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Items: 1 to 50 of 133

1.

Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response.

Lv Y, Hu F, Zhou Y, Wu F, Gaut BS.

BMC Genomics. 2019 Nov 15;20(1):864. doi: 10.1186/s12864-019-6245-5.

2.

EvoChromo: towards a synthesis of chromatin biology and evolution.

Drinnenberg IA, Berger F, Elsässer SJ, Andersen PR, Ausió J, Bickmore WA, Blackwell AR, Erwin DH, Gahan JM, Gaut BS, Harvey ZH, Henikoff S, Kao JY, Kurdistani SK, Lemos B, Levine MT, Luger K, Malik HS, Martín-Durán JM, Peichel CL, Renfree MB, Rutowicz K, Sarkies P, Schmitz RJ, Technau U, Thornton JW, Warnecke T, Wolfe KH.

Development. 2019 Sep 26;146(19). pii: dev178962. doi: 10.1242/dev.178962.

PMID:
31558570
3.

The population genetics of structural variants in grapevine domestication.

Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, Beridze T, Cantu D, Gaut BS.

Nat Plants. 2019 Sep;5(9):965-979. doi: 10.1038/s41477-019-0507-8. Epub 2019 Sep 9.

PMID:
31506640
4.

Phylogenetic shifts in gene body methylation correlate with gene expression and reflect trait conservation.

Seymour DK, Gaut BS.

Mol Biol Evol. 2019 Aug 27. pii: msz195. doi: 10.1093/molbev/msz195. [Epub ahead of print]

PMID:
31504743
5.

The genome-wide dynamics of purging during selfing in maize.

Roessler K, Muyle A, Diez CM, Gaut GRJ, Bousios A, Stitzer MC, Seymour DK, Doebley JF, Liu Q, Gaut BS.

Nat Plants. 2019 Sep;5(9):980-990. doi: 10.1038/s41477-019-0508-7. Epub 2019 Sep 2.

PMID:
31477888
6.

Living with Two Genomes: Grafting and Its Implications for Plant Genome-to-Genome Interactions, Phenotypic Variation, and Evolution.

Gaut BS, Miller AJ, Seymour DK.

Annu Rev Genet. 2019 Dec 3;53:195-215. doi: 10.1146/annurev-genet-112618-043545. Epub 2019 Aug 19.

PMID:
31424971
7.

Multiple introductions and population structure during the rapid expansion of the invasive Sahara mustard (Brassica tournefortii).

Winkler DE, Chapin KJ, François O, Garmon JD, Gaut BS, Huxman TE.

Ecol Evol. 2019 Jun 28;9(14):7928-7941. doi: 10.1002/ece3.5239. eCollection 2019 Jul.

8.

Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana).

Aguirre-Liguori JA, Gaut BS, Jaramillo-Correa JP, Tenaillon MI, Montes-Hernández S, García-Oliva F, Hearne SJ, Eguiarte LE.

Mol Ecol. 2019 Jun;28(11):2814-2830. doi: 10.1111/mec.15098. Epub 2019 Jun 7.

PMID:
30980686
9.

Loss of Gene Body Methylation in Eutrema salsugineum Is Associated with Reduced Gene Expression.

Muyle A, Gaut BS.

Mol Biol Evol. 2019 Jan 1;36(1):155-158. doi: 10.1093/molbev/msy204.

10.

Demography and its effects on genomic variation in crop domestication.

Gaut BS, Seymour DK, Liu Q, Zhou Y.

Nat Plants. 2018 Aug;4(8):512-520. doi: 10.1038/s41477-018-0210-1. Epub 2018 Jul 30. Review.

PMID:
30061748
11.

Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention.

Roessler K, Bousios A, Meca E, Gaut BS.

Genome Biol Evol. 2018 Mar 1;10(3):803-815. doi: 10.1093/gbe/evy043.

12.

Seasonal Changes in a Maize-Based Polyculture of Central Mexico Reshape the Co-occurrence Networks of Soil Bacterial Communities.

Rebollar EA, Sandoval-Castellanos E, Roessler K, Gaut BS, Alcaraz LD, Benítez M, Escalante AE.

Front Microbiol. 2017 Dec 18;8:2478. doi: 10.3389/fmicb.2017.02478. eCollection 2017.

13.

A convergent outcome: small genomes in mangroves.

Gaut BS.

New Phytol. 2018 Jan;217(1):5-7. doi: 10.1111/nph.14906. No abstract available.

14.

Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication.

Zhou Y, Massonnet M, Sanjak JS, Cantu D, Gaut BS.

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):11715-11720. doi: 10.1073/pnas.1709257114. Epub 2017 Oct 17.

15.

Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression.

González-González A, Hug SM, Rodríguez-Verdugo A, Patel JS, Gaut BS.

