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Items: 1 to 50 of 63

1.

Transcriptional Variation in Glucosinolate Biosynthetic Genes and Inducible Responses to Aphid Herbivory on Field-Grown Arabidopsis thaliana.

Sato Y, Tezuka A, Kashima M, Deguchi A, Shimizu-Inatsugi R, Yamazaki M, Shimizu KK, Nagano AJ.

Front Genet. 2019 Sep 11;10:787. doi: 10.3389/fgene.2019.00787. eCollection 2019.

2.

Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence.

Izuno A, Wicker T, Hatakeyama M, Copetti D, Shimizu KK.

G3 (Bethesda). 2019 Nov 5;9(11):3513-3520. doi: 10.1534/g3.119.400643.

3.

The current genomic landscape of western South America: Andes, Amazonia and Pacific Coast.

Barbieri C, Barquera R, Arias L, Sandoval JR, Acosta O, Zurita C, Aguilar-Campos A, Tito-Álvarez AM, Serrano-Osuna R, Gray R, Mafessoni F, Heggarty P, Shimizu KK, Fujita R, Stoneking M, Pugach I, Fehren-Schmitz L.

Mol Biol Evol. 2019 Jul 27. pii: msz174. doi: 10.1093/molbev/msz174. [Epub ahead of print]

PMID:
31350885
4.

A stigmatic gene confers interspecies incompatibility in the Brassicaceae.

Fujii S, Tsuchimatsu T, Kimura Y, Ishida S, Tangpranomkorn S, Shimosato-Asano H, Iwano M, Furukawa S, Itoyama W, Wada Y, Shimizu KK, Takayama S.

Nat Plants. 2019 Jul;5(7):731-741. doi: 10.1038/s41477-019-0444-6. Epub 2019 Jul 1.

PMID:
31263241
5.

Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana.

Sato Y, Shimizu-Inatsugi R, Yamazaki M, Shimizu KK, Nagano AJ.

BMC Plant Biol. 2019 Apr 27;19(1):163. doi: 10.1186/s12870-019-1705-2.

6.

Homeolog expression quantification methods for allopolyploids.

Kuo TCY, Hatakeyama M, Tameshige T, Shimizu KK, Sese J.

Brief Bioinform. 2018 Dec 27. doi: 10.1093/bib/bby121. [Epub ahead of print]

PMID:
30590436
7.

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica.

Paape T, Briskine RV, Halstead-Nussloch G, Lischer HEL, Shimizu-Inatsugi R, Hatakeyama M, Tanaka K, Nishiyama T, Sabirov R, Sese J, Shimizu KK.

Nat Commun. 2018 Sep 25;9(1):3909. doi: 10.1038/s41467-018-06108-1.

8.

Molecular basis of flowering under natural long-day conditions in Arabidopsis.

Song YH, Kubota A, Kwon MS, Covington MF, Lee N, Taagen ER, Laboy Cintrón D, Hwang DY, Akiyama R, Hodge SK, Huang H, Nguyen NH, Nusinow DA, Millar AJ, Shimizu KK, Imaizumi T.

Nat Plants. 2018 Oct;4(10):824-835. doi: 10.1038/s41477-018-0253-3. Epub 2018 Sep 24.

9.

The Nagoya Protocol could backfire on the Global South.

Deplazes-Zemp A, Abiven S, Schaber P, Schaepman M, Schaepman-Strub G, Schmid B, Shimizu KK, Altermatt F.

Nat Ecol Evol. 2018 Jun;2(6):917-919. doi: 10.1038/s41559-018-0561-z. No abstract available.

PMID:
29760439
10.

Reference-guided de novo assembly approach improves genome reconstruction for related species.

Lischer HEL, Shimizu KK.

BMC Bioinformatics. 2017 Nov 10;18(1):474. doi: 10.1186/s12859-017-1911-6.

11.

Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica.

Yew CL, Kakui H, Shimizu KK.

J Plant Res. 2018 Mar;131(2):349-358. doi: 10.1007/s10265-017-0982-9. Epub 2017 Oct 14.

PMID:
29032409
12.

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop.

Hatakeyama M, Aluri S, Balachadran MT, Sivarajan SR, Patrignani A, Grüter S, Poveda L, Shimizu-Inatsugi R, Baeten J, Francoijs KJ, Nataraja KN, Reddy YAN, Phadnis S, Ravikumar RL, Schlapbach R, Sreeman SM, Shimizu KK.

