Genome-wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet (Setaria italica L.)
Abstract Backgrounds Adapter proteins (APs) complex is a class of heterotetrameric complexes comprising of 4-subunits with important regulatory functions in eukaryotic cell membrane vesicle trafficking. Foxtail millet (Setaria italica L.) is a significant C4 model plant for monocotyledon studies, an...
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2025-01-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-024-05959-9 |
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| author | Dan Wang Min Su Jian-Hong Hao Zi-Dong Li Shuqi Dong Xiangyang Yuan Xiaorui Li Lulu Gao Xiaoqian Chu Guanghui Yang Jia-Gang Wang Huiling Du |
| author_facet | Dan Wang Min Su Jian-Hong Hao Zi-Dong Li Shuqi Dong Xiangyang Yuan Xiaorui Li Lulu Gao Xiaoqian Chu Guanghui Yang Jia-Gang Wang Huiling Du |
| author_sort | Dan Wang |
| collection | DOAJ |
| description | Abstract Backgrounds Adapter proteins (APs) complex is a class of heterotetrameric complexes comprising of 4-subunits with important regulatory functions in eukaryotic cell membrane vesicle trafficking. Foxtail millet (Setaria italica L.) is a significant C4 model plant for monocotyledon studies, and vesicle trafficking may plays a crucial role in various life activities related to growth and development. Despite this importance, studies on AP complexes in foxtail millet have been lacking. Results This research conducted genome-wide identification and systematical analysis of AP complexes in foxtail millet. 33 SiAP complex genes were identified and classified into 7 groups, distributed unevenly across 9 chromosomes in foxtail millet. Among these genes, 11 segmental duplication pairs were found. Out of the 33 SiAP complex genes, 24 exhibited collinear relationships with Setaria viridis, while only one showed relationship with Arabidopsis thaliana. Gene structure and motif composition were investigated to understand the function and evolution of these SiAP complex genes. Furthermore, these promoter region of the SiAP complex genes contains 49 cis-elements that are associated with responses to light, hormones, abiotic stress, growth and development. The interaction network between the SiAP complexes was analyzed, and there were strong interactions among the SiAP complex proteins. Expression patterns of SiAP complex genes in different organs and developmental stages of foxtail millet were investigated. The majority of the SiAP complex genes exhibited expressed in multiple tissues, with some genes being predominantly expressed in specific tissues. Subsequently, we selected SiAP4M and SiAP2M for validation of subcellular localization. The signal of 35 S:: SiAP4M: GFP (Long) and 35 S:: SiAP4M: GFP (Short) fused proteins were primarily observed in the nucleus, while the signal of 35 S:: SiAP2M: GFP fused proteins was widely distributed on the cell membrane and vesicles. Conclusions Overall, this study presents a comprehensive map of the SiAP complexes in foxtail millet. These findings not only administer to understanding the biological functions of AP complexes in foxtail millet growth and development but also offer insights for enhancing genetic breeding in this crop. |
| format | Article |
| id | doaj-art-e1f501c94a8a48b5a5fd6ce14acc4cad |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-e1f501c94a8a48b5a5fd6ce14acc4cad2025-02-02T12:15:26ZengBMCBMC Plant Biology1471-22292025-01-0125111610.1186/s12870-024-05959-9Genome-wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet (Setaria italica L.)Dan Wang0Min Su1Jian-Hong Hao2Zi-Dong Li3Shuqi Dong4Xiangyang Yuan5Xiaorui Li6Lulu Gao7Xiaoqian Chu8Guanghui Yang9Jia-Gang Wang10Huiling Du11College of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityCollege of Agriculture, Shanxi Agricultural UniversityAbstract Backgrounds Adapter proteins (APs) complex is a class of heterotetrameric complexes comprising of 4-subunits with important regulatory functions in eukaryotic cell membrane vesicle trafficking. Foxtail millet (Setaria italica L.) is a significant C4 model plant for monocotyledon studies, and vesicle trafficking may plays a crucial role in various life activities related to growth and development. Despite this importance, studies on AP complexes in foxtail millet have been lacking. Results This research conducted genome-wide identification and systematical analysis of AP complexes in foxtail millet. 33 SiAP complex genes were identified and classified into 7 groups, distributed unevenly across 9 chromosomes in foxtail millet. Among these genes, 11 segmental duplication pairs were found. Out of the 33 SiAP complex genes, 24 exhibited collinear relationships with Setaria viridis, while only one showed relationship with Arabidopsis thaliana. Gene structure and motif composition were investigated to understand the function and evolution of these SiAP complex genes. Furthermore, these promoter region of the SiAP complex genes contains 49 cis-elements that are associated with responses to light, hormones, abiotic stress, growth and development. The interaction network between the SiAP complexes was analyzed, and there were strong interactions among the SiAP complex proteins. Expression patterns of SiAP complex genes in different organs and developmental stages of foxtail millet were investigated. The majority of the SiAP complex genes exhibited expressed in multiple tissues, with some genes being predominantly expressed in specific tissues. Subsequently, we selected SiAP4M and SiAP2M for validation of subcellular localization. The signal of 35 S:: SiAP4M: GFP (Long) and 35 S:: SiAP4M: GFP (Short) fused proteins were primarily observed in the nucleus, while the signal of 35 S:: SiAP2M: GFP fused proteins was widely distributed on the cell membrane and vesicles. Conclusions Overall, this study presents a comprehensive map of the SiAP complexes in foxtail millet. These findings not only administer to understanding the biological functions of AP complexes in foxtail millet growth and development but also offer insights for enhancing genetic breeding in this crop.https://doi.org/10.1186/s12870-024-05959-9Adaptor protein complexVesicle traffickingSetaria italica L.Genome-wide identificationExpression patternsSubcellular localization |
| spellingShingle | Dan Wang Min Su Jian-Hong Hao Zi-Dong Li Shuqi Dong Xiangyang Yuan Xiaorui Li Lulu Gao Xiaoqian Chu Guanghui Yang Jia-Gang Wang Huiling Du Genome-wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet (Setaria italica L.) BMC Plant Biology Adaptor protein complex Vesicle trafficking Setaria italica L. Genome-wide identification Expression patterns Subcellular localization |
| title | Genome-wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet (Setaria italica L.) |
| title_full | Genome-wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet (Setaria italica L.) |
| title_fullStr | Genome-wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet (Setaria italica L.) |
| title_full_unstemmed | Genome-wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet (Setaria italica L.) |
| title_short | Genome-wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet (Setaria italica L.) |
| title_sort | genome wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet setaria italica l |
| topic | Adaptor protein complex Vesicle trafficking Setaria italica L. Genome-wide identification Expression patterns Subcellular localization |
| url | https://doi.org/10.1186/s12870-024-05959-9 |
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