Genome-Wide Identification and Expression Analysis of <i>Auxin Response Factor</i> (<i>ARF</i>) Gene Family in <i>Betula pendula</i>
As the key transcription factors regulating auxin responsive genes expression, auxin response factors (ARFs) play critical roles in diverse aspects of plant growth and development. <i>Betula pendula</i> is a valuable ornamental tree, and the information on <i>ARF</i> gene fam...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-12-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/10/1/27 |
| _version_ | 1797343534570799104 |
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| author | Huaizhi Mu Xuhong Jin Songtong Lv Sheng Long Yang Liu Le Chen Lin Lin |
| author_facet | Huaizhi Mu Xuhong Jin Songtong Lv Sheng Long Yang Liu Le Chen Lin Lin |
| author_sort | Huaizhi Mu |
| collection | DOAJ |
| description | As the key transcription factors regulating auxin responsive genes expression, auxin response factors (ARFs) play critical roles in diverse aspects of plant growth and development. <i>Betula pendula</i> is a valuable ornamental tree, and the information on <i>ARF</i> gene family of <i>B. pendula</i> is needed for better understanding. The publication of the genome sequence of <i>B. pendula</i> enable to analyze the bioinformatics information and expression pattern of <i>BpeARF</i> gene family on the genome-wide basis. In this study, physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, conserved domain, motif composition, and <i>cis</i>-acting element of <i>BpeARF</i> gene family were analyzed, and expression patterns of <i>BpeARF</i> genes were investigated using completely random design in different tissues and under exogenous NAA and drought treatments. A total of 17 <i>BpeARF</i> genes was identified from <i>B. pendula</i> genome, which were unevenly distributed on 13 chromosomes and encoded adequate proteins ranging from 613 to 1135 amino acids in length. Three <i>BpeARF</i> gene pairs were formed by segmental duplication, and the Ka/Ks values of these <i>BpeARF</i> gene pairs were less than 1. According to the phylogenetic relationship among <i>B. pendula</i>, <i>Betula platyphylla</i>, <i>Populus trichocarpa</i>, and <i>Arabidopsis thaliana</i>, the <i>BpeARF</i> genes were divided into four classes, and the intron/exon structure, conserved domain, and motif composition showed high similarity among the <i>BpeARF</i> genes within the same class. The <i>cis</i>-acting elements in the promoter regions of <i>BpeARF</i> genes were related to tissue development, hormone response, and stress resistance. Quantitative real-time PCR exhibited diverse expression patterns of <i>BpeARF</i> genes in different tissues and in response to exogenous auxin treatment and drought stress. The expressions of one, ten, seven, and three <i>BpeARF</i> genes were the high levels in buds, young leaves, stems, and roots, respectively. Under exogenous NAA treatment, six <i>BpeARF</i> genes in stems and roots were upregulated expression at all timepoints. Under drought stress, <i>BpeARF7</i> and <i>BpeARF15</i> were upregulated in stems and roots, and <i>BpeARF5</i> and <i>BpeARF6</i> were downregulated in leaves, stems, and roots. Our results provided valuable information for the classification and putative functions of <i>BpeARF</i> gene family, which may be helpful for selecting candidate genes and verifying gene function in the genetic engineering of birch trees in further research. |
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| language | English |
| last_indexed | 2024-03-08T10:49:03Z |
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| series | Horticulturae |
| spelling | doaj.art-300ee9a5385444e89ac87379173da0fa2024-01-26T16:49:42ZengMDPI AGHorticulturae2311-75242023-12-011012710.3390/horticulturae10010027Genome-Wide Identification and Expression Analysis of <i>Auxin Response Factor</i> (<i>ARF</i>) Gene Family in <i>Betula pendula</i>Huaizhi Mu0Xuhong Jin1Songtong Lv2Sheng Long3Yang Liu4Le Chen5Lin Lin6Key Laboratory of State Forestry Administration on Conservation and Efficient Utilization of Precious and Rare Forest Resource in Changbai Mountain, Engineering Research Centre of Forestry Biotechnology, Forestry College, Beihua University, Jilin 132013, ChinaKey Laboratory of State Forestry Administration on Conservation and Efficient Utilization of Precious and Rare Forest Resource in Changbai Mountain, Engineering Research Centre of Forestry Biotechnology, Forestry College, Beihua University, Jilin 132013, ChinaKey Laboratory of State Forestry Administration on Conservation and Efficient Utilization of Precious and Rare Forest Resource in Changbai Mountain, Engineering Research Centre of Forestry Biotechnology, Forestry College, Beihua University, Jilin 132013, ChinaKey Laboratory of State Forestry Administration on Conservation and Efficient Utilization of Precious and Rare Forest Resource in Changbai Mountain, Engineering Research Centre of