DNA Res. 2017 Sep 5. doi: 10.1093/dnares/dsx036. [Epub ahead of print]

13.

Duplicated pollen-pistil recognition loci control intraspecific unilateral incompatibility in Brassica rapa.

Takada Y, Murase K, Shimosato-Asano H, Sato T, Nakanishi H, Suwabe K, Shimizu KK, Lim YP, Takayama S, Suzuki G, Watanabe M.

Nat Plants. 2017 Jun 26;3:17096. doi: 10.1038/nplants.2017.96.

PMID:
28650458
14.

Positional bias in variant calls against draft reference assemblies.

Briskine RV, Shimizu KK.

BMC Genomics. 2017 Mar 28;18(1):263. doi: 10.1186/s12864-017-3637-2.

15.

The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae).

Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y.

Mol Ecol. 2017 Mar;26(6):1515-1532. doi: 10.1111/mec.14016. Epub 2017 Feb 8.

PMID:
28099775
16.

Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri.

Fischer MC, Rellstab C, Leuzinger M, Roumet M, Gugerli F, Shimizu KK, Holderegger R, Widmer A.

BMC Genomics. 2017 Jan 11;18(1):69. doi: 10.1186/s12864-016-3459-7.

17.

Erratum: The Cardamine hirsuta genome offers insight into the evolution of morphological diversity.

Gan X, Hay A, Kwantes M, Haberer G, Hallab A, Ioio RD, Hofhuis H, Pieper B, Cartolano M, Neumann U, Nikolov LA, Song B, Hajheidari M, Briskine R, Kougioumoutzi E, Vlad D, Broholm S, Hein J, Meksem K, Lightfoot D, Shimizu KK, Shimizu-Inatsugi R, Imprialou M, Kudrna D, Wing R, Sato S, Huijser P, Filatov D, X Mayer KF, Mott R, Tsiantis M.

Nat Plants. 2016 Nov 7;2:16189. doi: 10.1038/nplants.2016.189. No abstract available.

PMID:
27819656
18.

The Cardamine hirsuta genome offers insight into the evolution of morphological diversity.

Gan X, Hay A, Kwantes M, Haberer G, Hallab A, Ioio RD, Hofhuis H, Pieper B, Cartolano M, Neumann U, Nikolov LA, Song B, Hajheidari M, Briskine R, Kougioumoutzi E, Vlad D, Broholm S, Hein J, Meksem K, Lightfoot D, Shimizu KK, Shimizu-Inatsugi R, Imprialou M, Kudrna D, Wing R, Sato S, Huijser P, Filatov D, Mayer KF, Mott R, Tsiantis M.

Nat Plants. 2016 Oct 31;2(11):16167. doi: 10.1038/nplants.2016.167. Erratum in: Nat Plants. 2016 Nov 07;2:16189.

PMID:
27797353
19.

Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology.

Briskine RV, Paape T, Shimizu-Inatsugi R, Nishiyama T, Akama S, Sese J, Shimizu KK.

Mol Ecol Resour. 2017 Sep;17(5):1025-1036. doi: 10.1111/1755-0998.12604. Epub 2016 Oct 26.

PMID:
27671113
20.

Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri.

Rellstab C, Fischer MC, Zoller S, Graf R, Tedder A, Shimizu KK, Widmer A, Holderegger R, Gugerli F.

Heredity (Edinb). 2017 Feb;118(2):193-201. doi: 10.1038/hdy.2016.82. Epub 2016 Oct 5.

21.

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism.

Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, Guggisberg A, Paape T, Schmid K, Fedorenko OM, Holm S, Säll T, Schlötterer C, Marhold K, Widmer A, Sese J, Shimizu KK, Weigel D, Krämer U, Koch MA, Nordborg M.

Nat Genet. 2016 Sep;48(9):1077-82. doi: 10.1038/ng.3617. Epub 2016 Jul 18.

22.

Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica.

Paape T, Hatakeyama M, Shimizu-Inatsugi R, Cereghetti T, Onda Y, Kenta T, Sese J, Shimizu KK.

Mol Biol Evol. 2016 Nov;33(11):2781-2800. Epub 2016 Jul 12.

23.

Plant adaptive radiation mediated by polyploid plasticity in transcriptomes.

Shimizu-Inatsugi R, Terada A, Hirose K, Kudoh H, Sese J, Shimizu KK.

Mol Ecol. 2017 Jan;26(1):193-207. doi: 10.1111/mec.13738. Epub 2016 Aug 26.

