Comparative (pan)genomics

We believe pangenomics is the future of comparative genomics, which aims to understand the content, organization and evolution of genomes, and explain genotype-phenotype relationships. Motivated by large sequencing projects and a desire to link genomic variation to phenotypic variation, my team works on the transition from reference-based approaches to pangenomic approaches for comparative genomics.

We develop novel methods for pangenomics and apply them across the tree of life, with a focus on plants and plant pathogens. Our software:

PanTools
PanUtils
PanVA

Publications

Lactuca super-pangenome reduces bias towards reference genes in lettuce research

van Workum, F.J.M. , Mehrem, Sarah L. , Snoek, L.B. , Alderkamp, M.C. , Lapin, D.N. , Mulder, Flip F.M. , Van Den Ackerveken, Guido , de Ridder, D. , Schranz, M.E. , Smit, S. (2024)
Picochlorum sp. BPE23 genome assembly

Barten, R.J.P. , van Workum, F.J.M. , de Bakker, E. , Risse, J.E. , Kleisman, Michelle , Correia Navalho, S.A. , Smit, S. , Wijffels, R.H. , Nijveen, H. , Barbosa, M.J. (2022)
Visual Exploration of Genetic Sequence Variants in Pangenomes

van den Brandt, A. , Jonkheer, E.M. , van Workum, F.J.M. , Smit, S. , Vilanova, A. (2022)
PanTools v3: functional annotation, classification and phylogenomics

Jonkheer, E.M. , van Workum, F.J.M. , Sheikhizadeh Anari, S. , Brankovics, B. , de Haan, J.R. , Berke, Lidija , van der Lee, T.A.J. , de Ridder, D. , Smit, S. (2022) Bioinformatics (2022), Volume: 38, Issue: 18 - ISSN 1367-4803 - p. 4403-4405.
Genetic mechanisms underlying increased microalgal thermotolerance, maximal growth rate, and yield on light following adaptive laboratory evolution

Barten, R.J.P. , van Workum, F.J.M. , de Bakker, E. , Risse, J.E. , Kleisman, Michelle , Correia Navalho, S.A. , Smit, S. , Wijffels, R.H. , Nijveen, H. , Barbosa, M.J. (2022) BMC Biology (2022), Volume: 20 - ISSN 1741-7007
PanTools

Nijveen, H. , Smit, S. , Medema, M.H. , de Ridder, D. , van Dijk, A.D.J. , Jonkheer, E.M. , van der Hooft, J.J.J. , van Lankveld, T. , Moed, M. , van Workum, F.J.M. (2019) Wageningen: Wageningen University & Research
Hecaton

Wijfjes, R. , Smit, S. (2019) Wageningen: Wageningen University & Research
Integrative pangenome analysis of the Pectobacterium genus

Jonkheer, Eef , Brankovics, Balázs , Houwers, I.M. , van der Wolf, J.M. , Bonants, P.J.M. , Vreeburg, R.A.M. , Sheikhizadeh Anari, S. , de Ridder, D. , Smit, S. , van der Lee, T.A.J. (2019)
Pangenome analysis and its application on Pectobacterium

Jonkheer, Eef , Smit, S. , de Ridder, D. , Brankovics, Balázs , Houwers, I.M. , van der Wolf, J.M. , Bonants, P.J.M. , Vreeburg, R.A.M. , van der Lee, T.A.J. (2018)
Data from: Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

van Velzen, R. , Holmer, R. , Bu, F. , Rutten, L.J.J. , van Zeijl, A.L. , Liu, W. , Santuari, L. , Cao, Q. , Sharma, Trupti , Shen, D. , Roswanjaya, Yuda , Wardhani, T. , Seifi Kalhor, M. , Jansen, Joelle , van den Hoogen, D.J. , Gungor, Berivan , Hartog, M.V. , Hontelez, Jan , Verver, J.W.G. , Yang, Wei-Cai , Schijlen, E.G.W.M. , Repin, Rimi , Schilthuizen, M. , Schranz, M.E. , Heidstra, R. , Miyata, Kana , Fedorova, E. , Kohlen, W. , Bisseling, A.H.J. , Smit, S. , Geurts, R. (2018)

Publications

Lactuca super-pangenome reduces bias towards reference genes in lettuce research

Picochlorum sp. BPE23 genome assembly

Visual Exploration of Genetic Sequence Variants in Pangenomes

PanTools v3: functional annotation, classification and phylogenomics

Genetic mechanisms underlying increased microalgal thermotolerance, maximal growth rate, and yield on light following adaptive laboratory evolution

PanTools

Hecaton

Integrative pangenome analysis of the Pectobacterium genus

Pangenome analysis and its application on Pectobacterium

Data from: Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses