PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics
The plastid genome (plastome) represents an indispensable molecular resource for studying plant phylogeny and evolution. Although plastome size is much smaller than that of nuclear genomes, accurately and efficiently annotating and utilizing plastome sequences remain challenging. Therefore, a stream...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2025-07-01
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| Series: | Plant Diversity |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468265925000915 |
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| author | Na-Na Zhang Gregory W. Stull Xue-Jie Zhang Shou-Jin Fan Ting-Shuang Yi Xiao-Jian Qu |
| author_facet | Na-Na Zhang Gregory W. Stull Xue-Jie Zhang Shou-Jin Fan Ting-Shuang Yi Xiao-Jian Qu |
| author_sort | Na-Na Zhang |
| collection | DOAJ |
| description | The plastid genome (plastome) represents an indispensable molecular resource for studying plant phylogeny and evolution. Although plastome size is much smaller than that of nuclear genomes, accurately and efficiently annotating and utilizing plastome sequences remain challenging. Therefore, a streamlined phylogenomic pipeline spanning plastome annotation, phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome. Here, we develop PlastidHub, a novel web application employing innovative tools to analyze plastome sequences. In comparison with existing tools, key novel functionalities in PlastidHub include: (1) standardization of quadripartite structure; (2) improvement of annotation flexibility and consistency; (3) quantitative assessment of annotation completeness; (4) diverse extraction modes for canonical and specialized sequences; (5) intelligent screening of molecular markers for biodiversity studies; (6) gene-level visual comparison of structural variations and annotation completeness. PlastidHub features cloud-based web applications that do not require users to install, update, or maintain tools; detailed help documents including user guides, test examples, a static pop-up prompt box, and dynamic pop-up warning prompts when entering unreasonable parameter values; batch processing capabilities for all tools; intermediate results for secondary use; and easy-to-operate task flows between file upload and download. A key feature of PlastidHub is its interrelated task-based user interface design. Give that PlastidHub is easy to use without specialized computational skills or resources, this new platform should be widely used among botanists and evolutionary biologists, improving and expediting research employing the plastome. PlastidHub is available at https://www.plastidhub.cn. |
| format | Article |
| id | doaj-art-7c2ab304b88c439db8a3b2bf88ed9af5 |
| institution | Kabale University |
| issn | 2468-2659 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Plant Diversity |
| spelling | doaj-art-7c2ab304b88c439db8a3b2bf88ed9af52025-08-20T03:25:55ZengKeAi Communications Co., Ltd.Plant Diversity2468-26592025-07-0147454456010.1016/j.pld.2025.05.005PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomicsNa-Na Zhang0Gregory W. Stull1Xue-Jie Zhang2Shou-Jin Fan3Ting-Shuang Yi4Xiao-Jian Qu5College of Life Sciences, Shandong Normal University, Ji’nan 250358, China; Dongying Institute, Shandong Normal University, Dongying 257092, ChinaDepartment of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USACollege of Life Sciences, Shandong Normal University, Ji’nan 250358, China; Dongying Institute, Shandong Normal University, Dongying 257092, ChinaCollege of Life Sciences, Shandong Normal University, Ji’nan 250358, China; Dongying Institute, Shandong Normal University, Dongying 257092, China; Corresponding author. College of Life Sciences, Shandong Normal University, Ji'nan 250358, China.Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Corresponding author.College of Life Sciences, Shandong Normal University, Ji’nan 250358, China; Dongying Institute, Shandong Normal University, Dongying 257092, China; Corresponding author. College of Life Sciences, Shandong Normal University, Ji’nan 250358, China.The plastid genome (plastome) represents an indispensable molecular resource for studying plant phylogeny and evolution. Although plastome size is much smaller than that of nuclear genomes, accurately and efficiently annotating and utilizing plastome sequences remain challenging. Therefore, a streamlined phylogenomic pipeline spanning plastome annotation, phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome. Here, we develop PlastidHub, a novel web application employing innovative tools to analyze plastome sequences. In comparison with existing tools, key novel functionalities in PlastidHub include: (1) standardization of quadripartite structure; (2) improvement of annotation flexibility and consistency; (3) quantitative assessment of annotation completeness; (4) diverse extraction modes for canonical and specialized sequences; (5) intelligent screening of molecular markers for biodiversity studies; (6) gene-level visual comparison of structural variations and annotation completeness. PlastidHub features cloud-based web applications that do not require users to install, update, or maintain tools; detailed help documents including user guides, test examples, a static pop-up prompt box, and dynamic pop-up warning prompts when entering unreasonable parameter values; batch processing capabilities for all tools; intermediate results for secondary use; and easy-to-operate task flows between file upload and download. A key feature of PlastidHub is its interrelated task-based user interface design. Give that PlastidHub is easy to use without specialized computational skills or resources, this new platform should be widely used among botanists and evolutionary biologists, improving and expediting research employing the plastome. PlastidHub is available at https://www.plastidhub.cn.http://www.sciencedirect.com/science/article/pii/S2468265925000915AnnotationComparative genomicsPlastid phylogenomicsSequence processingVisualization |
| spellingShingle | Na-Na Zhang Gregory W. Stull Xue-Jie Zhang Shou-Jin Fan Ting-Shuang Yi Xiao-Jian Qu PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics Plant Diversity Annotation Comparative genomics Plastid phylogenomics Sequence processing Visualization |
| title | PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics |
| title_full | PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics |
| title_fullStr | PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics |
| title_full_unstemmed | PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics |
| title_short | PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics |
| title_sort | plastidhub an integrated analysis platform for plastid phylogenomics and comparative genomics |
| topic | Annotation Comparative genomics Plastid phylogenomics Sequence processing Visualization |
| url | http://www.sciencedirect.com/science/article/pii/S2468265925000915 |
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