image: PlastidHub is an integrated plastome analysis platform including 10 tool kits. THE Streamlined phylogenomic pipeline spanning plastome annotation, phylogenetic reconstruction and comparative genomics.
Credit: Xiao-Jian Qu
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.
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Contact the author: Xiao-Jian Qu, quxiaojian@sdnu.edu.cn
The publisher KeAi was established by Elsevier and China Science Publishing & Media Ltd to unfold quality research globally. In 2013, our focus shifted to open access publishing. We now proudly publish more than 100 world-class, open access, English language journals, spanning all scientific disciplines. Many of these are titles we publish in partnership with prestigious societies and academic institutions, such as the National Natural Science Foundation of China (NSFC).
Journal
Plant Diversity
Method of Research
Computational simulation/modeling
Subject of Research
Not applicable
Article Title
PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics
COI Statement
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.