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The Genomics of Cannabis and Its Close Relatives.

Kovalchuk I, Pellino M, Rigault P, van Velzen R, Ebersbach J, R Ashnest J, Mau M, Schranz ME, Alcorn J, Laprairie RB, McKay JK, Burbridge C, Schneider D, Vergara D, Kane NC, Sharbel TF.

Annu Rev Plant Biol. 2020 Mar 10. doi: 10.1146/annurev-arplant-081519-040203. [Epub ahead of print]


Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae.

Liu Z, Suarez Duran HG, Harnvanichvech Y, Stephenson MJ, Schranz ME, Nelson D, Medema MH, Osbourn A.

New Phytol. 2019 Nov 26. doi: 10.1111/nph.16338. [Epub ahead of print]


An influential meal: host plant dependent transcriptional variation in the beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae).

Breeschoten T, Ros VID, Schranz ME, Simon S.

BMC Genomics. 2019 Nov 13;20(1):845. doi: 10.1186/s12864-019-6081-7.


Genome Improvement and Genetic Map Construction for Aethionema arabicum, the First Divergent Branch in the Brassicaceae Family.

Nguyen TP, Mühlich C, Mohammadin S, van den Bergh E, Platts AE, Haas FB, Rensing SA, Schranz ME.

G3 (Bethesda). 2019 Nov 5;9(11):3521-3530. doi: 10.1534/g3.119.400657.


The alternative reality of plant mitochondrial DNA: One ring does not rule them all.

Kozik A, Rowan BA, Lavelle D, Berke L, Schranz ME, Michelmore RW, Christensen AC.

PLoS Genet. 2019 Aug 30;15(8):e1008373. doi: 10.1371/journal.pgen.1008373. eCollection 2019 Aug.


Recently duplicated sesterterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota.

Chen Q, Jiang T, Liu YX, Liu H, Zhao T, Liu Z, Gan X, Hallab A, Wang X, He J, Ma Y, Zhang F, Jin T, Schranz ME, Wang Y, Bai Y, Wang G.

Sci China Life Sci. 2019 Jul;62(7):947-958. doi: 10.1007/s11427-019-9521-2. Epub 2019 May 10.


Plastome based phylogenetics and younger crown node age in Pelargonium.

van de Kerke SJ, Shrestha B, Ruhlman TA, Weng ML, Jansen RK, Jones CS, Schlichting CD, Hosseini S, Mohammadin S, Schranz ME, Bakker FT.

Mol Phylogenet Evol. 2019 Aug;137:33-43. doi: 10.1016/j.ympev.2019.03.021. Epub 2019 Mar 26.


Association between vitamin content, plant morphology and geographical origin in a worldwide collection of the orphan crop Gynandropsis gynandra (Cleomaceae).

Sogbohossou EOD, Kortekaas D, Achigan-Dako EG, Maundu P, Stoilova T, Van Deynze A, de Vos RCH, Schranz ME.

Planta. 2019 Sep;250(3):933-947. doi: 10.1007/s00425-019-03142-1. Epub 2019 Mar 25.


Origins and geographic diversification of African rice (Oryza glaberrima).

Veltman MA, Flowers JM, van Andel TR, Schranz ME.

PLoS One. 2019 Mar 6;14(3):e0203508. doi: 10.1371/journal.pone.0203508. eCollection 2019.


Identifying and Engineering Genes for Parthenogenesis in Plants.

Vijverberg K, Ozias-Akins P, Schranz ME.

Front Plant Sci. 2019 Feb 19;10:128. doi: 10.3389/fpls.2019.00128. eCollection 2019. Review.


Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds.

Wilhelmsson PKI, Chandler JO, Fernandez-Pozo N, Graeber K, Ullrich KK, Arshad W, Khan S, Hofberger JA, Buchta K, Edger PP, Pires JC, Schranz ME, Leubner-Metzger G, Rensing SA.

BMC Genomics. 2019 Jan 30;20(1):95. doi: 10.1186/s12864-019-5452-4.


Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes.

Zhao T, Schranz ME.

Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2165-2174. doi: 10.1073/pnas.1801757116. Epub 2019 Jan 23.


Comparative analysis of repetitive sequences among species from the potato and the tomato clades.

Gaiero P, Vaio M, Peters SA, Schranz ME, de Jong H, Speranza PR.

