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Items: 40

1.

Shifting the limits in wheat research and breeding using a fully annotated reference genome.

International Wheat Genome Sequencing Consortium (IWGSC); IWGSC RefSeq principal investigators:, Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N; IWGSC whole-genome assembly principal investigators:, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG; Whole-genome sequencing and assembly:, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnère G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin AA; Hi-C data-based scaffolding:, Stein N, Mascher M, Himmelbach A; Whole-genome assembly quality control and analyses:, Choulet F, Keeble-Gagnère G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin AA, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V; Pseudomolecule assembly:, Choulet F, Keeble-Gagnère G, Mascher M, Josselin AA, Rogers J; RefSeq genome structure and gene analyses:, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnère G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Šimková H, Wicker T; Automated annotation:, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L; Manual gene curation:, Appels R, Rimbert H, Choulet F, Juhász A, Keeble-Gagnère G; Subgenome comparative analyses:, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnère G, Mayer KFX, Wicker T; Transposable elements:, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M; Phylogenomic analyses:, Lang D, Spannagl M, Appels R, Fischer I; Transcriptome analyses and RNA-seq data:, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH; Whole-genome methylome:, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A; Histone mark analyses:, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D; BAC chromosome MTP IWGSC–Bayer Whole-Genome Profiling (WGP) tags:, Rogers J, Jacobs J, Alaux M, Appels R, Bartoš J, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen OA, Šimková H, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S; Chromosome LTC mapping and physical mapping quality control:, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J; RH mapping:, Tiwari V, Gill B, Paux E, Poland J; Optical mapping:, Doležel J, Číhalíková J, Šimková H, Toegelová H, Vrána J; Recombination analyses:, Sourdille P, Darrier B; Gene family analyses:, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V; CBF gene family:, Barabaschi D, Cattivelli L; Dehydrin gene family:, Hernandez P, Galvez S, Budak H; NLR gene family:, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G; PPR gene family:, Small I, Melonek J, Zhou R; Prolamin gene family:, Juhász A, Belova T, Appels R, Olsen OA; WAK gene family:, Kanyuka K, King R; Stem solidness (SSt1) QTL team:, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D; Flowering locus C (FLC) gene team:, Rohde A, Golds T; Genome size analysis:, Doležel J, Čížková J, Tibbits J; MicroRNA and tRNA annotation:, Budak H, Akpinar BA, Biyiklioglu S; Genetic maps and mapping:, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N'Daiye A; BAC libraries and chromosome sorting:, Doležel J, Šimková H, Číhalíková J, Kubaláková M, Šafář J, Vrána J; BAC pooling, BAC library repository, and access:, Berges H, Bellec A, Vautrin S; IWGSC sequence and data repository and access:, Alaux M, Alfama F, Adam-Blondon AF, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H; Physical maps and BAC-based sequences:; 1A BAC sequencing and assembly:, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T; 1B BAC sequencing and assembly:, Choulet F, Paux E, Alberti A, Aury JM, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P; 1D, 4D, and 6D physical mapping:, Gill B, Kaur G, Luo M, Sehgal S; 2AL physical mapping:, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B; 2AS physical mapping:, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS; 2B, 2D, 4B, 5BL, and 5DL IWGSC–Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S; 3AL physical mapping:, Gill B, Kaur G, Luo M, Sehgal S; 3DS physical mapping and BAC sequencing and assembly:, Bartoš J, Holušová K, Plíhal O; 3DL BAC sequencing and assembly:, Clark MD, Heavens D, Kettleborough G, Wright J; 4A physical mapping, BAC sequencing, assembly, and annotation:, Valárik M, Abrouk M, Balcárková B, Holušová K, Hu Y, Luo M; 5BS BAC sequencing and assembly:, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E; 6B BAC sequencing and assembly:, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J; 7A physical mapping and BAC sequencing:, Appels R, Hayden M, Keeble-Gagnère G, Rigault P, Tibbits J; 7B physical mapping, BAC sequencing, and assembly:, Olsen OA, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B; 7DS BAC sequencing and assembly:, Šimková H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelová H, Tulpová Z, Visendi P; 7DL physical mapping and BAC sequencing:, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L; Figures:, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L; Manuscript writing team:, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Šimková H, Small I, Spannagl M, Swarbreck D, Uauy C.

