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Items: 15

1.

Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L.

Gazave E, Tassone EE, Ilut DC, Wingerson M, Datema E, Witsenboer HM, Davis JB, Grant D, Dyer JM, Jenks MA, Brown J, Gore MA.

Front Plant Sci. 2016 Apr 21;7:525. doi: 10.3389/fpls.2016.00525. eCollection 2016.

2.

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.

3.

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome.

Faino L, Seidl MF, Datema E, van den Berg GC, Janssen A, Wittenberg AH, Thomma BP.

MBio. 2015 Aug 18;6(4). pii: e00936-15. doi: 10.1128/mBio.00936-15.

4.

Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life.

Faddeeva A, Studer RA, Kraaijeveld K, Sie D, Ylstra B, Mariën J, op den Camp HJ, Datema E, den Dunnen JT, van Straalen NM, Roelofs D.

PLoS One. 2015 Jun 15;10(6):e0130600. doi: 10.1371/journal.pone.0130600. eCollection 2015.

5.

Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin.

de Boer JM, Datema E, Tang X, Borm TJ, Bakker EH, van Eck HJ, van Ham RC, de Jong H, Visser RG, Bachem CW.

BMC Genomics. 2015 May 10;16:374. doi: 10.1186/s12864-015-1578-1.

6.

Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome.

Tang X, Datema E, Guzman MO, de Boer JM, van Eck HJ, Bachem CW, Visser RG, de Jong H.

Mol Genet Genomics. 2014 Dec;289(6):1307-19. doi: 10.1007/s00438-014-0891-8. Epub 2014 Aug 9.

PMID:
25106953
7.

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.

8.

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.

9.

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology.

Nijkamp JF, van den Broek M, Datema E, de Kok S, Bosman L, Luttik MA, Daran-Lapujade P, Vongsangnak W, Nielsen J, Heijne WH, Klaassen P, Paddon CJ, Platt D, Kötter P, van Ham RC, Reinders MJ, Pronk JT, de Ridder D, Daran JM.

Microb Cell Fact. 2012 Mar 26;11:36. doi: 10.1186/1475-2859-11-36.

10.

Genome sequence and analysis of the tuber crop potato.

Potato Genome Sequencing Consortium, Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DM, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejía N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera Mdel R, Giuliano G, Pietrella M, Perrotta G, Facella P, O'Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JM, Nielsen KL, Sønderkær M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CW, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert Bt, Goverse A, van Ham RC, Visser RG.

Nature. 2011 Jul 10;475(7355):189-95. doi: 10.1038/nature10158.

PMID:
21743474
11.

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.

12.

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.

13.

FISH mapping and molecular organization of the major repetitive sequences of tomato.

Chang SB, Yang TJ, Datema E, van Vugt J, Vosman B, Kuipers A, Meznikova M, Szinay D, Lankhorst RK, Jacobsen E, de Jong H.

Chromosome Res. 2008;16(7):919-33. doi: 10.1007/s10577-008-1249-z. Epub 2008 Aug 13.

PMID:
18688733
14.

Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato.

Datema E, Mueller LA, Buels R, Giovannoni JJ, Visser RG, Stiekema WJ, van Ham RC.

BMC Plant Biol. 2008 Apr 11;8:34. doi: 10.1186/1471-2229-8-34.

15.

High-throughput bioinformatics with the Cyrille2 pipeline system.

Fiers MW, van der Burgt A, Datema E, de Groot JC, van Ham RC.

BMC Bioinformatics. 2008 Feb 12;9:96. doi: 10.1186/1471-2105-9-96.

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