Ann Bot. 2019 Feb 15;123(3):521-532. doi: 10.1093/aob/mcy186.


Efficient inference of homologs in large eukaryotic pan-proteomes.

Sheikhizadeh Anari S, de Ridder D, Schranz ME, Smit S.

BMC Bioinformatics. 2018 Sep 26;19(1):340. doi: 10.1186/s12859-018-2362-4.


The Functional Change and Deletion of FLC Homologs Contribute to the Evolution of Rapid Flowering in Boechera stricta.

Lee CR, Hsieh JW, Schranz ME, Mitchell-Olds T.

Front Plant Sci. 2018 Jul 31;9:1078. doi: 10.3389/fpls.2018.01078. eCollection 2018.


Lessons from Cleomaceae, the Sister of Crucifers.

Bayat S, Schranz ME, Roalson EH, Hall JC.

Trends Plant Sci. 2018 Sep;23(9):808-821. doi: 10.1016/j.tplants.2018.06.010. Epub 2018 Jul 11. Review.


DIACYLGLYCEROL ACYLTRANSFERASE1 Contributes to Freezing Tolerance.

Arisz SA, Heo JY, Koevoets IT, Zhao T, van Egmond P, Meyer AJ, Zeng W, Niu X, Wang B, Mitchell-Olds T, Schranz ME, Testerink C.

Plant Physiol. 2018 Aug;177(4):1410-1424. doi: 10.1104/pp.18.00503. Epub 2018 Jun 15.


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

van Velzen R, Holmer R, Bu F, Rutten L, van Zeijl A, Liu W, Santuari L, Cao Q, Sharma T, Shen D, Roswanjaya Y, Wardhani TAK, Kalhor MS, Jansen J, van den Hoogen J, Güngör B, Hartog M, Hontelez J, Verver J, Yang WC, Schijlen E, Repin R, Schilthuizen M, Schranz ME, Heidstra R, Miyata K, Fedorova E, Kohlen W, Bisseling T, Smit S, Geurts R.

Proc Natl Acad Sci U S A. 2018 May 15;115(20):E4700-E4709. doi: 10.1073/pnas.1721395115. Epub 2018 May 1.


New insights into the phylogeny of the TMBIM superfamily across the tree of life: Comparative genomics and synteny networks reveal independent evolution of the BI and LFG families in plants.

Gamboa-Tuz SD, Pereira-Santana A, Zhao T, Schranz ME, Castano E, Rodriguez-Zapata LC.

Mol Phylogenet Evol. 2018 Sep;126:266-278. doi: 10.1016/j.ympev.2018.04.032. Epub 2018 Apr 25.


Natural Variation within a Species for Traits Underpinning C4 Photosynthesis.

Reeves G, Singh P, Rossberg TA, Sogbohossou EOD, Schranz ME, Hibberd JM.

Plant Physiol. 2018 Jun;177(2):504-512. doi: 10.1104/pp.18.00168. Epub 2018 Apr 20.


Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses.

Edger PP, Hall JC, Harkess A, Tang M, Coombs J, Mohammadin S, Schranz ME, Xiong Z, Leebens-Mack J, Meyers BC, Sytsma KJ, Koch MA, Al-Shehbaz IA, Pires JC.

Am J Bot. 2018 Mar;105(3):463-469. doi: 10.1002/ajb2.1040. Epub 2018 Mar 25.


A roadmap for breeding orphan leafy vegetable species: a case study of Gynandropsis gynandra (Cleomaceae).

Sogbohossou EOD, Achigan-Dako EG, Maundu P, Solberg S, Deguenon EMS, Mumm RH, Hale I, Van Deynze A, Schranz ME.

Hortic Res. 2018 Jan 10;5:2. doi: 10.1038/s41438-017-0001-2. eCollection 2018.


Publisher correction: Young inversion with multiple linked QTLs under selection in a hybrid zone.

Lee CR, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Luis Goicoechea J, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, Kudrna D, Zhang J, Talag J, Golser W, Ghattas K, Schranz ME, Wing R, Lysak MA, Schmutz J, Rokhsar DS, Mitchell-Olds T.

Nat Ecol Evol. 2017 Oct;1(10):1585. doi: 10.1038/s41559-017-0310-8.


Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans.

Simon S, Sagasser S, Saccenti E, Brugler MR, Schranz ME, Hadrys H, Amato G, DeSalle R.

