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Items: 34

1.

Correcting palindromes in long reads after whole-genome amplification.

Warris S, Schijlen E, van de Geest H, Vegesna R, Hesselink T, Te Lintel Hekkert B, Sanchez Perez G, Medvedev P, Makova KD, de Ridder D.

BMC Genomics. 2018 Nov 6;19(1):798. doi: 10.1186/s12864-018-5164-1.

2.

The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.

Nishiyama T, Sakayama H, de Vries J, Buschmann H, Saint-Marcoux D, Ullrich KK, Haas FB, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson PKI, Janitza P, Kern R, Heyl A, Rümpler F, Villalobos LIAC, Clay JM, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington AJ, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan GV, Van Nieuwerburgh F, Deforce D, Chang C, Karol KG, Hedrich R, Ulvskov P, Glöckner G, Delwiche CF, Petrášek J, Van de Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theißen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing SA.

Cell. 2018 Jul 12;174(2):448-464.e24. doi: 10.1016/j.cell.2018.06.033.

PMID:
30007417
3.

A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.

Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F.

Nat Plants. 2018 Jul;4(7):473-484. doi: 10.1038/s41477-018-0166-1. Epub 2018 Jun 11.

PMID:
29892093
4.

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.

5.

Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis.

Zeng T, Holmer R, Hontelez J, Te Lintel-Hekkert B, Marufu L, de Zeeuw T, Wu F, Schijlen E, Bisseling T, Limpens E.

Plant J. 2018 May;94(3):411-425. doi: 10.1111/tpj.13908.

PMID:
29570877
6.

Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity.

Mommer L, Cotton TEA, Raaijmakers JM, Termorshuizen AJ, van Ruijven J, Hendriks M, van Rijssel SQ, van de Mortel JE, van der Paauw JW, Schijlen EGWM, Smit-Tiekstra AE, Berendse F, de Kroon H, Dumbrell AJ.

New Phytol. 2018 Apr;218(2):542-553. doi: 10.1111/nph.15036. Epub 2018 Feb 22.

7.

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development.

Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R, Di Pierro EA, Gouzy J, Rees DJG, Guérif P, Muranty H, Durel CE, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, Quesneville H, Weigel D, van de Weg E, Troggio M, Bucher E.

Nat Genet. 2017 Jul;49(7):1099-1106. doi: 10.1038/ng.3886. Epub 2017 Jun 5.

PMID:
28581499
8.

Corrigendum: The genome of Chenopodium quinoa.

Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B, Borm TJA, Ohyanagi H, Mineta K, Michell CT, Saber N, Kharbatia NM, Rupper RR, Sharp AR, Dally N, Boughton BA, Woo YH, Gao G, Schijlen EGWM, Guo X, Momin AA, Negrão S, Al-Babili S, Gehring C, Roessner U, Jung C, Murphy K, Arold ST, Gojobori T, van der Linden CG, van Loo EN, Jellen EN, Maughan PJ, Tester M.

Nature. 2017 May 25;545(7655):510. doi: 10.1038/nature22384. Epub 2017 May 10.

PMID:
28489823
9.

A footprint of desiccation tolerance in the genome of Xerophyta viscosa.

Costa MD, Artur MA, Maia J, Jonkheer E, Derks MF, Nijveen H, Williams B, Mundree SG, Jiménez-Gómez JM, Hesselink T, Schijlen EG, Ligterink W, Oliver MJ, Farrant JM, Hilhorst HW.

Nat Plants. 2017 Mar 27;3:17038. doi: 10.1038/nplants.2017.38.

PMID:
28346448
10.

The genome of Chenopodium quinoa.

Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B, Borm TJ, Ohyanagi H, Mineta K, Michell CT, Saber N, Kharbatia NM, Rupper RR, Sharp AR, Dally N, Boughton BA, Woo YH, Gao G, Schijlen EG, Guo X, Momin AA, Negrão S, Al-Babili S, Gehring C, Roessner U, Jung C, Murphy K, Arold ST, Gojobori T, Linden CG, van Loo EN, Jellen EN, Maughan PJ, Tester M.

Nature. 2017 Feb 16;542(7641):307-312. doi: 10.1038/nature21370. Epub 2017 Feb 8. Erratum in: Nature. 2017 May 25;545(7655):510.

PMID:
28178233
11.

Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere.

Schouten HJ, Vande Geest H, Papadimitriou S, Bemer M, Schaart JG, Smulders MJ, Perez GS, Schijlen E.

Plant Cell Rep. 2017 Mar;36(3):493-504. doi: 10.1007/s00299-017-2098-z. Epub 2017 Feb 2.

12.

Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen.

Vanheule A, Audenaert K, Warris S, van de Geest H, Schijlen E, Höfte M, De Saeger S, Haesaert G, Waalwijk C, van der Lee T.

BMC Genomics. 2016 Aug 23;17:670. doi: 10.1186/s12864-016-2941-6.

13.

A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus.

Sonnenberg AS, Gao W, Lavrijssen B, Hendrickx P, Sedaghat-Tellgerd N, Foulongne-Oriol M, Kong WS, Schijlen EG, Baars JJ, Visser RG.

Fungal Genet Biol. 2016 Aug;93:35-45. doi: 10.1016/j.fgb.2016.06.001. Epub 2016 Jun 8.

14.

Gene and transposable element methylation in great tit (Parus major) brain and blood.

Derks MF, Schachtschneider KM, Madsen O, Schijlen E, Verhoeven KJ, van Oers K.

BMC Genomics. 2016 May 4;17:332. doi: 10.1186/s12864-016-2653-y.

15.

First Complete Genome Sequence of the Dutch Veterinary Coxiella burnetii Strain NL3262, Originating from the Largest Global Q Fever Outbreak, and Draft Genome Sequence of Its Epidemiologically Linked Chronic Human Isolate NLhu3345937.

Kuley R, Smith HE, Janse I, Harders FL, Baas F, Schijlen E, Nabuurs-Franssen MH, Smits MA, Roest HI, Bossers A.

Genome Announc. 2016 Apr 21;4(2). pii: e00245-16. doi: 10.1128/genomeA.00245-16.

16.

Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry.

de Wit PJ, van der Burgt A, Ökmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE.

PLoS Genet. 2015 Dec 22;11(12):e1005775. doi: 10.1371/journal.pgen.1005775. eCollection 2015 Dec. No abstract available.

17.

Differentially expressed genes linked to natural variation in long-term memory formation in Cotesia parasitic wasps.

van Vugt JJ, Hoedjes KM, van de Geest HC, Schijlen EW, Vet LE, Smid HM.

Front Behav Neurosci. 2015 Sep 25;9:255. doi: 10.3389/fnbeh.2015.00255. eCollection 2015.

18.

The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology.

Derks MF, Smit S, Salis L, Schijlen E, Bossers A, Mateman C, Pijl AS, de Ridder D, Groenen MA, Visser ME, Megens HJ.

Genome Biol Evol. 2015 Jul 29;7(8):2321-32. doi: 10.1093/gbe/evv145.

19.

Learning-induced gene expression in the heads of two Nasonia species that differ in long-term memory formation.

Hoedjes KM, Smid HM, Schijlen EG, Vet LE, van Vugt JJ.

BMC Genomics. 2015 Mar 10;16:162. doi: 10.1186/s12864-015-1355-1.

20.

The genome of the stress-tolerant wild tomato species Solanum pennellii.

Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RC, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JK, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR.

Nat Genet. 2014 Sep;46(9):1034-8. doi: 10.1038/ng.3046. Epub 2014 Jul 27.

PMID:
25064008
21.

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing.

100 Tomato Genome Sequencing Consortium, Aflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, Finkers R, Wang J, Zhang G, Li N, Mao L, Bakker F, Dirks R, Breit T, Gravendeel B, Huits H, Struss D, Swanson-Wagner R, van Leeuwen H, van Ham RC, Fito L, Guignier L, Sevilla M, Ellul P, Ganko E, Kapur A, Reclus E, de Geus B, van de Geest H, Te Lintel Hekkert B, van Haarst J, Smits L, Koops A, Sanchez-Perez G, van Heusden AW, Visser R, Quan Z, Min J, Liao L, Wang X, Wang G, Yue Z, Yang X, Xu N, Schranz E, Smets E, Vos R, Rauwerda J, Ursem R, Schuit C, Kerns M, van den Berg J, Vriezen W, Janssen A, Datema E, Jahrman T, Moquet F, Bonnet J, Peters S.

