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Items: 1 to 50 of 86

1.

Genomic architecture of complex traits in loblolly pine.

De La Torre AR, Puiu D, Crepeau MW, Stevens K, Salzberg SL, Langley CH, Neale DB.

New Phytol. 2018 Oct 14. doi: 10.1111/nph.15535. [Epub ahead of print]

PMID:
30318590
2.

Genomic Variation Among and Within Six Juglans Species.

Stevens KA, Woeste K, Chakraborty S, Crepeau MW, Leslie CA, Martínez-García PJ, Puiu D, Romero-Severson J, Coggeshall M, Dandekar AM, Kluepfel D, Neale DB, Salzberg SL, Langley CH.

G3 (Bethesda). 2018 Jul 2;8(7):2153-2165. doi: 10.1534/g3.118.200030.

3.

Comparative Transcriptomics Among Four White Pine Species.

Baker EAG, Wegrzyn JL, Sezen UU, Falk T, Maloney PE, Vogler DR, Delfino-Mix A, Jensen C, Mitton J, Wright J, Knaus B, Rai H, Cronn R, Gonzalez-Ibeas D, Vasquez-Gross HA, Famula RA, Liu JJ, Kueppers LM, Neale DB.

G3 (Bethesda). 2018 May 4;8(5):1461-1474. doi: 10.1534/g3.118.200257.

4.

Environmental effects on fine-scale spatial genetic structure in four Alpine keystone forest tree species.

Mosca E, Di Pierro EA, Budde KB, Neale DB, González-Martínez SC.

Mol Ecol. 2018 Feb;27(3):647-658. doi: 10.1111/mec.14469. Epub 2018 Jan 29.

PMID:
29274175
5.

High rate of adaptive evolution in two widespread European pines.

Grivet D, Avia K, Vaattovaara A, Eckert AJ, Neale DB, Savolainen O, González-Martínez SC.

Mol Ecol. 2017 Dec;26(24):6857-6870. doi: 10.1111/mec.14402. Epub 2017 Dec 2.

PMID:
29110402
6.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Oct 1;6(10):1. doi: 10.1093/gigascience/gix072.

7.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Salzberg SL, Wegrzyn JL.

G3 (Bethesda). 2017 Sep 7;7(9):3157-3167. doi: 10.1534/g3.117.300078.

8.

Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles.

Cronn R, Dolan PC, Jogdeo S, Wegrzyn JL, Neale DB, St Clair JB, Denver DR.

BMC Genomics. 2017 Jul 24;18(1):558. doi: 10.1186/s12864-017-3916-y.

9.

Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.).

Ćalić I, Koch J, Carey D, Addo-Quaye C, Carlson JE, Neale DB.

BMC Genomics. 2017 Jul 20;18(1):547. doi: 10.1186/s12864-017-3931-z.

10.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Jan 1;6(1):1-4. doi: 10.1093/gigascience/giw016. Erratum in: Gigascience. 2017 Oct 1;6(10):1.

11.

Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA.

Lind BM, Friedline CJ, Wegrzyn JL, Maloney PE, Vogler DR, Neale DB, Eckert AJ.

Mol Ecol. 2017 Jun;26(12):3168-3185. doi: 10.1111/mec.14106. Epub 2017 May 6.

PMID:
28316116
12.

Novel Insights into Tree Biology and Genome Evolution as Revealed Through Genomics.

Neale DB, Martínez-García PJ, De La Torre AR, Montanari S, Wei XX.

Annu Rev Plant Biol. 2017 Apr 28;68:457-483. doi: 10.1146/annurev-arplant-042916-041049. Epub 2017 Feb 6. Review.

PMID:
28226237
13.

Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis.

Kujala ST, Knürr T, Kärkkäinen K, Neale DB, Sillanpää MJ, Savolainen O.

Heredity (Edinb). 2017 May;118(5):413-423. doi: 10.1038/hdy.2016.115. Epub 2016 Nov 30.

14.

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

Gonzalez-Ibeas D, Martinez-Garcia PJ, Famula RA, Delfino-Mix A, Stevens KA, Loopstra CA, Langley CH, Neale DB, Wegrzyn JL.

G3 (Bethesda). 2016 Dec 7;6(12):3787-3802. doi: 10.1534/g3.116.032805.

15.

Sequence of the Sugar Pine Megagenome.

Stevens KA, Wegrzyn JL, Zimin A, Puiu D, Crepeau M, Cardeno C, Paul R, Gonzalez-Ibeas D, Koriabine M, Holtz-Morris AE, Martínez-García PJ, Sezen UU, Marçais G, Jermstad K, McGuire PE, Loopstra CA, Davis JM, Eckert A, de Jong P, Yorke JA, Salzberg SL, Neale DB, Langley CH.

Genetics. 2016 Dec;204(4):1613-1626. Epub 2016 Oct 28.

16.

Quantitative trait loci influencing forking defects in an outbred pedigree of loblolly pine.

Xiong JS, McKeand SE, Isik F, Wegrzyn J, Neale DB, Zeng ZB, da Costa E Silva L, Whetten RW.

BMC Genet. 2016 Oct 18;17(1):138.

17.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols.

Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB.

Plant J. 2016 Sep;87(5):507-32. doi: 10.1111/tpj.13207. Epub 2016 Jul 18.