Science. 2018 Aug 17;361(6403). pii: eaar7191. doi: 10.1126/science.aar7191. Epub 2018 Aug 16.

PMID:
30115783
2.

A mosaic monoploid reference sequence for the highly complex genome of sugarcane.

Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K, Jenkins J, Martin G, Charron C, Hervouet C, Costet L, Yahiaoui N, Healey A, Sims D, Cherukuri Y, Sreedasyam A, Kilian A, Chan A, Van Sluys MA, Swaminathan K, Town C, Bergès H, Simmons B, Glaszmann JC, van der Vossen E, Henry R, Schmutz J, D'Hont A.

Nat Commun. 2018 Jul 6;9(1):2638. doi: 10.1038/s41467-018-05051-5.

3.

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data.

Madoui MA, Dossat C, d'Agata L, van Oeveren J, van der Vossen E, Aury JM.

BMC Bioinformatics. 2016 Mar 3;17:115. doi: 10.1186/s12859-016-0969-x.

4.

Elicitin recognition confers enhanced resistance to Phytophthora infestans in potato.

Du J, Verzaux E, Chaparro-Garcia A, Bijsterbosch G, Keizer LC, Zhou J, Liebrand TW, Xie C, Govers F, Robatzek S, van der Vossen EA, Jacobsen E, Visser RG, Kamoun S, Vleeshouwers VG.

Nat Plants. 2015 Mar 30;1(4):15034. doi: 10.1038/nplants.2015.34.

PMID:
27247034
5.

The Arabidopsis lectin receptor kinase LecRK-I.9 enhances resistance to Phytophthora infestans in Solanaceous plants.

Bouwmeester K, Han M, Blanco-Portales R, Song W, Weide R, Guo LY, van der Vossen EA, Govers F.

Plant Biotechnol J. 2014 Jan;12(1):10-6. doi: 10.1111/pbi.12111. Epub 2013 Aug 27.

6.

Comparative analysis of Solanum stoloniferum responses to probing by the green peach aphid Myzus persicae and the potato aphid Macrosiphum euphorbiae.

Alvarez AE, Broglia VG, Alberti D'Amato AM, Wouters D, van der Vossen E, Garzo E, Tjallingii WF, Dicke M, Vosman B.

Insect Sci. 2013 Apr;20(2):207-27. doi: 10.1111/j.1744-7917.2012.01505.x. Epub 2012 May 7.

PMID:
23955861
7.

Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity.

King AJ, Montes LR, Clarke JG, Affleck J, Li Y, Witsenboer H, van der Vossen E, van der Linde P, Tripathi Y, Tavares E, Shukla P, Rajasekaran T, van Loo EN, Graham IA.

Plant Biotechnol J. 2013 Oct;11(8):986-96. doi: 10.1111/pbi.12092. Epub 2013 Jul 30.

8.

Sequence-based SNP genotyping in durum wheat.

van Poecke RM, Maccaferri M, Tang J, Truong HT, Janssen A, van Orsouw NJ, Salvi S, Sanguineti MC, Tuberosa R, van der Vossen EA.

Plant Biotechnol J. 2013 Sep;11(7):809-17. doi: 10.1111/pbi.12072. Epub 2013 May 3.

9.

Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome.

Philippe R, Choulet F, Paux E, van Oeveren J, Tang J, Wittenberg AH, Janssen A, van Eijk MJ, Stormo K, Alberti A, Wincker P, Akhunov E, van der Vossen E, Feuillet C.

BMC Genomics. 2012 Jan 30;13:47. doi: 10.1186/1471-2164-13-47.

10.

A potato pathogenesis-related protein gene, StPRp27, contributes to race-nonspecific resistance against Phytophthora infestans.