PMID:
27352992
24.

Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations.

Izuno A, Hatakeyama M, Nishiyama T, Tamaki I, Shimizu-Inatsugi R, Sasaki R, Shimizu KK, Isagi Y.

J Plant Res. 2016 Jul;129(4):727-736. doi: 10.1007/s10265-016-0822-3. Epub 2016 Apr 6.

PMID:
27052216
25.

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species.

Menardo F, Praz CR, Wyder S, Ben-David R, Bourras S, Matsumae H, McNally KE, Parlange F, Riba A, Roffler S, Schaefer LK, Shimizu KK, Valenti L, Zbinden H, Wicker T, Keller B.

Nat Genet. 2016 Feb;48(2):201-5. doi: 10.1038/ng.3485. Epub 2016 Jan 11.

26.

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes.

Takeuchi Y, Chaffron S, Salcher MM, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, von Mering C, Pernthaler J, Shimizu KK.

Syst Appl Microbiol. 2015 Jul;38(5):330-9. doi: 10.1016/j.syapm.2015.05.006. Epub 2015 Jun 16.

27.

Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing.

Stockenhuber R, Zoller S, Shimizu-Inatsugi R, Gugerli F, Shimizu KK, Widmer A, Fischer MC.

PLoS One. 2015 Jun 10;10(6):e0128181. doi: 10.1371/journal.pone.0128181. eCollection 2015.

28.

Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae).

Tedder A, Carleial S, Gołębiewska M, Kappel C, Shimizu KK, Stift M.

PLoS One. 2015 Jun 3;10(6):e0126618. doi: 10.1371/journal.pone.0126618. eCollection 2015.

29.

Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae).

Tedder A, Helling M, Pannell JR, Shimizu-Inatsugi R, Kawagoe T, van Campen J, Sese J, Shimizu KK.

Ann Bot. 2015 Apr;115(5):763-76. doi: 10.1093/aob/mcv006. Epub 2015 Mar 16.

30.

Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia.

Kubo K, Paape T, Hatakeyama M, Entani T, Takara A, Kajihara K, Tsukahara M, Shimizu-Inatsugi R, Shimizu KK, Takayama S.

Nat Plants. 2015 Jan 8;1:14005. doi: 10.1038/nplants.2014.5.

PMID:
27246052
31.

Transcriptional characteristics and differences in Arabidopsis stigmatic papilla cells pre- and post-pollination.

Matsuda T, Matsushima M, Nabemoto M, Osaka M, Sakazono S, Masuko-Suzuki H, Takahashi H, Nakazono M, Iwano M, Takayama S, Shimizu KK, Okumura K, Suzuki G, Watanabe M, Suwabe K.

Plant Cell Physiol. 2015 Apr;56(4):663-73. doi: 10.1093/pcp/pcu209. Epub 2014 Dec 19.

32.

Nitrogen as a key regulator of flowering in Fagus crenata: understanding the physiological mechanism of masting by gene expression analysis.

Miyazaki Y, Maruyama Y, Chiba Y, Kobayashi MJ, Joseph B, Shimizu KK, Mochida K, Hiura T, Kon H, Satake A.

Ecol Lett. 2014 Oct;17(10):1299-309. doi: 10.1111/ele.12338. Epub 2014 Aug 7.

PMID:
25103959
33.

Efficient purging of deleterious mutations in plants with haploid selfing.

Szövényi P, Devos N, Weston DJ, Yang X, Hock Z, Shaw JA, Shimizu KK, McDaniel SF, Wagner A.

Genome Biol Evol. 2014 May 14;6(5):1238-52. doi: 10.1093/gbe/evu099.

34.

Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy.

Zozomová-Lihová J, Krak K, Mandáková T, Shimizu KK, Spaniel S, Vít P, Lysak MA.

Ann Bot. 2014 Apr;113(5):817-30. doi: 10.1093/aob/mcu012. Epub 2014 Feb 26.

35.

Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis.

Akama S, Shimizu-Inatsugi R, Shimizu KK, Sese J.

Nucleic Acids Res. 2014 Apr;42(6):e46. doi: 10.1093/nar/gkt1376. Epub 2014 Jan 13.

36.

Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps.

Fischer MC, Rellstab C, Tedder A, Zoller S, Gugerli F, Shimizu KK, Holderegger R, Widmer A.

Mol Ecol. 2013 Nov;22(22):5594-607. doi: 10.1111/mec.12521. Epub 2013 Oct 28.

37.

