Publications
Gutiérrez-Valencia J, Zervakis P-I, Postel Z, Fracassetti M, Losvik A, Mehrabi S, Bunikis I, Soler L, Hughes PW, Désamoré A, Laenen B, Abdelaziz M, Vinnere Pettersson O, Arroyo J, Slotte T. 2024. Genetic causes and genomic consequences of breakdown of distyly in Linum trigynum. Molecular Biology and Evolution, In press.
Olmedo-Vicente E, Désamoré A, Simón-Porcar VI, Slotte T, Arroyo J. 2023. Development of microsatellite markers for sister species Linum suffruticosum and Linum tenuifolium in their overlapping ranges. Molecular Biology Reports 50:7927-7933.
Gutiérrez-Valencia J, Fracassetti M, Berdan EL, Bunikis I, Soler L, Dainat J, Kutschera VE, Losvik A, Désamoré A, Hughes PW, Foroozani A, Laenen B, Pesquet E, Abdelaziz M, Vinnere Pettersson O, Nystedt B, Brennan A, Arroyo J, Slotte T. 2022. Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level. Current Biology 32: 4360-4371. bioRxiv doi: https://doi.org/10.1101/2022.05.27.493681
Birkeland S, Slotte T, Brysting AK, Gustafsson ALS, Hvidsten TR, Brochmann C, Nowak MD. 2022. What can the cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance? Molecular Ecology 31: 4271-4285. bioRxiv doi: https://doi.org/10.1101/2021.12.04.471218
Gutiérrez-Valencia J, Slotte T. 2022. Potato genomes pave the way to crop improvement. Nature. doi: 10.1038/d41586-022-01419-2 Invited perspective.
Berdan E*, Blanckaert A*, Butlin RK, Flatt T, Slotte T, Wielstra B. 2022. Mutation accumulation opposes polymorphism: Supergenes and the curious case of balanced lethals. Philosophical Transactions B 377: 20210199
Gutiérrez-Valencia J, Fracassetti M, Horvath R, Laenen B, Désamore A, Drouzas AD, Friberg M, Kolár F, Slotte T. 2022. Genomic signatures of sexual selection on pollen-expressed genes in Arabis alpina. Molecular Biology and Evolution 39: msab349. Preprint at bioRxiv, doi: https://doi.org/10.1101/2021.09.02.457912
Horvath R, Josephs EB, Pesquet E, Stinchcombe JR, Wright SI, Scofield D, Slotte T. 2021. Selection on accessible chromatin regions in Capsella grandiflora. Molecular Biology and Evolution 12: 5563-5575.
Bohutínská M, Vlček J, Yair S, Laenen B, Konečná V, Fracassetti M, Slotte T, Kolár F. 2021. Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives. Proceedings of the National Academy of Sciences of the USA 118: e2022713118. bioRxiv preprint doi: https://doi.org/10.1101/2020.03.24.005397
Yang X, Slotte T, Dainat J, Hambäck P. 2021. Genome assemblies of three closely related leaf beetle species (Galerucella spp). G3: Genes|Genomes|Genetics, In press, doi: 10.1093/g3journal/jkab214
Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology 30: 2710-2723.
Bachmann J, Tedder A, Fracassetti M, Steige KA, Lafon-Placette C, Köhler C, Slotte T. 2021. On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae). Heredity 127: 124-134.
Gutiérrez-Valencia J, Hughes W, Berdan EL, Slotte T. 2021. The genomic architecture and evolutionary fates of supergenes. Genome Biology and Evolution, In press. Arxiv Preprint at: arXiv:2012.11508
Dziasek K, Simon L, Lafon Placette C, Laenen B, Wärdig C, Santos-González J, Slotte T, Köhler C. 2021. Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm. PLoS Genetics 17: e1009370.
Nowak M, Birkeland S, Mandáková T, Choudhury RR, Guo X, Gustafsson L, Gizaw A, Schröder-Nielsen A, Fracassetti M, Brysting A, Rieseberg L, Slotte T, Parisod C, Lysak M, Brochmann C. 2020. The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. Molecular Ecology Resources 21: 661-676.
Dong Y, Majda M, Šimura J, Horvath R, Srivastava AK, Łangowski Ł, Eldridge T, Stacey N, Slotte T, Sadanandom A, Ljung K, Smith RS, Ostergaard L. 2020. HEARTBREAK controls post-translational modification of INDEHISCENT to regulate fruit morphology in Capsella. Current Biology 30: 3880-3888.e5.