Shi X, Tian Z, Liu J, van der Vossen EA, Xie C.

Mol Biol Rep. 2012 Feb;39(2):1909-16. doi: 10.1007/s11033-011-0937-5. Epub 2011 Jun 11.

PMID:
21667110
11.

Cloning and characterization of r3b; members of the r3 superfamily of late blight resistance genes show sequence and functional divergence.

Li G, Huang S, Guo X, Li Y, Yang Y, Guo Z, Kuang H, Rietman H, Bergervoet M, Vleeshouwers VG, van der Vossen EA, Qu D, Visser RG, Jacobsen E, Vossen JH.

Mol Plant Microbe Interact. 2011 Oct;24(10):1132-42. doi: 10.1094/MPMI-11-10-0276.

12.

High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.).

Trebbi D, Maccaferri M, de Heer P, Sørensen A, Giuliani S, Salvi S, Sanguineti MC, Massi A, van der Vossen EA, Tuberosa R.

Theor Appl Genet. 2011 Aug;123(4):555-69. doi: 10.1007/s00122-011-1607-7. Epub 2011 May 25.

PMID:
21611761
13.

A genome-wide genetic map of NB-LRR disease resistance loci in potato.

Bakker E, Borm T, Prins P, van der Vossen E, Uenk G, Arens M, de Boer J, van Eck H, Muskens M, Vossen J, van der Linden G, van Ham R, Klein-Lankhorst R, Visser R, Smant G, Bakker J, Goverse A.

Theor Appl Genet. 2011 Aug;123(3):493-508. doi: 10.1007/s00122-011-1602-z. Epub 2011 May 18.

14.

Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.).

Finkers-Tomczak A, Bakker E, de Boer J, van der Vossen E, Achenbach U, Golas T, Suryaningrat S, Smant G, Bakker J, Goverse A.

Theor Appl Genet. 2011 Feb;122(3):595-608. doi: 10.1007/s00122-010-1472-9. Epub 2010 Nov 4.

15.

Diversity, distribution, and evolution of Solanum bulbocastanum late blight resistance genes.

Lokossou AA, Rietman H, Wang M, Krenek P, van der Schoot H, Henken B, Hoekstra R, Vleeshouwers VG, van der Vossen EA, Visser RG, Jacobsen E, Vosman B.

Mol Plant Microbe Interact. 2010 Sep;23(9):1206-16. doi: 10.1094/MPMI-23-9-1206.

16.

Phytophthora infestans isolates lacking class I ipiO variants are virulent on Rpi-blb1 potato.

Champouret N, Bouwmeester K, Rietman H, van der Lee T, Maliepaard C, Heupink A, van de Vondervoort PJ, Jacobsen E, Visser RG, van der Vossen EA, Govers F, Vleeshouwers VG.

Mol Plant Microbe Interact. 2009 Dec;22(12):1535-45. doi: 10.1094/MPMI-22-12-1535.

17.

The genome of the cucumber, Cucumis sativus L.

Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J, Lin K, Jin W, Fei Z, Li G, Staub J, Kilian A, van der Vossen EA, Wu Y, Guo J, He J, Jia Z, Ren Y, Tian G, Lu Y, Ruan J, Qian W, Wang M, Huang Q, Li B, Xuan Z, Cao J, Asan, Wu Z, Zhang J, Cai Q, Bai Y, Zhao B, Han Y, Li Y, Li X, Wang S, Shi Q, Liu S, Cho WK, Kim JY, Xu Y, Heller-Uszynska K, Miao H, Cheng Z, Zhang S, Wu J, Yang Y, Kang H, Li M, Liang H, Ren X, Shi Z, Wen M, Jian M, Yang H, Zhang G, Yang Z, Chen R, Liu S, Li J, Ma L, Liu H, Zhou Y, Zhao J, Fang X, Li G, Fang L, Li Y, Liu D, Zheng H, Zhang Y, Qin N, Li Z, Yang G, Yang S, Bolund L, Kristiansen K, Zheng H, Li S, Zhang X, Yang H, Wang J, Sun R, Zhang B, Jiang S, Wang J, Du Y, Li S.

