Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa)
Abstract Background Auxin/indoleacetic acid (AUX/IAA) genes encoding short-lived proteins participate in AUX signaling transduction and play crucial roles in plant growth and development. Although the AUX/IAA gene family has been identified in many plants, a systematic analysis of AUX/IAA genes in B...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-06-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-023-04356-y |
| _version_ | 1797789866360045568 |
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| author | Huanwen Xu Yu Liu Shengmei Zhang Deju Shui Zhewen Xia Ji Sun |
| author_facet | Huanwen Xu Yu Liu Shengmei Zhang Deju Shui Zhewen Xia Ji Sun |
| author_sort | Huanwen Xu |
| collection | DOAJ |
| description | Abstract Background Auxin/indoleacetic acid (AUX/IAA) genes encoding short-lived proteins participate in AUX signaling transduction and play crucial roles in plant growth and development. Although the AUX/IAA gene family has been identified in many plants, a systematic analysis of AUX/IAA genes in Brassica rapa ssp. rapa has not yet been reported. Results We performed a comprehensive genome-wide analysis and found 89 AUX/IAA genes in turnip based on the conserved AUX/IAA domain (pfam02309). Phylogenetic analysis of AUX/IAA genes from turnip, Arabidopsis, and cabbage revealed that these genes cluster into six subgroups (A1, A2, A3, A4, B1, and B2). The motif distribution was also conservative among the internal members of the clade. Enhanced yellow fluorescent protein (EYFP) signals of BrrIAA-EYFPs showed that BrrIAA members functioned as nucleoproteins. Moreover, transcriptional analysis revealed that the expression patterns of AUX/IAA genes in turnip were tissue-dependent. Because orthologs have similar biological functions and interaction networks in plant growth and development, BrrIAA66 in turnip possibly played a role in embryo axis formation, vascular development, lateral root formation, and floral organ development by interacting with BrrARF19 and BrrTIR1. Conclusion These results provide a theoretical basis for further investigation of BrrAUX/IAA genes and lay the foundation for functional analysis of BrrIAA66 in turnip. |
| first_indexed | 2024-03-13T01:56:39Z |
| format | Article |
| id | doaj.art-ae7486f82d2a4ea79bbbda42b82e90c1 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-03-13T01:56:39Z |
| publishDate | 2023-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-ae7486f82d2a4ea79bbbda42b82e90c12023-07-02T11:11:56ZengBMCBMC Plant Biology1471-22292023-06-0123111310.1186/s12870-023-04356-yGenome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa)Huanwen Xu0Yu Liu1Shengmei Zhang2Deju Shui3Zhewen Xia4Ji Sun5College of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences)Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural SciencesCollege of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences)College of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences)Wenzhou Lucheng District Agricultural Industry InstituteCollege of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology (Wenzhou Academy of Agricultural Sciences)Abstract Background Auxin/indoleacetic acid (AUX/IAA) genes encoding short-lived proteins participate in AUX signaling transduction and play crucial roles in plant growth and development. Although the AUX/IAA gene family has been identified in many plants, a systematic analysis of AUX/IAA genes in Brassica rapa ssp. rapa has not yet been reported. Results We performed a comprehensive genome-wide analysis and found 89 AUX/IAA genes in turnip based on the conserved AUX/IAA domain (pfam02309). Phylogenetic analysis of AUX/IAA genes from turnip, Arabidopsis, and cabbage revealed that these genes cluster into six subgroups (A1, A2, A3, A4, B1, and B2). The motif distribution was also conservative among the internal members of the clade. Enhanced yellow fluorescent protein (EYFP) signals of BrrIAA-EYFPs showed that BrrIAA members functioned as nucleoproteins. Moreover, transcriptional analysis revealed that the expression patterns of AUX/IAA genes in turnip were tissue-dependent. Because orthologs have similar biological functions and interaction networks in plant growth and development, BrrIAA66 in turnip possibly played a role in embryo axis formation, vascular development, lateral root formation, and floral organ development by interacting with BrrARF19 and BrrTIR1. Conclusion These results provide a theoretical basis for further investigation of BrrAUX/IAA genes and lay the foundation for functional analysis of BrrIAA66 in turnip.https://doi.org/10.1186/s12870-023-04356-yGenome-wide analysisAUX/IAA gene familyPhylogenetic relationshipExpression analysisBrassica rapa ssp. rapa |
| spellingShingle | Huanwen Xu Yu Liu Shengmei Zhang Deju Shui Zhewen Xia Ji Sun Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa) BMC Plant Biology Genome-wide analysis AUX/IAA gene family Phylogenetic relationship Expression analysis Brassica rapa ssp. rapa |
| title | Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa) |
| title_full | Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa) |
| title_fullStr | Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa) |
| title_full_unstemmed | Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa) |
| title_short | Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa) |
| title_sort | genome wide identification and expression analysis of the aux iaa gene family in turnip brassica rapa ssp rapa |
| topic | Genome-wide analysis AUX/IAA gene family Phylogenetic relationship Expression analysis Brassica rapa ssp. rapa |
| url | https://doi.org/10.1186/s12870-023-04356-y |
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