Publications

Journal publications

18. Sander A. Peters and Charles J. Underwood. 2022. “Technology-driven approaches for meiosis research in tomato and wild relatives.” Plant Reproduction (Online in advance) https://doi.org/10.1007/s00497-022-00450-7

17. Willem M. J. van Rengs, Maximilian H. W. Schmidt, Sieglinde Effgen, Duyen Bao Le, Yazhong Wang, Mohd Waznul Adly Mohd Zaidan, Bruno Huettel, Henk J. Schouten, Björn Usadel, and Charles J. Underwood. 2022. “A Chromosome Scale Tomato Genome Built from Complementary PacBio and Nanopore Sequences Alone Reveals Extensive Linkage Drag during Breeding.” The Plant Journal 110(2) 572-588.

16. Charles J. Underwood and Raphael Mercier. 2022. “Engineering Apomixis: Clonal Seeds Approaching the Fields.” Annual Review of Plant Biology 73:201-225.

15. Charles J. Underwood, Kitty Vijverberg, Diana Rigola, Shunsuke Okamoto, Carla Oplaat, Rik Op Den Camp, Tatyana Radoeva, Stephen E. Schauer, Joke Fierens, Kim Jansen, Sandra Mansveld, Marco Busscher, Wei Xiong, Erwin Datema, Koen Nijbroek, Evert-Jan Blom, Ross A. Bicknell, Andrew Catanach, Sylvia K. Erasmuson, Christopher Winefield, Arjen J. van Tunen, Marcel Prins, Michael E. Schranz, and Peter J. van Dijk. 2022. “A PARTHENOGENESIS Allele from Apomictic Dandelion Can Induce Egg Cell Division without Fertilization in Lettuce.” Nature Genetics 54:84-93. https://doi.org/10.1038/s41588-021-00984-y

14. Longfei Zhu, Nadia Fernández-Jiménez, Maja Szymanska-Lejman, Alexandre Pelé, Charles J. Underwood, Heïdi Serra, Christophe Lambing, Julia Dluzewska, Tomasz Bieluszewski, Mónica Pradillo, Ian R. Henderson, and Piotr A. Ziolkowski. 2021. “Natural Variation Identifies SNI1, the SMC5/6 Component, as a Modifier of Meiotic Crossover in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America 118(33).

13. Rosanna Petrella, Mara Cucinotta, Marta A. Mendes, Charles J. Underwood, and Lucia Colombo. 2021. “The Emerging Role of Small RNAs in Ovule Development, a Kind of Magic.” Plant Reproduction 34(4):335–51.

12. Yazhong Wang, Willem M. J. Van Rengs, Mohd Waznul Adly Mohd Zaidan, and Charles J. Underwood. 2021. “Meiosis in Crops: From Genes to Genomes.” Journal of Experimental Botany 72(18):6091–6109.

11. Charles J. Underwood and Kyuha Choi. 2019. “Heterogeneous Transposable Elements as Silencers, Enhancers and Targets of Meiotic Recombination.” Chromosoma 128(3):279–96.

10. Charles J. Underwood, Kyuha Choi, Christophe Lambing, Xiaohui Zhao, Heïdi Serra, Filipe Borges, Joe Simorowski, Evan Ernst, Yannick Jacob, Ian R. Henderson, and Robert A. Martienssen. 2018. “Epigenetic Activation of Meiotic Recombination near Arabidopsis Thaliana Centromeres via Loss of H3K9me2 and Non-CG DNA Methylation.” Genome Research 28(4):519–31.

9. Kyuha Choi, Xiaohui Zhao, Andrew J. Tock, Christophe Lambing, Charles J. Underwood, Thomas J. Hardcastle, Heïdi Serra, Juhyun Kim, Hyun Seob Cho, Jaeil Kim, Piotr A. Ziolkowski, Nataliya E. Yelina, Ildoo Hwang, Robert A. Martienssen, and Ian R. Henderson. 2018. “Nucleosomes and DNA Methylation Shape Meiotic DSB Frequency in Arabidopsis Thaliana Transposons and Gene Regulatory Regions.” Genome Research 28(4):532–46.

8. Heïdi Serra, Christophe Lambing, Catherine H. Griffin, Stephanie D. Topp, Divyashree C. Nageswaran, Charles J. Underwood, Piotr A. Ziolkowski, Mathilde Séguéla-Arnaud, Joiselle B. Fernandes, Raphaël Mercier, and Ian R. Henderson. 2018. “Massive Crossover Elevation via Combination of HEI10 and Recq4a Recq4b during Arabidopsis Meiosis.” Proceedings of the National Academy of Sciences 115(10):2437–42.

7. Gregory W. Vurture, Fritz J. Sedlazeck, Maria Nattestad, Charles J. Underwood, Han Fang, James Gurtowski, and Michael C. Schatz. 2017. “GenomeScope: Fast Reference-Free Genome Profiling from Short Reads.” Bioinformatics.

