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Items: 1 to 50 of 93

1.

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense.

Wang M, Tu L, Yuan D, Zhu, Shen C, Li J, Liu F, Pei L, Wang P, Zhao G, Ye Z, Huang H, Yan F, Ma Y, Zhang L, Liu M, You J, Yang Y, Liu Z, Huang F, Li B, Qiu P, Zhang Q, Zhu L, Jin S, Yang X, Min L, Li G, Chen LL, Zheng H, Lindsey K, Lin Z, Udall JA, Zhang X.

Nat Genet. 2019 Feb;51(2):224-229. doi: 10.1038/s41588-018-0282-x. Epub 2018 Dec 3.

PMID:
30510239
2.

Genomic Structural Variations Within Five Continental Populations of Drosophila melanogaster.

Long E, Evans C, Chaston J, Udall JA.

G3 (Bethesda). 2018 Oct 3;8(10):3247-3253. doi: 10.1534/g3.118.200631.

3.

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping.

Udall JA, Dawe RK.

Plant Cell. 2018 Jan;30(1):7-14. doi: 10.1105/tpc.17.00514. Epub 2017 Dec 20. Review.

4.

Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing.

Grover CE, Arick MA 2nd, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, Wendel JF.

Genome Biol Evol. 2017 Dec 1;9(12):3328-3344. doi: 10.1093/gbe/evx248.

5.

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.

Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM.

BMC Plant Biol. 2017 Feb 3;17(1):37. doi: 10.1186/s12870-017-0981-y.

6.

Genome-wide divergence, haplotype distribution and population demographic histories for Gossypium hirsutum and Gossypium barbadense as revealed by genome-anchored SNPs.

Reddy UK, Nimmakayala P, Abburi VL, Reddy CV, Saminathan T, Percy RG, Yu JZ, Frelichowski J, Udall JA, Page JT, Zhang D, Shehzad T, Paterson AH.

Sci Rep. 2017 Jan 27;7:41285. doi: 10.1038/srep41285.

7.

Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds.

Hu G, Hovav R, Grover CE, Faigenboim-Doron A, Kadmon N, Page JT, Udall JA, Wendel JF.

Genome Biol Evol. 2016 Dec 1;8(12):3765-3783. doi: 10.1093/gbe/evw280.

8.

The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly.

Clouse JW, Adhikary D, Page JT, Ramaraj T, Deyholos MK, Udall JA, Fairbanks DJ, Jellen EN, Maughan PJ.

Plant Genome. 2016 Mar;9(1). doi: 10.3835/plantgenome2015.07.0062. Erratum in: Plant Genome. 2016 Nov;9(3):.

9.

Widespread natural variation of DNA methylation within angiosperms.

Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ.

Genome Biol. 2016 Sep 27;17(1):194.

10.

OMWare: a tool for efficient assembly of genome-wide physical maps.

Sharp AR, Udall JA.

BMC Bioinformatics. 2016 Jul 25;17 Suppl 7:241. doi: 10.1186/s12859-016-1099-1.

11.

Correction: DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton.

Page JT, Liechty ZS, Alexander RH, Clemons K, Hulse-Kemp AM, Ashrafi H, Van Deynze A, Stelly DM, Udall JA.

PLoS Genet. 2016 Jul 22;12(7):e1006206. doi: 10.1371/journal.pgen.1006206. eCollection 2016 Jul.

12.

Genome Mapping in Plant Comparative Genomics.

Chaney L, Sharp AR, Evans CR, Udall JA.

Trends Plant Sci. 2016 Sep;21(9):770-780. doi: 10.1016/j.tplants.2016.05.004. Epub 2016 Jun 8. Review.

PMID:
27289181
13.

Independent Domestication of Two Old World Cotton Species.

Renny-Byfield S, Page JT, Udall JA, Sanders WS, Peterson DG, Arick MA 2nd, Grover CE, Wendel JF.

Genome Biol Evol. 2016 Jul 2;8(6):1940-7. doi: 10.1093/gbe/evw129.

14.

DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton.

Page JT, Liechty ZS, Alexander RH, Clemons K, Hulse-Kemp AM, Ashrafi H, Van Deynze A, Stelly DM, Udall JA.

PLoS Genet. 2016 May 11;12(5):e1006012. doi: 10.1371/journal.pgen.1006012. eCollection 2016 May. Erratum in: PLoS Genet. 2016 Jul;12(7):e1006206.

15.

Re-evaluating the phylogeny of allopolyploid Gossypium L.

Grover CE, Gallagher JP, Jareczek JJ, Page JT, Udall JA, Gore MA, Wendel JF.

