PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics

doi:10.1016/j.pld.2025.05.005

Plant Diversity ›› 2025, Vol. 47 ›› Issue (04): 544-560.DOI: 10.1016/j.pld.2025.05.005

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PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics

Na-Na Zhang (张娜娜)^a,b, Gregory W. Stull^c, Xue-Jie Zhang (张学杰)^a,b, Shou-Jin Fan (樊守金)^a,b, Ting-Shuang Yi (伊廷双)^d, Xiao-Jian Qu (曲小健)^a,b

a. College of Life Sciences, Shandong Normal University, Ji'nan 250358, China;
b. Dongying Institute, Shandong Normal University, Dongying 257092, China;
c. Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA;
d. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China

Received:2025-03-13 Revised:2025-05-06 Online:2025-08-13 Published:2025-08-13
Contact: Shou-Jin Fan (樊守金),E-mail:fansj@sdnu.edu.cn;Ting-Shuang Yi (伊廷双),E-mail:tingshuangyi@mail.kib.ac.cn;Xiao-Jian Qu (曲小健),E-mail:quxiaojian@sdnu.edu.cn
Supported by:
This study was funded by the Natural Science Foundation of Shandong Province (ZR2020QC022), the Science and Technology Basic Resources Investigation Program of China (No. 2019FY100900), the Major Program for Basic Research Project of Yunnan Province (202401BC070001), Yunnan Revitalization Talent Support Program: Yunling Scholar Project to Tingshuang Yi, and the open research project of “Cross Cooperative Team” of the Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences.

PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics

Na-Na Zhang (张娜娜)^a,b, Gregory W. Stull^c, Xue-Jie Zhang (张学杰)^a,b, Shou-Jin Fan (樊守金)^a,b, Ting-Shuang Yi (伊廷双)^d, Xiao-Jian Qu (曲小健)^a,b

a. College of Life Sciences, Shandong Normal University, Ji'nan 250358, China;
b. Dongying Institute, Shandong Normal University, Dongying 257092, China;
c. Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA;
d. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China

通讯作者: Shou-Jin Fan (樊守金),E-mail:fansj@sdnu.edu.cn;Ting-Shuang Yi (伊廷双),E-mail:tingshuangyi@mail.kib.ac.cn;Xiao-Jian Qu (曲小健),E-mail:quxiaojian@sdnu.edu.cn
基金资助:
This study was funded by the Natural Science Foundation of Shandong Province (ZR2020QC022), the Science and Technology Basic Resources Investigation Program of China (No. 2019FY100900), the Major Program for Basic Research Project of Yunnan Province (202401BC070001), Yunnan Revitalization Talent Support Program: Yunling Scholar Project to Tingshuang Yi, and the open research project of “Cross Cooperative Team” of the Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences.

Abstract

Abstract: 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.

Key words: Annotation, Comparative genomics, Plastid phylogenomics, Sequence processing, Visualization

摘要： 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.

关键词: Annotation, Comparative genomics, Plastid phylogenomics, Sequence processing, Visualization

Na-Na Zhang (张娜娜), Gregory W. Stull, Xue-Jie Zhang (张学杰), Shou-Jin Fan (樊守金), Ting-Shuang Yi (伊廷双), Xiao-Jian Qu (曲小健). PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics[J]. Plant Diversity, 2025, 47(04): 544-560.

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PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics

PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics

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