Plant J. 2014 Oct;80(1):136-48. doi: 10.1111/tpj.12616. Epub 2014 Sep 3.

22.

A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens.

Lin YF, Severing EI, Te Lintel Hekkert B, Schijlen E, Aarts MG.

Front Plant Sci. 2014 Jun 20;5:261. doi: 10.3389/fpls.2014.00261. eCollection 2014.

23.

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry.

de Wit PJ, van der Burgt A, Ökmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE.

PLoS Genet. 2012;8(11):e1003088. doi: 10.1371/journal.pgen.1003088. Epub 2012 Nov 29. Erratum in: PLoS Genet. 2015 Dec;11(12):e1005775.

24.

Solanum lycopersicum cv. Heinz 1706 chromosome 6: distribution and abundance of genes and retrotransposable elements.

Peters SA, Datema E, Szinay D, van Staveren MJ, Schijlen EG, van Haarst JC, Hesselink T, Abma-Henkens MH, Bai Y, de Jong H, Stiekema WJ, Klein Lankhorst RM, van Ham RC.

Plant J. 2009 Jun;58(5):857-69. doi: 10.1111/j.1365-313X.2009.03822.x. Epub 2009 Feb 4.

25.

Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors.

Butelli E, Titta L, Giorgio M, Mock HP, Matros A, Peterek S, Schijlen EG, Hall RD, Bovy AG, Luo J, Martin C.

Nat Biotechnol. 2008 Nov;26(11):1301-8. doi: 10.1038/nbt.1506. Epub 2008 Oct 26.

PMID:
18953354
26.

High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6.

Szinay D, Chang SB, Khrustaleva L, Peters S, Schijlen E, Bai Y, Stiekema WJ, van Ham RC, de Jong H, Klein Lankhorst RM.

Plant J. 2008 Nov;56(4):627-37. doi: 10.1111/j.1365-313X.2008.03626.x. Epub 2008 Sep 18.

27.

RNA interference silencing of chalcone synthase, the first step in the flavonoid biosynthesis pathway, leads to parthenocarpic tomato fruits.

Schijlen EG, de Vos CH, Martens S, Jonker HH, Rosin FM, Molthoff JW, Tikunov YM, Angenent GC, van Tunen AJ, Bovy AG.

Plant Physiol. 2007 Jul;144(3):1520-30. Epub 2007 May 3.

28.

Metabolic engineering of flavonoids in tomato (Solanum lycopersicum): the potential for metabolomics.

Bovy A, Schijlen E, Hall RD.

Metabolomics. 2007;3:399-412. Epub 2007 Sep 9.

29.

Pathway engineering for healthy phytochemicals leading to the production of novel flavonoids in tomato fruit.

Schijlen E, Ric de Vos CH, Jonker H, van den Broeck H, Molthoff J, van Tunen A, Martens S, Bovy A.

Plant Biotechnol J. 2006 Jul;4(4):433-44.

30.

Transgenic flavonoid tomato intake reduces C-reactive protein in human C-reactive protein transgenic mice more than wild-type tomato.

Rein D, Schijlen E, Kooistra T, Herbers K, Verschuren L, Hall R, Sonnewald U, Bovy A, Kleemann R.

J Nutr. 2006 Sep;136(9):2331-7.

PMID:
16920850
31.

Modification of flavonoid biosynthesis in crop plants.

Schijlen EG, Ric de Vos CH, van Tunen AJ, Bovy AG.

Phytochemistry. 2004 Oct;65(19):2631-48. Review.

PMID:
15464151
32.

Effect of diets fortified with tomatoes or onions with variable quercetin-glycoside content on azoxymethane-induced aberrant crypt foci in the colon of rats.

Femia AP, Caderni G, Ianni M, Salvadori M, Schijlen E, Collins G, Bovy A, Dolara P.

Eur J Nutr. 2003 Dec;42(6):346-52.

PMID:
14673608
33.

High-flavonol tomatoes resulting from the heterologous expression of the maize transcription factor genes LC and C1.

Bovy A, de Vos R, Kemper M, Schijlen E, Almenar Pertejo M, Muir S, Collins G, Robinson S, Verhoeyen M, Hughes S, Santos-Buelga C, van Tunen A.

Plant Cell. 2002 Oct;14(10):2509-26.

34.

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