Nat Genet. 2009 Dec;41(12):1275-81. doi: 10.1038/ng.475. Epub 2009 Nov 1.

PMID:
19881527
18.

In planta expression screens of Phytophthora infestans RXLR effectors reveal diverse phenotypes, including activation of the Solanum bulbocastanum disease resistance protein Rpi-blb2.

Oh SK, Young C, Lee M, Oliva R, Bozkurt TO, Cano LM, Win J, Bos JI, Liu HY, van Damme M, Morgan W, Choi D, Van der Vossen EA, Vleeshouwers VG, Kamoun S.

Plant Cell. 2009 Sep;21(9):2928-47. doi: 10.1105/tpc.109.068247. Epub 2009 Sep 30.

19.

Exploiting knowledge of R/Avr genes to rapidly clone a new LZ-NBS-LRR family of late blight resistance genes from potato linkage group IV.

Lokossou AA, Park TH, van Arkel G, Arens M, Ruyter-Spira C, Morales J, Whisson SC, Birch PR, Visser RG, Jacobsen E, van der Vossen EA.

Mol Plant Microbe Interact. 2009 Jun;22(6):630-41. doi: 10.1094/MPMI-22-6-0630.

20.

Mapping and cloning of late blight resistance genes from Solanum venturii using an interspecific candidate gene approach.

Pel MA, Foster SJ, Park TH, Rietman H, van Arkel G, Jones JD, Van Eck HJ, Jacobsen E, Visser RG, Van der Vossen EA.

Mol Plant Microbe Interact. 2009 May;22(5):601-15. doi: 10.1094/MPMI-22-5-0601.

21.

Rpi-vnt1.1, a Tm-2(2) homolog from Solanum venturii, confers resistance to potato late blight.

Foster SJ, Park TH, Pel M, Brigneti G, Sliwka J, Jagger L, van der Vossen E, Jones JD.

Mol Plant Microbe Interact. 2009 May;22(5):589-600. doi: 10.1094/MPMI-22-5-0589.

22.

Genetic mapping and transcription analyses of resistance gene loci in potato using NBS profiling.

Brugmans B, Wouters D, van Os H, Hutten R, van der Linden G, Visser RG, van Eck HJ, van der Vossen EA.

Theor Appl Genet. 2008 Nov;117(8):1379-88. doi: 10.1007/s00122-008-0871-7. Epub 2008 Sep 20.

PMID:
18806994
23.

Cross-species bacterial artificial chromosome-fluorescence in situ hybridization painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements.

Tang X, Szinay D, Lang C, Ramanna MS, van der Vossen EA, Datema E, Lankhorst RK, de Boer J, Peters SA, Bachem C, Stiekema W, Visser RG, de Jong H, Bai Y.

Genetics. 2008 Nov;180(3):1319-28. doi: 10.1534/genetics.108.093211. Epub 2008 Sep 14.

24.

Effector genomics accelerates discovery and functional profiling of potato disease resistance and phytophthora infestans avirulence genes.

Vleeshouwers VG, Rietman H, Krenek P, Champouret N, Young C, Oh SK, Wang M, Bouwmeester K, Vosman B, Visser RG, Jacobsen E, Govers F, Kamoun S, Van der Vossen EA.

PLoS One. 2008 Aug 6;3(8):e2875. doi: 10.1371/journal.pone.0002875.

25.

Allele mining in Solanum: conserved homologues of Rpi-blb1 are identified in Solanum stoloniferum.

Wang M, Allefs S, van den Berg RG, Vleeshouwers VG, van der Vossen EA, Vosman B.

Theor Appl Genet. 2008 May;116(7):933-43. doi: 10.1007/s00122-008-0725-3. Epub 2008 Feb 15.

PMID:
18274723
26.