The more the merrier: recent hybridization and polyploidy in cardamine.

Mandáková T, Kovarík A, Zozomová-Lihová J, Shimizu-Inatsugi R, Shimizu KK, Mummenhoff K, Marhold K, Lysak MA.

Plant Cell. 2013 Sep;25(9):3280-95. doi: 10.1105/tpc.113.114405. Epub 2013 Sep 30.

38.

Cell type-specific transcriptome of Brassicaceae stigmatic papilla cells from a combination of laser microdissection and RNA sequencing.

Osaka M, Matsuda T, Sakazono S, Masuko-Suzuki H, Maeda S, Sewaki M, Sone M, Takahashi H, Nakazono M, Iwano M, Takayama S, Shimizu KK, Yano K, Lim YP, Suzuki G, Suwabe K, Watanabe M.

Plant Cell Physiol. 2013 Nov;54(11):1894-906. doi: 10.1093/pcp/pct133. Epub 2013 Sep 20.

39.

Effects of pollen availability and the mutation bias on the fixation of mutations disabling the male specificity of self-incompatibility.

Tsuchimatsu T, Shimizu KK.

J Evol Biol. 2013 Oct;26(10):2221-32. doi: 10.1111/jeb.12219. Epub 2013 Aug 28.

40.

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph.

Wicker T, Oberhaensli S, Parlange F, Buchmann JP, Shatalina M, Roffler S, Ben-David R, Doležel J, Šimková H, Schulze-Lefert P, Spanu PD, Bruggmann R, Amselem J, Quesneville H, Ver Loren van Themaat E, Paape T, Shimizu KK, Keller B.

Nat Genet. 2013 Sep;45(9):1092-6. doi: 10.1038/ng.2704. Epub 2013 Jul 14.

41.

Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss.

Szövényi P, Ricca M, Hock Z, Shaw JA, Shimizu KK, Wagner A.

Mol Biol Evol. 2013 Aug;30(8):1929-39. doi: 10.1093/molbev/mst095. Epub 2013 May 17.

PMID:
23686659
42.

Mass flowering of the tropical tree Shorea beccariana was preceded by expression changes in flowering and drought-responsive genes.

Kobayashi MJ, Takeuchi Y, Kenta T, Kume T, Diway B, Shimizu KK.

Mol Ecol. 2013 Sep;22(18):4767-82. doi: 10.1111/mec.12344. Epub 2013 May 8.

43.

Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus.

Ogura A, Yoshida MA, Moritaki T, Okuda Y, Sese J, Shimizu KK, Sousounis K, Tsonis PA.

Sci Rep. 2013;3:1432. doi: 10.1038/srep01432.

44.

Recent loss of self-incompatibility by degradation of the male component in allotetraploid Arabidopsis kamchatica.

Tsuchimatsu T, Kaiser P, Yew CL, Bachelier JB, Shimizu KK.

PLoS Genet. 2012;8(7):e1002838. doi: 10.1371/journal.pgen.1002838. Epub 2012 Jul 26.

45.
46.

In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus Nepenthes.

Takeuchi Y, Salcher MM, Ushio M, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, von Mering C, Pernthaler J, Shimizu KK.

PLoS One. 2011;6(9):e25144. doi: 10.1371/journal.pone.0025144. Epub 2011 Sep 16.

47.

Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology.

Shimizu KK, Kudoh H, Kobayashi MJ.

Ann Bot. 2011 Sep;108(4):777-87. doi: 10.1093/aob/mcr180. Epub 2011 Aug 17. Review.

48.

Coexistence of trichome variation in a natural plant population: a combined study using ecological and candidate gene approaches.

Kawagoe T, Shimizu KK, Kakutani T, Kudoh H.

PLoS One. 2011;6(7):e22184. doi: 10.1371/journal.pone.0022184. Epub 2011 Jul 19.

49.

Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation.

Yoshida MA, Ishikura Y, Moritaki T, Shoguchi E, Shimizu KK, Sese J, Ogura A.

Gene. 2011 Sep 1;483(1-2):63-71. doi: 10.1016/j.gene.2011.05.027. Epub 2011 Jun 6.

PMID:
21672613
50.

Using knockout mutants to reveal the growth costs of defensive traits.

Züst T, Joseph B, Shimizu KK, Kliebenstein DJ, Turnbull LA.

Proc Biol Sci. 2011 Sep 7;278(1718):2598-603. doi: 10.1098/rspb.2010.2475. Epub 2011 Jan 26.

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