Hong Ma

Huck Chair in Plant Reproductive Development and Evolution; Professor of Biology

Hong Ma

Research Summary

Plant development under favorable and stressful conditions; phylogeny and evolutionary biology of plant groups containing major crops and ecologically important species.

Huck Graduate Students

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Publication Tags

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Genes Phylogeny Genome Magnoliopsida Angiosperms Gene Rosaceae Transcriptome Radiation History Polyploidy Angiospermae Gene Duplication Arabidopsis Poaceae Transcription Factors Malus Datasets Brassicaceae Fruit Alchemilla Climate Droughts Angiosperm Divergence

Most Recent Publications

Preferential retention of the slowly evolving gene in pairs of duplicates in angiosperm genomes

Lin‐Bo Wang, Hong Ma, Juan Lin, Journal of Systematics and Evolution

Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae

Lei Zhao, Ying Yang, Xiao Qu, Hong Ma, Yi Hu, Hong Li, Ting Yi, De Li, 2023, Annals of botany on p. 199-214

Telomere-to-telomere genome assembly of bitter melon (<i>Momordica charantia</i> L. var. <i>abbreviata</i> Ser.) reveals fruit development, composition and ripening genetic characteristics

Anzhen Fu, Yanyan Zheng, Jing Guo, Donald Grierson, Xiaoyan Zhao, Changlong Wen, Ye Liu, Jian Li, Xuewen Zhang, Ying Yu, Hong Ma, Qing Wang, Jinhua Zuo, 2023, Horticulture Research

Tree2GD: a phylogenomic method to detect large-scale gene duplication events

Duoyuan Chen, Taikui Zhang, Yamao Chen, Hong Ma, Ji Qi, 2022, Bioinformatics on p. 5317-5321

DNA polymerase epsilon binds histone H3.1-H4 and recruits MORC1 to mediate meiotic heterochromatin condensation

Cong Wang, Jiyue Huang, Yingping Li, Jun Zhang, Chengpeng He, Tianyang Li, Danhua Jiang, Aiwu Dong, Hong Ma, Gregory P. Copenhaver, Yingxiang Wang, 2022, Proceedings of the National Academy of Sciences of the United States of America

Preferential retention of the slowly evolving gene in pairs of duplicates in angiosperm genomes

Lin Bo Wang, Hong Ma, Juan Lin, 2022, Journal of Systematics and Evolution on p. 848-858

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Bin Bin Liu, Chen Ren, Myounghai Kwak, Richard G.J. Hodel, Chao Xu, Jian He, Wen Bin Zhou, Chien Hsun Huang, Hong Ma, Guan Ze Qian, De Yuan Hong, Jun Wen, 2022, Journal of Integrative Plant Biology on p. 1020-1043

A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C<sub>4</sub> photosynthesis

Weichen Huang, Lin Zhang, J. Travis Columbus, Yi Hu, Yiyong Zhao, Lin Tang, Zhenhua Guo, Wenli Chen, Michael McKain, Madelaine Bartlett, Chien Hsun Huang, De Zhu Li, Song Ge, Hong Ma, 2022, Molecular Plant on p. 755-777

Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution

Lin Zhang, Xinxin Zhu, Yiyong Zhao, Jing Guo, Taikui Zhang, Weichen Huang, Jie Huang, Yi Hu, Chien Hsun Huang, Hong Ma, 2022, Molecular Biology and Evolution

Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)

Diego F. Morales-Briones, Berit Gehrke, Chien Hsun Huang, Aaron Liston, Hong Ma, Hannah E. Marx, David C. Tank, Ya Yang, 2022, Systematic Biology on p. 190-207

Most-Cited Papers

The Amborella genome and the evolution of flowering plants

Claude W. DePamphilis, Jeffrey D. Palmer, Steve Rounsley, David Sankoff, Stephan C. Schuster, Jetty S.S. Ammiraju, W. Bradley Barbazuk, Srikar Chamala, Andre S. Chanderbali, Ronald Determann, Ma Hong, Paula Ralph, Jason Talag, Lynn Tomsho, Brandon Walts, Stefan Wanke, Rod A. Wing, Tien Hao Chang, Tianying Lan, Douglas E. Soltis, Siwaret Arikit, Michael J. Axtell, Saravanaraj Ayyampalayam, James M. Burnette, Emanuele De Paoli, Nina P. Farrell, Alex Harkess, Yuannian Jiao, James Leebens-Mack, Kun Liu, Wenbin Mei, Blake C. Meyers, Saima Shahid, Eric Wafula, Susan R. Wessler, Jixian Zhai, Xiaoyu Zhang, Victor A. Albert, Lorenzo Carretero-Paulet, Eric Lyons, Haibao Tang, Chunfang Zheng, Naomi S. Altman, Feng Chen, Jian Qun Chen, Vincent Chiang, Joshua P. Der, Bruno Fogliani, Chunce Guo, Jesper Harholt, Claudette Job, Dominique Job, Sangtae Kim, Hongzhi Kong, Guanglin Li, N. Li, Jie Liu, Jongsun Park, Xinshuai Qi, Loïc Rajjou, Valérie Burtet-Sarramegna, Ron Sederoff, Ying Hsuan Sun, Peter Ulvskov, Matthieu Villegente, Jia Yu Xue, Ting Feng Yeh, Xianxian Yu, Juan J. Acosta, Riva A. Bruenn, Alexandre De Kochko, Luis R. Herrera-Estrella, Enrique Ibarra-Laclette, Matias Kirst, Solon P. Pissis, Valérie Poncet, Pamela S. Soltis, 2013, Science