6. Charles J. Underwood, Ian R. Henderson, and Robert A. Martienssen. 2017. “Genetic and Epigenetic Variation of Transposable Elements in Arabidopsis.” Current Opinion in Plant Biology 36:135–41.

5. Piotr A. Ziolkowski*, Charles J. Underwood*, Christophe Lambing, Marina Martinez-Garcia, Emma J. Lawrence, Liliana Ziolkowska, Catherine Griffin, Kyuha Choi, F. Chris H. Franklin, Robert A. Martienssen, and Ian R. Henderson. 2017. “Natural Variation and Dosage of the HEI10 Meiotic E3 Ligase Control Arabidopsis Crossover Recombination.” Genes & Development 31(3):306–17. *co-first author.

4. Kyuha Choi, Carsten Reinhard, Heïdi Serra, Piotr A. Ziolkowski, Charles J. Underwood, Xiaohui Zhao, Thomas J. Hardcastle, Nataliya E. Yelina, Catherine Griffin, Matthew Jackson, Christine Mézard, Gil McVean, Gregory P. Copenhaver, and Ian R. Henderson. 2016. “Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes.” PLOS Genetics 12(7):e1006179.

3. Kyuha Choi, Juhyun Kim, Sebastian Y. Müller, Mijin Oh, Charles Underwood, Ian Henderson, and Ilha Lee. 2016. “Regulation of MicroRNA-Mediated Developmental Changes by the SWR1 Chromatin Remodeling Complex.” Plant Physiology 171(2):1128–43.

2. Charles J. Underwood and Robert A. Martienssen. 2015. “Argonautes Team up to Silence Transposable Elements in Arabidopsis.” The EMBO Journal 34(5):579–80.

1. Yannick Jacob, Elisa Bergamin, Mark T. A. Donoghue, Vanessa Mongeon, Chantal LeBlanc, Philipp Voigt, Charles J. Underwood, Joseph S. Brunzelle, Scott D. Michaels, Danny Reinberg, Jean-François Couture, and Robert A. Martienssen. 2014. “Selective Methylation of Histone H3 Variant H3.1 Regulates Heterochromatin Replication.” Science (New York, N.Y.) 343(6176):1249–53.

 

Pre-prints

4. Willem M. J. van Rengs, Maximilian H. W. Schmidt, Sieglinde Effgen, Yazhong Wang, Mohd Waznul Adly Mohd Zaidan, Bruno Huettel, Henk J. Schouten, Björn Usadel, and Charles J. Underwood. 2021. “A Gap-Free Tomato Genome Built from Complementary PacBio and Nanopore Long DNA Sequences Reveals Extensive Linkage Drag during Breeding.” BioRxiv 456472.

3. Kyuha Choi, Xiaohui Zhao, Christophe Lambing, Charles J. Underwood, Thomas J. Hardcastle, Heidi Serra, Andrew J. Tock, Piotr A. Ziolkowski, Nataliya E. Yelina, Robert A. Martienssen, and Ian R. Henderson. 2017. “Nucleosomes and DNA Methylation Shape Meiotic DSB Frequency in Arabidopsis Transposons and Gene Regulatory Regions.” BioRxiv 160911.

2. Charles J. Underwood, Kyuha Choi, Christophe Lambing, Xiaohui Zhao, Heidi Serra, Filipe Borges, Joe Simorowski, Evan Ernst, Yannick Jacob, Ian R. Henderson, and Robert A. Martienssen. 2017. “Epigenetic Activation of Meiotic Recombination in Arabidopsis Centromeres via Loss of H3K9me2 and Non-CG DNA Methylation.” BioRxiv 160929.

1. Gregory W. Vurture, Fritz J. Sedlazeck, Maria Nattestad, Charles J. Underwood, Han Fang, James Gurtowski, and Michael Schatz. 2017. “GenomeScope: Fast Reference-Free Genome Profiling from Short Reads.” BioRxiv 075978

 

Book chapters

1.     Peter J. van Dijk and Charles J. Underwood. 2018. “Sexual Reproduction vs Unisexual; Asexual Reproduction, Plants.” Encyclopedia of Reproduction (Elsevier).

 

Published patent applications

3. Charles J. Underwood, Diana Rigola, Peter J. van Dijk, Rik H. M. Op den Camp, Michael E. Schranz and Catharina A. Vijverberg. “Gene for Parthenogenesis.” WO2020239984.

2. Charles J. Underwood, Ian R. Henderson and Robert A. Martienssen. “Control of meiotic crossover in maize.” WO2018005752.

1. Piotr A. Ziolkowski, Charles J. Underwood, Robert A. Martienssen and Ian R. Henderson. “Methods to increase meiotic crossover frequency in plants.” WO2018104724.