Sci Rep. 2017 Oct 19;7(1):13547. doi: 10.1038/s41598-017-13176-8.


Young inversion with multiple linked QTLs under selection in a hybrid zone.

Lee CR, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Goicoechea JL, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, Kudrna D, Zhang J, Talag J, Golser W, Ghattas K, Schranz ME, Wing R, Lysak MA, Schmutz J, Rokhsar DS, Mitchell-Olds T.

Nat Ecol Evol. 2017 Apr 3;1(5):119. doi: 10.1038/s41559-017-0119. Erratum in: Nat Ecol Evol. 2017 Oct;1(10 ):1585.


Anatolian origins and diversification of Aethionema, the sister lineage of the core Brassicaceae.

Mohammadin S, Peterse K, van de Kerke SJ, Chatrou LW, Dönmez AA, Mummenhoff K, Pires JC, Edger PP, Al-Shehbaz IA, Schranz ME.

Am J Bot. 2017 Jul;104(7):1042-1054. doi: 10.3732/ajb.1700091.


Flowering Locus C (FLC) Is a Potential Major Regulator of Glucosinolate Content across Developmental Stages of Aethionema arabicum (Brassicaceae).

Mohammadin S, Nguyen TP, van Weij MS, Reichelt M, Schranz ME.

Front Plant Sci. 2017 May 26;8:876. doi: 10.3389/fpls.2017.00876. eCollection 2017.


Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation.

Zhao T, Holmer R, de Bruijn S, Angenent GC, van den Burg HA, Schranz ME.

Plant Cell. 2017 Jun;29(6):1278-1292. doi: 10.1105/tpc.17.00312. Epub 2017 Jun 5.


Network approaches for plant phylogenomic synteny analysis.

Zhao T, Schranz ME.

Curr Opin Plant Biol. 2017 Apr;36:129-134. doi: 10.1016/j.pbi.2017.03.001. Epub 2017 Mar 19. Review.


Collinearity between potato (Solanum tuberosum L.) and wild relatives assessed by comparative cytogenetic mapping.

Gaiero P, van de Belt J, Vilaró F, Schranz ME, Speranza P, de Jong H.

Genome. 2017 Mar;60(3):228-240. doi: 10.1139/gen-2016-0150. Epub 2016 Nov 14.


Developmental Control and Plasticity of Fruit and Seed Dimorphism in Aethionema arabicum.

Lenser T, Graeber K, Cevik ÖS, Adigüzel N, Dönmez AA, Grosche C, Kettermann M, Mayland-Quellhorst S, Mérai Z, Mohammadin S, Nguyen TP, Rümpler F, Schulze C, Sperber K, Steinbrecher T, Wiegand N, Strnad M, Scheid OM, Rensing SA, Schranz ME, Theißen G, Mummenhoff K, Leubner-Metzger G.

Plant Physiol. 2016 Nov;172(3):1691-1707. Epub 2016 Oct 4.


Tracing ancestor rice of Suriname Maroons back to its African origin.

van Andel TR, Meyer RS, Aflitos SA, Carney JA, Veltman MA, Copetti D, Flowers JM, Havinga RM, Maat H, Purugganan MD, Wing RA, Schranz ME.

Nat Plants. 2016 Oct 3;2:16149. doi: 10.1038/nplants.2016.149.


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

Sheikhizadeh S, Schranz ME, Akdel M, de Ridder D, Smit S.

Bioinformatics. 2016 Sep 1;32(17):i487-i493. doi: 10.1093/bioinformatics/btw455.


Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana.

Fransz P, Linc G, Lee CR, Aflitos SA, Lasky JR, Toomajian C, Ali H, Peters J, van Dam P, Ji X, Kuzak M, Gerats T, Schubert I, Schneeberger K, Colot V, Martienssen R, Koornneef M, Nordborg M, Juenger TE, de Jong H, Schranz ME.

Plant J. 2016 Oct;88(2):159-178. doi: 10.1111/tpj.13262. Epub 2016 Sep 13.


Flower power and the mustard bomb: Comparative analysis of gene and genome duplications in glucosinolate biosynthetic pathway evolution in Cleomaceae and Brassicaceae.

van den Bergh E, Hofberger JA, Schranz ME.

Am J Bot. 2016 Jul;103(7):1212-22. doi: 10.3732/ajb.1500445. Epub 2016 Jun 16.


Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida.

Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D'Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus SL, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C.