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

Liping Zeng, Qiang Zhang, Renran Sun, Hongzhi Kong, Ning Zhang, Hong Ma, 2014, Nature Communications

Evolution of rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication

Yezi Xiang, Chien Hsun Huang, Yi Hu, Jun Wen, Shisheng Li, Tingshuang Yi, Hongyi Chen, Jun Xiang, Hong Ma, 2017, Molecular Biology and Evolution on p. 262-281

Resolution of brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution

Chien Hsun Huang, Renran Sun, Yi Hu, Liping Zeng, Ning Zhang, Liming Cai, Qiang Zhang, Marcus A. Koch, Ihsan Al-Shehbaz, Patrick P. Edger, J. Chris Pires, Dun Yan Tan, Yang Zhong, Hong Ma, 2016, Molecular Biology and Evolution on p. 394-412

RNA-seq analyses of multiple meristems of soybean: Novel and alternative transcripts, evolutionary and functional implications

Lei Wang, Chenlong Cao, Qibin Ma, Qiaoying Zeng, Haifeng Wang, Zhihao Cheng, Genfeng Zhu, Ji Qi, Hong Ma, Hai Nian, Yingxiang Wang, 2014, BMC Plant Biology

The water lily genome and the early evolution of flowering plants

Liangsheng Zhang, Fei Chen, Xingtan Zhang, Zhen Li, Yiyong Zhao, Rolf Lohaus, Xiaojun Chang, Wei Dong, Simon Y.W. Ho, Xing Liu, Aixia Song, Junhao Chen, Wenlei Guo, Zhengjia Wang, Yingyu Zhuang, Haifeng Wang, Xuequn Chen, Juan Hu, Yanhui Liu, Yuan Qin, Kai Wang, Shanshan Dong, Yang Liu, Shouzhou Zhang, Xianxian Yu, Qian Wu, Liangsheng Wang, Xueqing Yan, Yuannian Jiao, Hongzhi Kong, Xiaofan Zhou, Cuiwei Yu, Yuchu Chen, Fan Li, Jihua Wang, Wei Chen, Xinlu Chen, Qidong Jia, Chi Zhang, Yifan Jiang, Wanbo Zhang, Guanhua Liu, Jianyu Fu, Feng Chen, Hong Ma, Yves Van de Peer, Haibao Tang, 2020, Nature on p. 79-84

The NAC family transcription factor OsNAP confers abiotic stress response through the ABA pathway

Xu Chen, Yaofeng Wang, Bo Lv, Jie Li, Liqiong Luo, Songchong Lu, Xuan Zhang, Hong Ma, Feng Ming, 2014, Plant and Cell Physiology on p. 604-619

Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

Ren Ren, Haifeng Wang, Chunce Guo, Ning Zhang, Liping Zeng, Yamao Chen, Hong Ma, Ji Qi, 2018, Molecular Plant on p. 414-428

Flower development under drought stress: Morphological and transcriptomic analyses reveal acute responses and long-term acclimation in Arabidopsis

Zhao Su, Xuan Ma, Huihong Guo, Noor Liyana Sukiran, Bin Guo, Sarah M. Assmann, Hong Ma, 2013, Plant Cell on p. 3785-3807

The hornwort genome and early land plant evolution

Jian Zhang, Xin Xing Fu, Rui Qi Li, Xiang Zhao, Yang Liu, Ming He Li, Arthur Zwaenepoel, Hong Ma, Bernard Goffinet, Yan Long Guan, Jia Yu Xue, Yi Ying Liao, Qing Feng Wang, Qing Hua Wang, Jie Yu Wang, Guo Qiang Zhang, Zhi Wen Wang, Yu Jia, Mei Zhi Wang, Shan Shan Dong, Jian Fen Yang, Yuan Nian Jiao, Ya Long Guo, Hong Zhi Kong, An Ming Lu, Huan Ming Yang, Shou Zhou Zhang, Yves Van de Peer, Zhong Jian Liu, Zhi Duan Chen, 2020, Nature Plants on p. 107-118

News Articles Featuring Hong Ma

May 23, 2023

Orchids’ ability to grow on other plants independently evolved multiple times

The most extensive study of the genetic relationships among orchids to date reveals that the flower’s ability to grow on other plants evolved independently multiple times.

Full Article

Mar 10, 2022

How grasses like wheat can grow in the cold

A new, large-scale analysis of the relationships among members of the largest subfamily of grasses, which includes wheat and barley, reveals gene-duplication events that contributed to the adaptation of the plants to cooler temperatures.

Full Article

Mar 01, 2022

A new molecular family tree of grasses

The evolutionary relationships among grasses — including important crop plants like wheat, rice, corn, and sugarcane — have been clarified in a new molecular study of the grass family tree. Having a clear picture of the relationships among the grasses can help understanding of how important crop traits like seed size or disease resistance evolves and eventually could inform manipulation of these traits to increase crop yields.

Full Article

Jan 03, 2020

Water lily genome expands picture of the early evolution of flowering plants

The newly reported genome sequence of a water lily sheds light on the early evolution of angiosperms, the group of all flowering plants. An international team of researchers, including scientists at Penn State, used high-throughput next-generation sequencing technology to read out the water lily’s (Nymphaea colorata) genome and transcriptome — the set of all genes expressed as RNAs.

Full Article