Forestry Biotechnology, Forestry College, Beihua University, Jilin 132013, ChinaKey Laboratory of State Forestry Administration on Conservation and Efficient Utilization of Precious and Rare Forest Resource in Changbai Mountain, Engineering Research Centre of Forestry Biotechnology, Forestry College, Beihua University, Jilin 132013, ChinaKey Laboratory of State Forestry Administration on Conservation and Efficient Utilization of Precious and Rare Forest Resource in Changbai Mountain, Engineering Research Centre of Forestry Biotechnology, Forestry College, Beihua University, Jilin 132013, ChinaKey Laboratory of State Forestry Administration on Conservation and Efficient Utilization of Precious and Rare Forest Resource in Changbai Mountain, Engineering Research Centre of Forestry Biotechnology, Forestry College, Beihua University, Jilin 132013, ChinaAs the key transcription factors regulating auxin responsive genes expression, auxin response factors (ARFs) play critical roles in diverse aspects of plant growth and development. <i>Betula pendula</i> is a valuable ornamental tree, and the information on <i>ARF</i> gene family of <i>B. pendula</i> is needed for better understanding. The publication of the genome sequence of <i>B. pendula</i> enable to analyze the bioinformatics information and expression pattern of <i>BpeARF</i> gene family on the genome-wide basis. In this study, physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, conserved domain, motif composition, and <i>cis</i>-acting element of <i>BpeARF</i> gene family were analyzed, and expression patterns of <i>BpeARF</i> genes were investigated using completely random design in different tissues and under exogenous NAA and drought treatments. A total of 17 <i>BpeARF</i> genes was identified from <i>B. pendula</i> genome, which were unevenly distributed on 13 chromosomes and encoded adequate proteins ranging from 613 to 1135 amino acids in length. Three <i>BpeARF</i> gene pairs were formed by segmental duplication, and the Ka/Ks values of these <i>BpeARF</i> gene pairs were less than 1. According to the phylogenetic relationship among <i>B. pendula</i>, <i>Betula platyphylla</i>, <i>Populus trichocarpa</i>, and <i>Arabidopsis thaliana</i>, the <i>BpeARF</i> genes were divided into four classes, and the intron/exon structure, conserved domain, and motif composition showed high similarity among the <i>BpeARF</i> genes within the same class. The <i>cis</i>-acting elements in the promoter regions of <i>BpeARF</i> genes were related to tissue development, hormone response, and stress resistance. Quantitative real-time PCR exhibited diverse expression patterns of <i>BpeARF</i> genes in different tissues and in response to exogenous auxin treatment and drought stress. The expressions of one, ten, seven, and three <i>BpeARF</i> genes were the high levels in buds, young leaves, stems, and roots, respectively. Under exogenous NAA treatment, six <i>BpeARF</i> genes in stems and roots were upregulated expression at all timepoints. Under drought stress, <i>BpeARF7</i> and <i>BpeARF15</i> were upregulated in stems and roots, and <i>BpeARF5</i> and <i>BpeARF6</i> were downregulated in leaves, stems, and roots. Our results provided valuable information for the classification and putative functions of <i>BpeARF</i> gene family, which may be helpful for selecting candidate genes and verifying gene function in the genetic engineering of birch trees in further research.https://www.mdpi.com/2311-7524/10/1/27birchauxin response factorgene family identificationexpression pattern |
| spellingShingle | Huaizhi Mu Xuhong Jin Songtong Lv Sheng Long Yang Liu Le Chen Lin Lin Genome-Wide Identification and Expression Analysis of <i>Auxin Response Factor</i> (<i>ARF</i>) Gene Family in <i>Betula pendula</i> Horticulturae birch auxin response factor gene family identification expression pattern |
| title | Genome-Wide Identification and Expression Analysis of <i>Auxin Response Factor</i> (<i>ARF</i>) Gene Family in <i>Betula pendula</i> |
| title_full | Genome-Wide Identification and Expression Analysis of <i>Auxin Response Factor</i> (<i>ARF</i>) Gene Family in <i>Betula pendula</i> |
| title_fullStr | Genome-Wide Identification and Expression Analysis of <i>Auxin Response Factor</i> (<i>ARF</i>) Gene Family in <i>Betula pendula</i> |
| title_full_unstemmed | Genome-Wide Identification and Expression Analysis of <i>Auxin Response Factor</i> (<i>ARF</i>) Gene Family in <i>Betula pendula</i> |
| title_short | Genome-Wide Identification and Expression Analysis of <i>Auxin Response Factor</i> (<i>ARF</i>) Gene Family in <i>Betula pendula</i> |
| title_sort | genome wide identification and expression analysis of i auxin response factor i i arf i gene family in i betula pendula i |
| topic | birch auxin response factor gene family identification expression pattern |
| url | https://www.mdpi.com/2311-7524/10/1/27 |
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