Mol Phylogenet Evol. 2015 Nov;92:45-52. doi: 10.1016/j.ympev.2015.05.023. Epub 2015 Jun 4.

PMID:
26049043
16.

Insights into transcriptomes of big and low sagebrush.

Huynh MD, Page JT, Richardson BA, Udall JA.

PLoS One. 2015 May 28;10(5):e0127593. doi: 10.1371/journal.pone.0127593. eCollection 2015.

17.

Methods for mapping and categorization of DNA sequence reads from allopolyploid organisms.

Page JT, Udall JA.

BMC Genet. 2015;16 Suppl 2:S4. doi: 10.1186/1471-2156-16-S2-S4. Epub 2015 Apr 23.

18.

Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Singh SK, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM.

G3 (Bethesda). 2015 Apr 22;5(6):1187-209. doi: 10.1534/g3.115.018416.

19.

BamBam: genome sequence analysis tools for biologists.

Page JT, Liechty ZS, Huynh MD, Udall JA.

BMC Res Notes. 2014 Nov 24;7:829. doi: 10.1186/1756-0500-7-829.

20.

Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium.

Yurchenko OP, Park S, Ilut DC, Inmon JJ, Millhollon JC, Liechty Z, Page JT, Jenks MA, Chapman KD, Udall JA, Gore MA, Dyer JM.

BMC Plant Biol. 2014 Nov 18;14:312. doi: 10.1186/s12870-014-0312-5.

21.

Genomic reduction assisted single nucleotide polymorphism discovery using 454-pyrosequencing.

Maughan PJ, Udall JA, Jellen EN.

Methods Mol Biol. 2015;1245:169-82. doi: 10.1007/978-1-4939-1966-6_13.

PMID:
25373757
22.

Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts.

Hulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda AB, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM.

BMC Genomics. 2014 Oct 30;15:945. doi: 10.1186/1471-2164-15-945.

23.
24.

The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

Naoumkina M, Thyssen G, Fang DD, Hinchliffe DJ, Florane C, Yeater KM, Page JT, Udall JA.

PLoS One. 2014 Mar 5;9(3):e90830. doi: 10.1371/journal.pone.0090830. eCollection 2014.

25.

Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT, Udall JA, Wang X, Paterson AH, Wendel JF.

Genome Biol Evol. 2014 Mar;6(3):559-71. doi: 10.1093/gbe/evu037.

26.

De novo genome assembly of the fungal plant pathogen Pyrenophora semeniperda.

Soliai MM, Meyer SE, Udall JA, Elzinga DE, Hermansen RA, Bodily PM, Hart AA, Coleman CE.

PLoS One. 2014 Jan 27;9(1):e87045. doi: 10.1371/journal.pone.0087045. eCollection 2014.

27.

Polyploidy and the petal transcriptome of Gossypium.

Rambani A, Page JT, Udall JA.

BMC Plant Biol. 2014 Jan 6;14:3. doi: 10.1186/1471-2229-14-3.

28.

RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Jones DC, Campbell BT.

PLoS One. 2013 Dec 6;8(12):e82634. doi: 10.1371/journal.pone.0082634. eCollection 2013.

29.

Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.).

Tyagi P, Gore MA, Bowman DT, Campbell BT, Udall JA, Kuraparthy V.

Theor Appl Genet. 2014 Feb;127(2):283-95. doi: 10.1007/s00122-013-2217-3. Epub 2013 Oct 30.

PMID:
24170350
30.

Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

Page JT, Huynh MD, Liechty ZS, Grupp K, Stelly D, Hulse AM, Ashrafi H, Van Deynze A, Wendel JF, Udall JA.

G3 (Bethesda). 2013 Oct 3;3(10):1809-18. doi: 10.1534/g3.113.007229.

31.

PolyCat: a resource for genome categorization of sequencing reads from allopolyploid organisms.

Page JT, Gingle AR, Udall JA.

G3 (Bethesda). 2013 Mar;3(3):517-25. doi: 10.1534/g3.112.005298. Epub 2013 Mar 1.

32.

Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata; Asteraceae).

Richardson BA, Page JT, Bajgain P, Sanderson SC, Udall JA.

Am J Bot. 2012 Dec;99(12):1962-75. doi: 10.3732/ajb.1200373. Epub 2012 Nov 30.

33.

Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton.

Salmon A, Udall JA, Jeddeloh JA, Wendel J.

G3 (Bethesda). 2012 Aug;2(8):921-30. doi: 10.1534/g3.112.003392. Epub 2012 Aug 1.

34.

Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton.

Flagel LE, Wendel JF, Udall JA.

BMC Genomics. 2012 Jul 6;13:302. doi: 10.1186/1471-2164-13-302.

35.

Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach.

Bushakra JM, Stephens MJ, Atmadjaja AN, Lewers KS, Symonds VV, Udall JA, Chagné D, Buck EJ, Gardiner SE.

Theor Appl Genet. 2012 Jul;125(2):311-27. doi: 10.1007/s00122-012-1835-5. Epub 2012 Mar 8.

PMID:
22398438
36.

Development and mapping of SNP assays in allotetraploid cotton.

Byers RL, Harker DB, Yourstone SM, Maughan PJ, Udall JA.

Theor Appl Genet. 2012 May;124(7):1201-14. doi: 10.1007/s00122-011-1780-8. Epub 2012 Jan 18.

37.

Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics.

Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA.

Genome Biol Evol. 2011;3:1312-23. doi: 10.1093/gbe/evr106. Epub 2011 Oct 13.

38.

Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata).

Bajgain P, Richardson BA, Price JC, Cronn RC, Udall JA.

BMC Genomics. 2011 Jul 18;12:370. doi: 10.1186/1471-2164-12-370.

39.

Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication.

Rapp RA, Haigler CH, Flagel L, Hovav RH, Udall JA, Wendel JF.

BMC Biol. 2010 Nov 15;8:139. doi: 10.1186/1741-7007-8-139.

40.

Homoeologous nonreciprocal recombination in polyploid cotton.

Salmon A, Flagel L, Ying B, Udall JA, Wendel JF.

New Phytol. 2010 Apr;186(1):123-34. doi: 10.1111/j.1469-8137.2009.03093.x. Epub 2009 Nov 19.

41.

Characterization of Salt Overly Sensitive 1 (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd.).

Maughan PJ, Turner TB, Coleman CE, Elzinga DB, Jellen EN, Morales JA, Udall JA, Fairbanks DJ, Bonifacio A.

Genome. 2009 Jul;52(7):647-57. doi: 10.1139/G09-041.

PMID:
19767895
42.

Genomic expression dominance in allopolyploids.

Rapp RA, Udall JA, Wendel JF.

BMC Biol. 2009 May 1;7:18. doi: 10.1186/1741-7007-7-18.

43.

Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (gossypium).

Chaudhary B, Flagel L, Stupar RM, Udall JA, Verma N, Springer NM, Wendel JF.

Genetics. 2009 Jun;182(2):503-17. doi: 10.1534/genetics.109.102608. Epub 2009 Apr 10.

44.

Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense.

Chaudhary B, Hovav R, Rapp R, Verma N, Udall JA, Wendel JF.

Evol Dev. 2008 Sep-Oct;10(5):567-82. doi: 10.1111/j.1525-142X.2008.00272.x.

PMID:
18803775
45.

Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton.

Hovav R, Chaudhary B, Udall JA, Flagel L, Wendel JF.

Genetics. 2008 Jul;179(3):1725-33. doi: 10.1534/genetics.108.089656. Epub 2008 Jun 18.

46.

Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant.

Hovav R, Udall JA, Chaudhary B, Rapp R, Flagel L, Wendel JF.

Proc Natl Acad Sci U S A. 2008 Apr 22;105(16):6191-5. doi: 10.1073/pnas.0711569105. Epub 2008 Apr 17.

47.

The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism.

Hovav R, Udall JA, Chaudhary B, Hovav E, Flagel L, Hu G, Wendel JF.

PLoS Genet. 2008 Feb;4(2):e25. doi: 10.1371/journal.pgen.0040025.

48.

A majority of cotton genes are expressed in single-celled fiber.

Hovav R, Udall JA, Hovav E, Rapp R, Flagel L, Wendel JF.

Planta. 2008 Jan;227(2):319-29. Epub 2007 Sep 12.

PMID:
17849148
49.

Analyses of a multi-parent population derived from two diverse alfalfa germplasms: testcross evaluations and phenotype-DNA associations.

Maureira-Butler IJ, Udall JA, Osborn TC.

Theor Appl Genet. 2007 Oct;115(6):859-67. Epub 2007 Aug 4.

PMID:
17676305
50.

Spotted cotton oligonucleotide microarrays for gene expression analysis.

Udall JA, Flagel LE, Cheung F, Woodward AW, Hovav R, Rapp RA, Swanson JM, Lee JJ, Gingle AR, Nettleton D, Town CD, Chen ZJ, Wendel JF.

BMC Genomics. 2007 Mar 27;8:81.

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