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

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, Defeng , Purwana Roswanjaya, Yuda , Wardhani, T. , Seifi Kalhor, M. , Jansen, Joelle , van den Hoogen, D.J. , Güngör, Berivan , Hartog, M.V. , Hontelez, J. , Verver, Jan , 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) Proceedings of the National Academy of Sciences of the United States of America (2018), Volume: 115, Issue: 20 - ISSN 0027-8424 - p. E4700-E4709.
Computational pan-genomics: status, promises and challenges

Marschall, Tobias , de Ridder, D. , Sheikhizadeh Anari, S. , Smit, S. (2018) Briefings in Bioinformatics (2018), Volume: 19, Issue: 1 - ISSN 1467-5463 - p. 118-135.
Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia

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. , Purwana Roswanjaya, Yuda , Wardhani, T. , Seifi Kalhor, M. , Jansen, Joelle , van den Hoogen, D.J. , Gungor, Berivan , Hartog, M.V. , Hontelez, J. , Verver, J.W.G. , Yang, W.C. , 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. (2017)
NCBI-compliant genome submissions: tips and tricks to save time and money

Pirovano, Walter , Boetzer, Marten , Derks, M.F.L. , Smit, S. (2017) Briefings in Bioinformatics (2017), Volume: 18, Issue: 2 - ISSN 1467-5463 - p. 179-182.
Beauveria bassiana Genome sequencing and assembly

Valero Jimenez, C.A. , Faino, L. , Spring in 'T Veld, Daphne , Smit, S. , Zwaan, B.J. , van Kan, J.A.L. (2016)
Genome Sequence of Madurella mycetomatis mm55, Isolated from a Human Mycetoma Case in Sudan

Smit, S. , Derks, M.F.L. , Bervoets, Sander , Fahal, Ahmed , van Leeuwen, Willem , van Belkum, Alex , van de Sande, Wendy W.J. (2016) Genome Announcements (2016), Volume: 4, Issue: 3 - ISSN 2169-8287
PanTools: representation, storage and exploration of pan-genomic data

Sheikhizadeh Anari, S. , Schranz, M.E. , Akdel, Mehmet , de Ridder, D. , Smit, S. (2016) Bioinformatics (2016), Volume: 32, Issue: 17 - ISSN 1367-4803 - p. i487-i493.
Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta

Faddeeva-Vakhrusheva, Anna , Derks, M.F.L. , Anvar, Seyed Yahya , Agamennone, Valeria , Suring, Wouter , Smit, S. , van Straalen, Nico M. , Roelofs, Dick (2016) Genome Biology and Evolution (2016), Volume: 8, Issue: 7 - ISSN 1759-6653 - p. 2106-2117.
Wolbachia endosymbiont of Operophtera brumata strain:Ob_Wba Genome sequencing and assembly

Derks, M.F.L. , Smit, S. , Salis, L. , Schijlen, E.G.W.M. , Bossers, A. , Mateman, C. , Pijl, A.S. , de Ridder, D. , Groenen, M.A.M. , Visser, M.E. , Megens, H.J.W.C. (2015)
Operophtera brumata isolate:WM2013NL Genome sequencing and assembly

Derks, M.F.L. , Smit, S. , Salis, L. , Schijlen, E.G.W.M. , Bossers, A. , Mateman, C. , Pijl, A.S. , de Ridder, D. , Groenen, M.A.M. , Visser, M.E. , Megens, H.J.W.C. (2015)

Publications

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

Computational pan-genomics: status, promises and challenges

Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia

NCBI-compliant genome submissions: tips and tricks to save time and money

Beauveria bassiana Genome sequencing and assembly

Genome Sequence of Madurella mycetomatis mm55, Isolated from a Human Mycetoma Case in Sudan

PanTools: representation, storage and exploration of pan-genomic data

Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta

Wolbachia endosymbiont of Operophtera brumata strain:Ob_Wba Genome sequencing and assembly

Operophtera brumata isolate:WM2013NL Genome sequencing and assembly