wu Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.) BMC Genomics Flax Transcription factor WRKY Phylogenetic analysis Expression patterns |
author_facet |
Hongmei Yuan Wendong Guo Lijuan Zhao Ying Yu Si Chen Lei Tao Lili Cheng Qinghua Kang Xixia Song Jianzhong Wu Yubo Yao Wengong Huang Ying Wu Yan Liu Xue Yang Guangwen Wu |
author_sort |
Hongmei Yuan |
title |
Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.) |
title_short |
Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.) |
title_full |
Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.) |
title_fullStr |
Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.) |
title_full_unstemmed |
Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.) |
title_sort |
genome-wide identification and expression analysis of the wrky transcription factor family in flax (linum usitatissimum l.) |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2021-05-01 |
description |
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. |
topic |
Flax Transcription factor WRKY Phylogenetic analysis Expression patterns |
url |
https://doi.org/10.1186/s12864-021-07697-w |
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