Novel online 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 streamlined phylogenomic pipeline spanning plastome annotation, phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.

Back in 2022, Dr. Xiao-Jian Qu, who is affiliated to the College of Life Sciences, Shandong Normal University, conceived the idea of creating an integrated freely available analysis platform to address this problem. Now, in an article published in the KeAi journal Plant Diversity, Qu and his colleagues presented a novel online analysis platform, known as PlastidHub, with an interrelated task-based user interface design.

In comparison with existing tools such as GeSeq, CPGAVAS2, PhyloSuite and Geneious, PlastidHub possesses several key novel functionalities, including: (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; and (6) gene-level visual comparison of structural variations and annotation completeness.

“Given that PlastidHub is easy to use without specialized computational skills or resources, it would be widely used among botanists and evolutionary biologists, improving and expediting research employing the plastome,” says Qu. “In particular, as plastid research grows in importance—from evolutionary studies to crop engineering—PlastidHub’s innovations ensure scientists spend less time troubleshooting and more time on discovery.”

With its speed, accuracy, and ease of use, PlastidHub is poised to become a go-to for plastid phylogenomics labs worldwide.

Contact the author: Xiao-Jian Qu, quxiaojian@sdnu.edu.cn

Funder: 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.

Journal: Plant Diversity

DOI: https://doi.org/10.1016/j.pld.2025.05.005

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

Conflict of interest: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.