The Rpi-blb2 gene from Solanum bulbocastanum is an Mi-1 gene homolog conferring broad-spectrum late blight resistance in potato.

van der Vossen EA, Gros J, Sikkema A, Muskens M, Wouters D, Wolters P, Pereira A, Allefs S.

Plant J. 2005 Oct;44(2):208-22.

27.

The late blight resistance locus Rpi-bib3 from Solanum bulbocastanum belongs to a major late blight R gene cluster on chromosome 4 of potato.

Park TH, Gros J, Sikkema A, Vleeshouwers VG, Muskens M, Allefs S, Jacobsen E, Visser RG, van der Vossen EA.

Mol Plant Microbe Interact. 2005 Jul;18(7):722-9.

28.

Characterization and high-resolution mapping of a late blight resistance locus similar to R2 in potato.

Park TH, Vleeshouwers VG, Huigen DJ, van der Vossen EA, van Eck HJ, Visser RG.

Theor Appl Genet. 2005 Aug;111(3):591-7. Epub 2005 May 21.

PMID:
15909136
29.

Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato.

Huang S, van der Vossen EA, Kuang H, Vleeshouwers VG, Zhang N, Borm TJ, van Eck HJ, Baker B, Jacobsen E, Visser RG.

Plant J. 2005 Apr;42(2):251-61.

30.

A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis.

Bakker E, Achenbach U, Bakker J, van Vliet J, Peleman J, Segers B, van der Heijden S, van der Linde P, Graveland R, Hutten R, van Eck H, Coppoolse E, van der Vossen E, Bakker J, Goverse A.

Theor Appl Genet. 2004 Jun;109(1):146-52. Epub 2004 Feb 25.

PMID:
14985978
31.

An ancient R gene from the wild potato species Solanum bulbocastanum confers broad-spectrum resistance to Phytophthora infestans in cultivated potato and tomato.

van der Vossen E, Sikkema A, Hekkert Bt, Gros J, Stevens P, Muskens M, Wouters D, Pereira A, Stiekema W, Allefs S.

Plant J. 2003 Dec;36(6):867-82.

32.

Genetic and physical mapping of homologues of the virus resistance gene Rx1 and the cyst nematode resistance gene Gpa2 in potato.

Bakker E, Butterbach P, Rouppe van der Voort J, van der Vossen E, van Vliet J, Bakker J, Goverse A.

Theor Appl Genet. 2003 May;106(8):1524-31. Epub 2003 Mar 25.

PMID:
12750796
33.

Homologues of a single resistance-gene cluster in potato confer resistance to distinct pathogens: a virus and a nematode.

van der Vossen EA, van der Voort JN, Kanyuka K, Bendahmane A, Sandbrink H, Baulcombe DC, Bakker J, Stiekema WJ, Klein-Lankhorst RM.

Plant J. 2000 Sep;23(5):567-76.

34.
35.
36.

cis-preferential stimulation of alfalfa mosaic virus RNA 3 accumulation by the viral coat protein.

van der Vossen EA, Reusken CB, Bol JF.

Virology. 1996 Jun 1;220(1):163-70.

37.

Characterization of sequences controlling the synthesis of alfalfa mosaic virus subgenomic RNA in vivo.

van der Vossen EA, Notenboom T, Bol JF.

Virology. 1995 Oct 1;212(2):663-72.

38.

Early and late functions of alfalfa mosaic virus coat protein can be mutated separately.

van der Vossen EA, Neeleman L, Bol JF.

Virology. 1994 Aug 1;202(2):891-903.

PMID:
8030250
39.

Infection of tobacco with alfalfa mosaic virus cDNAs sheds light on the early function of the coat protein.

Neeleman L, Van der Vossen EA, Bol JF.

Virology. 1993 Oct;196(2):883-7.

PMID:
8372454
40.

Role of the 5' leader sequence of alfalfa mosaic virus RNA 3 in replication and translation of the viral RNA.

van der Vossen EA, Neeleman L, Bol JF.

Nucleic Acids Res. 1993 Mar 25;21(6):1361-7.

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