Yang X, Fors L, Slotte T, Theopold U, Binzer-Panchal M, Wheat CW, Hambäck P. 2020. Differential expression of immune genes between two closely related beetle species with different immunocompetence following attack by Asecodes parviclava. Genome Biology and Evolution 12: 522-534. https://doi.org/10.1093/gbe/evaa075
Mattila TM**, Laenen B, Horvath R, Hämälä T, Savolainen O, Slotte T**. 2019. Impact of demography on linked selection in two outcrossing Brassicaceae species. Ecology and Evolution, Early online access, https://doi.org/10.1002/ece3.5463. **Corresponding authors
Bachmann JA*, Tedder A*, Laenen B*, Fracassetti M, Désamoré A, Lafon-Placette C, Steige KA, Callot C, Marande W, Neuffer B, Bérgès H, Köhler C, Castric V, Slotte T. 2019. Genetic basis and timing of a major mating system shift in Capsella. New Phytologist, 224: 505-517 Preprint available at BioRxiv doi: https://doi.org/10.1101/425389
Parducci L, Alsos IG, Unneberg P, Pedersen MW, Han L, Lammers Y, Salonen SJ, Väliranta MM, Slotte T, Wohlfarth B. 2019. Shotgun environmental DNA, pollen and macrofossil analysis of Lateglacial lake sediments from southern Sweden. Frontiers in Ecology and Evolution, https://doi.org/10.3389/fevo.2019.00189
Koenig D, Hagmann J, Li R, Bemm F, Slotte T, Neuffer B, Wright SI, Weigel D. 2019. Long-term balancing selection drives evolution of immunity genes in Capsella. eLife 8:e43606. BioRxiv doi: https://doi.org/10.1101/477612 (Preprint posted November 27, 2018)
Monnahan P*, Kolár F*, Baduel P*, Sailer C, Koch J, Horvath R, Laenen B, Schmickl R, Paajanen P, Srámková G, Bohutínska M, Arnold B, Weisman CM, Marhold K, Slotte T, Bomblies K, Yant L. 2019. Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nature Ecology and Evolution, https://doi.org/10.1038/s41559-019-0807-4 BioRxiv doi: https://doi.org/10.1101/411041 *These authors contributed equally.
Horvath R, Laenen B, Takuno S, Slotte T. 2019. Single-cell expression noise and gene-body methylation in Arabidopsis thaliana. Heredity, Advance Online Access.
Mattila TM, Laenen B, Slotte T. 2018. Population genomics of transitions to selfing in Brassicaceae model systems. Book chapter in: “Statistical Population Genomics” (Dutheil JY, Ed), Springer, In press. Arxiv preprint. http://arxiv.org/abs/1809.04872 (September 13, 2018, revised January 7, 2019)
Lafon-Placette C, Hatorangan MR, Steige KA, Cornille A, Lascoux M, Slotte T, Köhler C. 2018. Paternally expressed imprinted genes associate with hybridization barriers in Capsella. Nature Plants 4:352-357.
Plue J, Kimberley A, Slotte T. 2018. Interspecific variation in ploidy as a key plant trait outlining local extinction risks and community patterns in fragmented landscapes. Functional Ecology 32: 2095-2116 doi/10.1111/1365-2435.13127
Bachmann J*, Tedder A*, Laenen B, Steige K, Slotte T. 2018. Targeted long-read sequencing of a locus under long-term balancing selection in Capsella. G3: Genes | Genomes | Genetics 8:1327-1333. *These authors contributed equally.
Laenen B*, Tedder A*, Nowak MD, Toräng P, Wunder J, Wötzel S, Steige KA, Kourmpetis Y, Odong T, Drouzas AD, Bink M, Ågren J, Coupland G and Slotte T. 2018. Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina. Proceedings of the National Academy of Sciences of the USA 115:816-821. https://doi:10.1073/pnas.1707492115 . bioRxiv doi: https://doi.org/10.1101/127209 *These authors contributed equally.
Ahmed E*, Parducci L*, Unneberg P, Ågren R, Schenk F, Rattray JE, Han L, Muschitiello F, Pedersen MW, Smittenberg RH, Yamoah KA, Slotte T, Wohlfarth B. 2018. Archaeal community changes in Lateglacial lake sediments: evidence from ancient DNA. Quaternary Science Reviews 181:19-29 *These authors contributed equally.
Horvath R, Slotte T. 2017. The role of small RNA-based epigenetic silencing for purifying selection on transposable elements in Capsella grandiflora. Genome Biology and Evolution 9: 2911-2920 https://doi.org/10.1093/gbe/evx206
Steige KA, Laenen B, Reimegård J, Scofield DG, Slotte T. 2017. Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora. Proceedings of the National Academy of Sciences of the USA. 114:1087-1092. *These authors contributed equally.
Hatorangan MR, Laenen B, Steige KA, Slotte T, Köhler C. 2016. Rapid evolution of genomic imprinting in two species of the Brassicaceae. The Plant Cell. 28:1815-1827
Steige KA, Slotte T. 2016. Genomic legacies of the progenitors and the evolutionary consequences of allopolyploidy. Current Opinion in Plant Biology 30:88-93
Rebernig CA, Lafon-Placette C, Hatorangan MR, Slotte T, Köhler C. 2015. Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus are Established in the Endosperm. PLoS Genetics 11: e1005295.
Steige KA, Reimegård J, Koenig D, Scofield DG, Slotte T. 2015. Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella. Molecular Biology and Evolution 32:2501-2514. BioRxiv preprint.
