Publications

20 publications

† Equal contribution · * Corresponding author.

Journal articles

2026

Hybridization and incomplete lineage sorting characterize the evolutionary history of two East Asian clades of Stewartia (Theaceae).

Han-Yang Lin, Miao Sun, Jian-Jun Jin, Cheng-Xin Fu, Douglas E Soltis, Pamela S Soltis, Yun-Peng Zhao^*.

Molecular Phylogenetics and Evolution 214: 108472.

2026

Phylogenetic Resolution and Conflict in the Species-Rich Flowering Plant Family Leguminosae.

Rong Zhang, Gregory W Stull, Jian-Jun Jin, Yin-Huan Wang, Ying Guo, Zhi-Yun Yang, Hong-Tao Li, Kai-Lun An, Joseph L M Charboneau, Ryan A Folk, Domingos Cardoso, Luciano Paganucci de Queiroz, Anne Bruneau, Pamela S Soltis, Douglas E Soltis, Stephen A Smith, De-Zhu Li^*, Ting-Shuang Yi^*.

Systematic Biology 75(2): 236–258. Full text

2023

More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae).

Matias Köhler^*, Marcelo Reginato, Jian-Jun Jin, Lucas C Majure^*.

Annals of Botany 132(4): 771–786. Full text

2023

Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto-nuclear discordance and provides new insights into generic relationships.

Xiao-Gang Fu^†, Shui-Yin Liu^†, Robin van Velzen, Gregory W. Stull, Qin Tian, Yun-Xia Li, Ryan A. Folk, Robert P. Guralnick, Heather R. Kates, Jian-Jun Jin, Zhong-Hu Li, Douglas E. Soltis, Pamela S. Soltis, Ting-Shuang Yi^*.

Journal of Systematics and Evolution 61(5): 806–826.

2022

Comparative genomics of orobanchaceous species with different parasitic lifestyles reveals the origin and stepwise evolution of plant parasitism.

Yuxing Xu, Jingxiong Zhang, Canrong Ma, Yunting Lei, Guojing Shen, Jianjun Jin, Deren A.R. Eaton, Jianqiang Wu^*.

Molecular Plant 15(8): 1384–1399.

2021

Plastid phylogenomic insights into relationships of all flowering plant families.

Hong-Tao Li^†, Yang Luo^†, Lu Gan^†, Peng-Fei Ma^†, Lian-Ming Gao^†, Jun-Bo Yang^†, Jie Cai^†, Matthew A. Gitzendanner, Peter W. Fritsch, Ting Zhang, Jian-Jun Jin, Chun-Xia Zeng, Hong Wang, Wen-Bin Yu, Rong Zhang, Michelle van der Bank, Richard G. Olmstead, Peter M. Hollingsworth, Mark W. Chase, Douglas E. Soltis, Pamela S. Soltis, Ting-Shuang Yi^*, De-Zhu Li^*.

BMC Biology 19(1): 232.

2020

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes.

Jian-Jun Jin^†, Wen-Bin Yu^†, Jun-Bo Yang, Yu Song, Claude W dePamphilis, Ting-Shuang Yi^*, De-Zhu Li^*.

Genome Biology 21: 241.

2020

Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae.

Rong Zhang^†, Yin-Huan Wang^†, Jian-Jun Jin^†, Gregory W Stull, Anne Bruneau, Domingos Cardoso, Luciano Paganucci De Queiroz, Michael J Moore, Shu-Dong Zhang, Si-Yun Chen, Jian Wang, De-Zhu Li^*, Ting-Shuang Yi^*.

Systematic Biology 69(4): 613–622. Full text

2020

The Loss of the Inverted Repeat in the Putranjivoid Clade of Malpighiales.

Dong-Min Jin, Susann Wicke, Lu Gan, Jun-Bo Yang^*, Jian-Jun Jin^*, Ting-Shuang Yi^*.

Frontiers in Plant Science 11: 942.

