Ghent University Academic Bibliography

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Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Lucas Prost (UGent) , Quinten Bafort (UGent) , Antoine Van de Vloet (UGent) , Fabricio De Almeida Silva (UGent) , Yunn Thet Paing (UGent) , Griet Casteleyn (UGent) , Sofie D'hondt (UGent) , Olivier De Clerck (UGent) and Yves Van de Peer (UGent)

(2025) NEW PHYTOLOGIST. 245(22). p.869-884
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doubletrouble : an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications

Fabricio De Almeida Silva (UGent) and Yves Van de Peer (UGent)

(2025) BIOINFORMATICS. 41(2).
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Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris

Si‐Jie Liu, Zhengtai Liu, Bing‐Yan Shao, Tao Li, Xinning Zhu, Ren Wang, Lei Shi, Sheng Xu, Yves Van de Peer (UGent) and Jia‐Yu Xue

(2025) PLANT JOURNAL. 121(2).
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Novel adaptive immune systems in pristine Antarctic soils

Marc W. Van Goethem, Oliver K. I. Bezuidt, Rian Pierneef, Surendra Vikram, David W. Hopkins, Thomas Aspray, Grant Hall, Stephan Woodborne, Ian D. Hogg, Trent R. Northen, et al.

(2025) SCIENTIFIC REPORTS. 15(1).
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Flavonoids and anthocyanins in seagrasses : implications for climate change adaptation and resilience

Jana Botes, Xiao Ma (UGent) , Jiyang Chang (UGent) , Yves Van de Peer (UGent) and Dave Kenneth Berger

(2025) FRONTIERS IN PLANT SCIENCE. 15.
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Water lily pond : a multiomics database for water lilies

Chengjun Zhao, Ji Zhang, Yayu Chen, Lishuang Yang, Hongliang Chen, Yufan Liang, Wenquan Wang, Shuang He, Yunqing Luo, Junyu Zhang, et al.

(2025) HORTICULTURE RESEARCH. 12(6).
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SOI : robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics

Ren-Gang Zhang, Hong-Yun Shang, Richard Ian Milne, Fabricio De Almeida Silva (UGent) , Hengchi Chen (UGent) , Min-Jie Zhou, Heng Shu, Kai-Hua Jia, Yves Van de Peer (UGent) and Yong-Peng Ma

(2025) NUCLEIC ACIDS RESEARCH. 53(7).
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Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii

Antoine Van de Vloet (UGent) , Lucas Prost Boxoen (UGent) , Quinten Bafort (UGent) , Yunn Thet Paing (UGent) , Griet Casteleyn (UGent) , Lucile Jomat, Stéphane D. Lemaire, Olivier De Clerck (UGent) and Yves Van de Peer (UGent)

(2025) NEW PHYTOLOGIST. 246(3). p.1403-1412
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Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls

Zahin Ali, Qiao Wen Tan, Peng Ken Lim, Hengchi Chen (UGent) , Lukas Pfeifer, Irene Julca, Jia Min Lee, Birgit Classen, Sophie de Vries, Jan de Vries, et al.

(2025) NATURE PLANTS. 11. p.1028-1048
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Untangling the gordian knot : the intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects

Bart Geens, Stijn Goossens, Jia Li (UGent) , Yves Van de Peer (UGent) and Jozef Vanden Broeck

(2024) MOLECULAR AND CELLULAR ENDOCRINOLOGY. 585.
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wgd v2 : a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Hengchi Chen (UGent) , Arthur Zwaenepoel and Yves Van de Peer (UGent)

(2024) BIOINFORMATICS. 40(5).
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Origin and evolution of the triploid cultivated banana genome

Xiuxiu Li, Sheng Yu, Zhihao Cheng, Xiaojun Chang, Yingzi Yun, Mengwei Jiang, Xuequn Chen, Xiaohui Wen, Hua Li, Wenjun Zhu, et al.

(2024) NATURE GENETICS. 56(1). p.136-142
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High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar

Tian-Le Shi, Kai-Hua Jia, Yu-Tao Bao, Shuai Nie, Xue-Chan Tian, Xue-Mei Yan, Zhao-Yang Chen, Zhi-Chao Li, Shi-Wei Zhao, Hai-Yao Ma, et al.

(2024) PLANT PHYSIOLOGY. 195(1). p.652-670
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The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, et al.

(2024) NATURE GENETICS. 56(4). p.721-731
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Interspecific transfer of genetic information through polyploid bridges

Felipe Kauai Pereira (UGent) , Quinten Bafort (UGent) , Frederik Mortier (UGent) , Marc Van Montagu (UGent) , Dries Bonte (UGent) and Yves Van de Peer (UGent)

(2024) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 121(21).
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Convergent and/or parallel evolution of RNA‐binding proteins in angiosperms after polyploidization

Liangyu Guo, Shuo Wang, Xi Jiao, Xiaoxue Ye, Deyin Deng, Hua Liu, Yan Li, Yves Van de Peer (UGent) and Wenwu Wu

(2024) NEW PHYTOLOGIST. 242(3). p.1377-1393
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Understanding polyploid establishment : temporary persistence or stable coexistence?

Frederik Mortier (UGent) , Quinten Bafort (UGent) , Silvija Milosavljević (UGent) , Felipe Kauai Pereira (UGent) , Lucas Prost (UGent) , Yves Van de Peer (UGent) and Dries Bonte (UGent)

(2024) OIKOS. 2024(5).
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How temperature modulates the expression of pathogenesis-related molecules of the cross-kingdom pathogen Lasiodiplodia hormozganensis

Carina Félix, Rodrigo Silva Meneses, Micael F. M. Gonçalves, Ana S. Duarte, Jesus V. Jorrín-Novo, Yves Van de Peer (UGent) , Dieter Deforce (UGent) , Filip Van Nieuwerburgh (UGent) , Artur Alves and Ana C. Esteves

(2024) SCIENCE OF THE TOTAL ENVIRONMENT. 927.
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Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

Xiao Ma (UGent) , Steffen Vanneste (UGent) , Jiyang Chang (UGent) , Luca Ambrosino, Kerrie Barry, Till Bayer, Alexander A. Bobrov, LoriBeth Boston, Justin E. Campbell, Hengchi Chen, et al.

(2024) NATURE PLANTS. 10. p.240-255
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Optimized tetraploidization strategies in tissue culture for Lolium, Festuca, and Festulolium

Marlies Peeters (UGent) , Isabelle Maryns (UGent) , An Ghesquière, Katrijn Van Laere, Yves Van de Peer (UGent) , Tom Ruttink (UGent) and Leen Leus

(2024) BIOLOGIA PLANTARUM. 68. p.70-76

Academic Bibliography

Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

doubletrouble : an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications

Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris

Novel adaptive immune systems in pristine Antarctic soils

Flavonoids and anthocyanins in seagrasses : implications for climate change adaptation and resilience

Water lily pond : a multiomics database for water lilies

SOI : robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics

Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii

Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls

Untangling the gordian knot : the intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects

wgd v2 : a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Origin and evolution of the triploid cultivated banana genome

High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Interspecific transfer of genetic information through polyploid bridges

Convergent and/or parallel evolution of RNA‐binding proteins in angiosperms after polyploidization

Understanding polyploid establishment : temporary persistence or stable coexistence?

How temperature modulates the expression of pathogenesis-related molecules of the cross-kingdom pathogen Lasiodiplodia hormozganensis

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

Optimized tetraploidization strategies in tissue culture for Lolium, Festuca, and Festulolium

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