Douglas GM*, Gos G*, Steige KA*, Salcedo A, Holm K, Josephs EB, Arunkumar R, Ågren JA, Hazzouri K, Wang W, Platts AE, Williamson RJ, Neuffer B, Lascoux M**, Slotte T**, Wright SI**. 2015. Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris. Proceedings of the National Academy of Sciences of the USA. 112:2806-2811 BioRxiv preprint. *These authors contributed equally, **Corresponding authors
Slotte T. 2014. The impact of linked selection on plant genomic variation. Briefings in Functional Genomics. 13:268-275.
Brandvain Y, Slotte T, Hazzouri K, Wright SI, Coop G. 2013. Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella. PLoS Genetics. 9:e1003754.
Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F, Guo Y, Steige K, Platts AE, Escobar JS, Newman LK, Wang W, Mandakova T, Vello E, Smith SM, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu TT, Blanchette M, Clark RM, Quesneville H, Nordborg M, Gaut BS, Lysak MA, Jenkins J, Grimwood J, Prochnick S, Shu S, Rokhsar D, Schmutz J, Weigel D, Wright SI. 2013. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature Genetics 45:831-835.
Wright SI, Kalisz S, Slotte T. 2013. Evolutionary consequences of self-fertilization in plants. Proceedings of the Royal Academy of Sciences Series B Biological Sciences 280:20130133. doi: 10.1098/rspb.2013.0133
Gos G, Slotte T, Wright SI. Signatures of balancing selection are maintained at disease resistance loci following mating system evolution and a population bottleneck in the genus Capsella. BMC Evolutionary Biology 12:152.
St. Onge KR, Foxe JP, Li J, Li H, Holm K, Corcoran P, Slotte T, Lascoux M, Wright SI. 2012. Coalescent-based analysis distinguishes between allo- and autopolyploid origin in Shepherd’s Purse (Capsella bursa-pastoris). Molecular Biology and Evolution 29:1721-1733.
Slotte T*, Hazzouri KM*, Stern DL, Andolfatto P, Wright SI. 2012. Genetic architecture and adaptive significance of the selfing syndrome in Capsella. Evolution 66:1360-1374.
Slotte T*, Bataillon T*, Hansen TT, St. Onge KR, Wright SI, Schierup MH. 2011. Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biology and Evolution 3:1210-1219
Qiu S*, Zeng K*, Slotte T, Wright SI, Charlesworth D. 2011. Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species. Genome Biology and Evolution 3:868-880
St. Onge KR, Källman T, Slotte T, Lascoux M, Palmé AE. 2011. Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems. Molecular Ecology 20(16):3306-3320 doi:10.1111/j.1365-294X.2011.05189.x
Slotte T, Foxe JP, Hazzouri KH, Wright SI. 2010. Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Molecular Biology and Evolution 27(8): 1813-1821 doi:10.1093/molbev/msq062
Slotte T, Huang H-R, Holm K, Ceplitis A, St. Onge K, Chen J, Lagercrantz U, Lascoux M. 2009. Splicing variation at a FLOWERING LOCUS C homoeolog is associated with flowering time variation in the tetraploid Capsella bursa-pastoris. Genetics 183: 337-345 doi: 10.1534/genetics.109.103705
Foxe JP*, Slotte T*, Stahl EA, Neuffer B, Hurka H, Wright SI. 2009. Recent speciation associated with the evolution of selfing in Capsella. Proceedings of the National Academy of Sciences USA 106(13): 5241-5245 *Joint first authorship. Evaluated in Faculty of 1000
Guo Y-L*, Bechsgaard JS*, Slotte T, Neuffer B, Lascoux M, Weigel D, Schierup MH. 2009. Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck. Proceedings of the National Academy of Sciences USA 106(13): 5246-5251 *Joint first authorship. Evaluated in Faculty of 1000
Slotte T, Huang H, Lascoux M, Ceplitis A. 2008. Polyploid speciation did not confer instant reproductive isolation in Capsella. Molecular Biology and Evolution 25(7): 1478-1481
Slotte T, Holm K, McIntyre LM, Lagercrantz U, Lascoux M. 2007. Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae). Plant Physiology 145(1): 160-173
Slotte T, Ceplitis A, Neuffer B, Hurka H, Lascoux M. 2006. Intrageneric phylogeny of Capsella (Brassicaceae) and the origin of the tetraploid C. bursa-pastoris based on chloroplast and nuclear DNA sequences. American Journal of Botany 93(11): 1714-1724
*These authors contributed equally.
Preprints
Gutiérrez-Valencia J, Zervakis P-I, Postel Z, Fracassetti M, Losvik A, Mehrabi S, Bunikis I, Soler L, Hughes PW, Désamoré A, Laenen B, Abdelaziz M, Vinnere Pettersson O, Arroyo J, Slotte T. 2023. Genomic analyses elucidate the causes and consequences of breakdown of distyly in Linum trigynum. bioRxiv preprint. doi: https://www.biorxiv.org/content/10.1101/2023.11.16.567348v1
Yang, X, Wheat C, Slotte T, Hambäck P. 2022. Lineage-specific targets of positive selection in three leaf beetles with different defence capacity against a parasitic wasp. Authorea preprint. DOI: 10.22541/au.166754711.16782535/v1
Slotte Lab 