2020

Born migrators: Historical biogeography of the cosmopolitan family Cannabaceae.

Jian-Jun Jin, Mei-Qing Yang, Peter W. Fritsch, Robin van Velzen, De-Zhu Li^*, Ting-Shuang Yi^*.

Journal of Systematics and Evolution 58(4): 461–473.

2020

Plastome structural conservation and evolution in the clusioid clade of Malpighiales.

Dong-Min Jin, Jian-Jun Jin, Ting-Shuang Yi^*.

Scientific Reports 10(1): 9091.

2020

Plastid phylogenomics improve phylogenetic resolution in the Lauraceae.

Yu Song^†, Wen-Bin Yu^†, Yun-Hong Tan^†, Jian-Jun Jin, Bo Wang, Jun-Bo Yang^*, Bing Liu^*, Richard T. Corlett^*.

Journal of Systematics and Evolution 58(4): 423–439.

2019

Plastid phylogenomic insights into the evolution of Caryophyllales.

Gang Yao^†, Jian-Jun Jin^†, Hong-Tao Li, Jun-Bo Yang, Venkata Shiva Mandala, Matthew Croley, Rebecca Mostow, Norman A Douglas, Mark W Chase, Maarten J M Christenhusz, Douglas E Soltis, Pamela S Soltis, Stephen A Smith, Samuel F Brockington, Michael J Moore, Ting-Shuang Yi^*, De-Zhu Li^*.

Molecular Phylogenetics and Evolution 134: 74–86.

2019

Assembly and comparative analyses of the mitochondrial genome of Castanospermum australe (Papilionoideae, Leguminosae).

Rong Zhang, Jian-Jun Jin, Michael J. Moore, Ting-Shuang Yi^*.

Australian Systematic Botany 32(6): 484–494.

2018

Plastome characteristics of Cannabaceae.

Huanlei Zhang, Jianjun Jin, Michael J. Moore, Tingshuang Yi^*, Dezhu Li^*.

Plant Diversity 40(3): 127–137. Full text

2018

Plastid genome evolution in the early-diverging legume subfamily Cercidoideae (Fabaceae).

Yin-Huan Wang, Susann Wicke, Hong Wang, Jian-Jun Jin, Si-Yun Chen, Shu-Dong Zhang, De-Zhu Li^*, Ting-Shuang Yi^*.

Frontiers in Plant Science 9: 138.

2017

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics.

Shu-Dong Zhang^†, Jian-Jun Jin^†, Si-Yun Chen, Mark W. Chase, Douglas E. Soltis, Hong-Tao Li, Jun-Bo Yang, De-Zhu Li^*, Ting-Shuang Yi^*.

New Phytologist 214(3): 1355–1367.

2017

Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae).

Xiao-Jian Qu, Jian-Jun Jin, Shu-Miaw Chaw, De-Zhu Li^*, Ting-Shuang Yi^*.

Scientific Reports 7: 41005.

2017

Evolutionary Comparisons of the Chloroplast Genome in Lauraceae and Insights into Loss Events in the Magnoliids.

Yu Song, Wen-Bin Yu, Yunhong Tan, Bing Liu, Xin Yao, Jianjun Jin, Michael Padmanaba, Jun-Bo Yang^*, Richard T Corlett^*.

Genome Biology and Evolution 9(9): 2354–2364. Full text

Chapters & reports

2026

Preserved Botanical Science Collections Support and Facilitate Restoration.

Matthew C. Pace, Jie Cai, JianJun Jin, Robert F. C. Naczi.

In: Grover, E. C., Bartholomew, D. C., De Vitis, M., Sanderson, E. W., and Diazgranados, M. (eds.). Scaling Ecosystem Restoration Through Botanical Garden Networks, pp. 28–32. Botanic Gardens Conservation International. Technical report chapter.

I prefer writing my name as JianJun Jin; its capitalization reflects the three characters of my Chinese name. In publications, my name has also appeared as Jian-Jun Jin or Jianjun Jin, following different conventions.