Mol Biol Evol. 2017 Nov 1;34(11):2839-2855. doi: 10.1093/molbev/msx216.

16.

Connecting genomic patterns of local adaptation and niche suitability in teosintes.

Aguirre-Liguori JA, Tenaillon MI, Vázquez-Lobo A, Gaut BS, Jaramillo-Correa JP, Montes-Hernandez S, Souza V, Eguiarte LE.

Mol Ecol. 2017 Aug;26(16):4226-4240. doi: 10.1111/mec.14203. Epub 2017 Jul 4.

PMID:
28612956
17.

How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes.

Minio A, Lin J, Gaut BS, Cantu D.

Front Plant Sci. 2017 May 17;8:826. doi: 10.3389/fpls.2017.00826. eCollection 2017. No abstract available.

18.

The Evolutionary Dynamics of Orthologs That Shift in Gene Body Methylation between Arabidopsis Species.

Takuno S, Seymour DK, Gaut BS.

Mol Biol Evol. 2017 Jun 1;34(6):1479-1491. doi: 10.1093/molbev/msx099.

PMID:
28333248
19.

Considerations and complications of mapping small RNA high-throughput data to transposable elements.

Bousios A, Gaut BS, Darzentas N.

Mob DNA. 2017 Feb 15;8:3. doi: 10.1186/s13100-017-0086-z. eCollection 2017.

20.

Deleterious Variants in Asian Rice and the Potential Cost of Domestication.

Liu Q, Zhou Y, Morrell PL, Gaut BS.

Mol Biol Evol. 2017 Apr 1;34(4):908-924. doi: 10.1093/molbev/msw296.

PMID:
28087781
21.

Evolutionary patterns of genic DNA methylation vary across land plants.

Takuno S, Ran JH, Gaut BS.

Nat Plants. 2016 Jan 25;2:15222. doi: 10.1038/nplants.2015.222.

PMID:
27249194
22.

CG Methylation Covaries with Differential Gene Expression between Leaf and Floral Bud Tissues of Brachypodium distachyon.

Roessler K, Takuno S, Gaut BS.

PLoS One. 2016 Mar 7;11(3):e0150002. doi: 10.1371/journal.pone.0150002. eCollection 2016.

23.

Mechanistic and evolutionary questions about epigenetic conflicts between transposable elements and their plant hosts.

Bousios A, Gaut BS.

Curr Opin Plant Biol. 2016 Apr;30:123-33. doi: 10.1016/j.pbi.2016.02.009. Epub 2016 Mar 4. Review.

PMID:
26950253
24.

A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response.

Bousios A, Diez CM, Takuno S, Bystry V, Darzentas N, Gaut BS.

Genome Res. 2016 Feb;26(2):226-37. doi: 10.1101/gr.193763.115. Epub 2015 Dec 2.

25.

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication.

Gaut BS, Díez CM, Morrell PL.

Trends Genet. 2015 Dec;31(12):709-719. doi: 10.1016/j.tig.2015.10.002. Epub 2015 Nov 18. Review.

PMID:
26603610
26.

The jury may be out, but it is important that it deliberates: a response to Besnard and Rubio de Casas about olive domestication.

Díez CM, Gaut BS.

New Phytol. 2016 Jan;209(2):471-3. doi: 10.1111/nph.13780. Epub 2015 Nov 24. No abstract available.

27.

First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes.

Rodríguez-Verdugo A, Tenaillon O, Gaut BS.

Mol Biol Evol. 2016 Jan;33(1):25-39. doi: 10.1093/molbev/msv228. Epub 2015 Oct 24.

28.

The phenotypic signature of adaptation to thermal stress in Escherichia coli.

Hug SM, Gaut BS.

BMC Evol Biol. 2015 Sep 2;15:177. doi: 10.1186/s12862-015-0457-3.

29.

Evolution Is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution: (Nei Lecture, SMBE 2014, Puerto Rico).

Gaut BS.

Mol Biol Evol. 2015 Jul;32(7):1661-71. doi: 10.1093/molbev/msv105. Epub 2015 May 26.

PMID:
26012904
30.

Olive domestication and diversification in the Mediterranean Basin.

Diez CM, Trujillo I, Martinez-Urdiroz N, Barranco D, Rallo L, Marfil P, Gaut BS.

New Phytol. 2015 Apr;206(1):436-47. doi: 10.1111/nph.13181. Epub 2014 Nov 24.

31.

Different tradeoffs result from alternate genetic adaptations to a common environment.

Rodríguez-Verdugo A, Carrillo-Cisneros D, González-González A, Gaut BS, Bennett AF.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12121-6. doi: 10.1073/pnas.1406886111. Epub 2014 Aug 4.

32.

The complex domestication history of the common bean.

Gaut BS.