Nat Plants. 2016 May 27;2(6):16074. doi: 10.1038/nplants.2016.74.


Transcriptomes of Eight Arabidopsis thaliana Accessions Reveal Core Conserved, Genotype- and Organ-Specific Responses to Flooding Stress.

van Veen H, Vashisht D, Akman M, Girke T, Mustroph A, Reinen E, Hartman S, Kooiker M, van Tienderen P, Schranz ME, Bailey-Serres J, Voesenek LA, Sasidharan R.

Plant Physiol. 2016 Oct;172(2):668-689. Epub 2016 May 15.


Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants.

Davin N, Edger PP, Hefer CA, Mizrachi E, Schuetz M, Smets E, Myburg AA, Douglas CJ, Schranz ME, Lens F.

Plant J. 2016 Jun;86(5):376-90. doi: 10.1111/tpj.13157.


Comparative paleogenomics of crucifers: ancestral genomic blocks revisited.

Lysak MA, Mandáková T, Schranz ME.

Curr Opin Plant Biol. 2016 Apr;30:108-15. doi: 10.1016/j.pbi.2016.02.001. Epub 2016 Mar 4. Review.


Whole-genome duplications followed by tandem duplications drive diversification of the protein modifier SUMO in Angiosperms.

Hammoudi V, Vlachakis G, Schranz ME, van den Burg HA.

New Phytol. 2016 Jul;211(1):172-85. doi: 10.1111/nph.13911. Epub 2016 Mar 2.


Natural variation in rosette size under salt stress conditions corresponds to developmental differences between Arabidopsis accessions and allelic variation in the LRR-KISS gene.

Julkowska MM, Klei K, Fokkens L, Haring MA, Schranz ME, Testerink C.

J Exp Bot. 2016 Apr;67(8):2127-38. doi: 10.1093/jxb/erw015. Epub 2016 Feb 11.


Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae.

Mohammadin S, Edger PP, Pires JC, Schranz ME.

BMC Plant Biol. 2015 Sep 11;15:217. doi: 10.1186/s12870-015-0603-5.


Nicotinate O-Glucosylation Is an Evolutionarily Metabolic Trait Important for Seed Germination under Stress Conditions in Arabidopsis thaliana.

Li W, Zhang F, Chang Y, Zhao T, Schranz ME, Wang G.

Plant Cell. 2015 Jul;27(7):1907-24. doi: 10.1105/tpc.15.00223. Epub 2015 Jun 26.


Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants.

Hofberger JA, Ramirez AM, Bergh Ev, Zhu X, Bouwmeester HJ, Schuurink RC, Schranz ME.

PLoS One. 2015 Jun 5;10(6):e0128808. doi: 10.1371/journal.pone.0128808. eCollection 2015.


Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes.

Mandáková T, Schranz ME, Sharbel TF, de Jong H, Lysak MA.

Plant J. 2015 Jun;82(5):785-93. doi: 10.1111/tpj.12849. Erratum in: Plant J. 2017 Apr;90(1):217.


Introgression browser: high-throughput whole-genome SNP visualization.

Aflitos SA, Sanchez-Perez G, de Ridder D, Fransz P, Schranz ME, de Jong H, Peters SA.

Plant J. 2015 Apr;82(1):174-82. doi: 10.1111/tpj.12800.


A complex interplay of tandem- and whole-genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae.

Hofberger JA, Nsibo DL, Govers F, Bouwmeester K, Schranz ME.

Genome Biol Evol. 2015 Jan 28;7(3):720-34. doi: 10.1093/gbe/evv020.


Abiotic stress QTL in lettuce crop-wild hybrids: comparing greenhouse and field experiments.

Hartman Y, Hooftman DA, Uwimana B, Schranz ME, van de Wiel CC, Smulders MJ, Visser RG, Michelmore RW, van Tienderen PH.

Ecol Evol. 2014 Jun;4(12):2395-409. doi: 10.1002/ece3.1060. Epub 2014 May 17.


Identification of quantitative trait loci and a candidate locus for freezing tolerance in controlled and outdoor environments in the overwintering crucifer Boechera stricta.

Heo JY, Feng D, Niu X, Mitchell-Olds T, Van Tienderen PH, Tomes D, Schranz ME.

Plant Cell Environ. 2014 Nov;37(11):2459-69. doi: 10.1111/pce.12365. Epub 2014 Jun 9.

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