JianJun Jin

Profile

My primary goal is to develop innovative tools that transform our understanding of plant biodiversity, while fostering international collaborations that synergize computational and organismal research for important evolutionary insights. I investigate both theoretical and practical questions about how biodiversity originates and is maintained, and how to quantify it. This involves the development of new models, methods, and software tools that contribute to the broader biodiversity research community. Fundamental questions that motivate my research include how to achieve precise genome assembly from mixtures, how to reconstruct evolutionary history accurately with genomic data, and how genomes and phenotypic traits evolve during the diversification of a lineage.

My research allows me to delve deep into plant phylogenetics, gaining extensive experience by working on the phylogenomics and evolution of diverse plant lineages, including Cannabaceae, Rosaceae, Fabaceae, and Caryophyllales. A notable achievement has been the development of GetOrganelle, a widely utilized tool for efficient and accurate organelle genome assembly.

Most recently, my research has focused on the evolution of the fascinating hyperdiverse plant genus Pedicularis. Leading fieldwork in Hengduan Mountains, a biodiversity hotspot, I collect ultrafine-level floral 3D models, transcriptomes and genomes, to study the parallel evolution of floral morphologies and the adaptation of Pedicularis. With a goals rooted in the analysis of empirical data, I have proposed a novel framework for the evolutionary analysis of 3D morphologies, implemented it in a novel Python package PhyloShape. PhyloShape is under development and aims to provide a general toolkit for morphology evolution analysis using a 3D model dataset.

Selected publications
Jian-Jun Jin, Wen-Bin Yu, Jun-Bo Yang, Yu Song, Claude W. dePamphilis, Ting-Shuang Yi, De-Zhu Li.2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes.
Genome Biology. 21. https://doi.org/10.1186/s13059-020-02154-5. **1000+ citations

Rong Zhang, Yin-Huan Wang, Jian-Jun Jin, Greg Stull, Anne Bruneau, Domingos Cardoso, Luciano Paganucci de Queiroz, Michael J. Moore, Jian Wang, Shu-Dong Zhang, Si-Yun Chen, De-Zhu Li, Ting-Shuang Yi. 2020. Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae. Systematic Biology. 69: 613–622. https://doi.org/10.1093/sysbio/syaa013

Dong-Min Jin, Susann Wicke, Lu Gan, Jun-Bo Yang, Jian-Jun Jin, Ting-Shuang Yi. 2020. The Loss of the Inverted Repeat in the Putranjivoid Clade of Malpighiales. Frontiers in Plant Science. 11. https://doi.org/10.3389/fpls.2020.00942

Jian-Jun Jin, Mei-Qing Yang, De-Zhu Li, Peter W. Fritsch, Ting-Shuang Yi. 2020. Born Migrators: historical biogeography of cosmopolitan family Cannabaceae. Journal of Systematics and Evolution. 58: 461-473. https://doi.org/10.1111/jse.12552