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

The plastome (plastid genome) represents an indispensable molecular data source for studying plant phylogeny and evolution. Although plastome size is much smaller than that of nuclear genome, accurate and efficient annotation and of use plastome sequences are not simple tasks. Therefore, a streamlined phylogenomic pipeline from plastome annotation to phylogenetic reconstruction and comparative genomics would greatly facilitate research using this important organellar genome. Here we develop PlastidHub, a new web application that primarily uses novel tools to analyze plastome sequences. In comparison with existing tools, new 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) visual comparison of structural variations and annotation completeness at the gene-level. PlastidHub has the following 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 functionalities for all tools; intermediate result documents for secondary use; and easy-to-operate task flows between file upload and download. Interrelated task-based user interface design is the most important feature of PlastidHub. Give that PlastidHub is easy to use without specialized computational skills or resources, this new platform should become widely used among botanists and evolutionary biologists, improving and expediting research employing the plastome. PlastidHub is available at https://www.plastidhub.cn.