Nat Genet. 2014 Jul;46(7):663-4. doi: 10.1038/ng.3017.

PMID:
24965727
33.

Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome.

Diez CM, Meca E, Tenaillon MI, Gaut BS.

PLoS Genet. 2014 Apr 17;10(4):e1004298. doi: 10.1371/journal.pgen.1004298. eCollection 2014 Apr.

34.

Epigenetics and plant genome evolution.

Diez CM, Roessler K, Gaut BS.

Curr Opin Plant Biol. 2014 Apr;18:1-8. doi: 10.1016/j.pbi.2013.11.017. Epub 2013 Dec 25. Review.

PMID:
24424204
35.

The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing.

Achaz G, Rodriguez-Verdugo A, Gaut BS, Tenaillon O.

Adv Exp Med Biol. 2014;781:211-31. doi: 10.1007/978-94-007-7347-9_11.

PMID:
24277302
36.

The Capsella rubella genome and the genomic consequences of rapid mating system evolution.

Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F, Guo YL, Steige K, Platts AE, Escobar JS, Newman LK, Wang W, Mandáková T, Vello E, Smith LM, Henz SR, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu TT, Blanchette M, Clark RM, Quesneville H, Nordborg M, Gaut BS, Lysak MA, Jenkins J, Grimwood J, Chapman J, Prochnik S, Shu S, Rokhsar D, Schmutz J, Weigel D, Wright SI.

Nat Genet. 2013 Jul;45(7):831-5. doi: 10.1038/ng.2669. Epub 2013 Jun 9.

PMID:
23749190
37.

Genome size variation in wild and cultivated maize along altitudinal gradients.

Díez CM, Gaut BS, Meca E, Scheinvar E, Montes-Hernandez S, Eguiarte LE, Tenaillon MI.

New Phytol. 2013 Jul;199(1):264-76. doi: 10.1111/nph.12247. Epub 2013 Apr 2.

38.

Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress.

Rodríguez-Verdugo A, Gaut BS, Tenaillon O.

BMC Evol Biol. 2013 Feb 22;13:50. doi: 10.1186/1471-2148-13-50.

39.

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence.

Takuno S, Gaut BS.

Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1797-802. doi: 10.1073/pnas.1215380110. Epub 2013 Jan 14.

40.

Inferences from the historical distribution of wild and domesticated maize provide ecological and evolutionary insight.

Hufford MB, Martínez-Meyer E, Gaut BS, Eguiarte LE, Tenaillon MI.

PLoS One. 2012;7(11):e47659. doi: 10.1371/journal.pone.0047659. Epub 2012 Nov 14.

41.

Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica).

Vonholdt BM, Takuno S, Gaut BS.

Mol Biol Evol. 2012 Oct;29(10):3193-203. Epub 2012 May 15.

PMID:
22593226
42.

The molecular diversity of adaptive convergence.

Tenaillon O, Rodríguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD, Gaut BS.

Science. 2012 Jan 27;335(6067):457-61. doi: 10.1126/science.1212986.

43.

Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.

Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, Kanamori H, Matsumoto T, Itoh T, Gaut BS.

Genome Biol Evol. 2011;3:1357-68. doi: 10.1093/gbe/evr111. Epub 2011 Oct 31.

44.

Mapping salinity tolerance during Arabidopsis thaliana germination and seedling growth.

DeRose-Wilson L, Gaut BS.

PLoS One. 2011;6(8):e22832. doi: 10.1371/journal.pone.0022832. Epub 2011 Aug 12.

45.

Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly.

Takuno S, Gaut BS.

Mol Biol Evol. 2012 Jan;29(1):219-27. doi: 10.1093/molbev/msr188. Epub 2011 Aug 2.

PMID:
21813466
46.

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.

Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL.

Nat Genet. 2011 May;43(5):476-81. doi: 10.1038/ng.807. Epub 2011 Apr 10.

47.

Factors that contribute to variation in evolutionary rate among Arabidopsis genes.

Yang L, Gaut BS.

Mol Biol Evol. 2011 Aug;28(8):2359-69. doi: 10.1093/molbev/msr058. Epub 2011 Mar 9.

PMID:
21389272
48.

Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians.

Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J.

Genome Biol Evol. 2011;3:219-29. doi: 10.1093/gbe/evr008. Epub 2011 Feb 4.

49.

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata.

Hollister JD, Smith LM, Guo YL, Ott F, Weigel D, Gaut BS.

Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2322-7. doi: 10.1073/pnas.1018222108. Epub 2011 Jan 20.

50.

Lowly expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degradation.

Yang L, Takuno S, Waters ER, Gaut BS.

Mol Biol Evol. 2011 Mar;28(3):1193-203. doi: 10.1093/molbev/msq298. Epub 2010 Nov 8.

PMID:
21059790

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