18.

Evaluation of a bilayered, micropatterned hydrogel dressing for full-thickness wound healing.

Magin CM, Neale DB, Drinker MC, Willenberg BJ, Reddy ST, La Perle KM, Schultz GS, Brennan AB.

Exp Biol Med (Maywood). 2016 May;241(9):986-95. doi: 10.1177/1535370216640943. Epub 2016 Mar 31.

19.

A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda.

Westbrook JW, Chhatre VE, Wu LS, Chamala S, Neves LG, Muñoz P, Martínez-García PJ, Neale DB, Kirst M, Mockaitis K, Nelson CD, Peter GF, Davis JM, Echt CS.

G3 (Bethesda). 2015 Jun 11;5(8):1685-94. doi: 10.1534/g3.115.019588.

20.

Micro- and macro-geographic scale effect on the molecular imprint of selection and adaptation in Norway spruce.

Scalfi M, Mosca E, Di Pierro EA, Troggio M, Vendramin GG, Sperisen C, La Porta N, Neale DB.

PLoS One. 2014 Dec 31;9(12):e115499. doi: 10.1371/journal.pone.0115499. eCollection 2014.

21.

Discovering candidate genes that regulate resin canal number in Pinus taeda stems by integrating genetic analysis across environments, ages, and populations.

Westbrook JW, Walker AR, Neves LG, Munoz P, Resende MF Jr, Neale DB, Wegrzyn JL, Huber DA, Kirst M, Davis JM, Peter GF.

New Phytol. 2015 Jan;205(2):627-41. doi: 10.1111/nph.13074. Epub 2014 Sep 30.

22.

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines.

DeGiorgio M, Syring J, Eckert AJ, Liston A, Cronn R, Neale DB, Rosenberg NA.

BMC Evol Biol. 2014 Mar 29;14:67. doi: 10.1186/1471-2148-14-67.

23.

Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.

Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, Dejong PJ, Mockaitis K, Main D, Langley CH, Neale DB.

Genetics. 2014 Mar;196(3):891-909. doi: 10.1534/genetics.113.159996.

24.

Sequencing and assembly of the 22-gb loblolly pine genome.

Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH.

Genetics. 2014 Mar;196(3):875-90. doi: 10.1534/genetics.113.159715.

25.

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.

Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH.

Genome Biol. 2014 Mar 4;15(3):R59. doi: 10.1186/gb-2014-15-3-r59.

26.

Multilocus analyses reveal little evidence for lineage-wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus).

Eckert AJ, Bower AD, Jermstad KD, Wegrzyn JL, Knaus BJ, Syring JV, Neale DB.

Mol Ecol. 2013 Nov;22(22):5635-50. doi: 10.1111/mec.12514. Epub 2013 Oct 18.

PMID:
24134614
27.

The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae).

Eckert AJ, Wegrzyn JL, Liechty JD, Lee JM, Cumbie WP, Davis JM, Goldfarb B, Loopstra CA, Palle SR, Quesada T, Langley CH, Neale DB.

Genetics. 2013 Dec;195(4):1353-72. doi: 10.1534/genetics.113.157198. Epub 2013 Oct 11.

28.

Environmental versus geographical determinants of genetic structure in two subalpine conifers.

Mosca E, González-Martínez SC, Neale DB.

New Phytol. 2014 Jan;201(1):180-92. doi: 10.1111/nph.12476. Epub 2013 Sep 16.

29.

Insights into the loblolly pine genome: characterization of BAC and fosmid sequences.

Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA.

PLoS One. 2013 Sep 4;8(9):e72439. doi: 10.1371/journal.pone.0072439. eCollection 2013.

30.

Association of loblolly pine xylem development gene expression with single-nucleotide polymorphisms.

Palle SR, Seeve CM, Eckert AJ, Wegrzyn JL, Neale DB, Loopstra CA.

Tree Physiol. 2013 Jul;33(7):763-74. doi: 10.1093/treephys/tpt054.

PMID:
23933831
31.

Open access to tree genomes: the path to a better forest.

Neale DB, Langley CH, Salzberg SL, Wegrzyn JL.

Genome Biol. 2013 Jun 24;14(6):120. doi: 10.1186/gb-2013-14-6-120.

32.

Adaptive evolution of Mediterranean pines.

Grivet D, Climent J, Zabal-Aguirre M, Neale DB, Vendramin GG, González-Martínez SC.

Mol Phylogenet Evol. 2013 Sep;68(3):555-66. doi: 10.1016/j.ympev.2013.03.032. Epub 2013 Apr 13.

PMID:
23591087
33.

Association genetics of oleoresin flow in loblolly pine: discovering genes and predicting phenotype for improved resistance to bark beetles and bioenergy potential.

Westbrook JW, Resende MF Jr, Munoz P, Walker AR, Wegrzyn JL, Nelson CD, Neale DB, Kirst M, Huber DA, Gezan SA, Peter GF, Davis JM.

New Phytol. 2013 Jul;199(1):89-100. doi: 10.1111/nph.12240. Epub 2013 Mar 28.

34.

CartograTree: connecting tree genomes, phenotypes and environment.

Vasquez-Gross HA, Yu JJ, Figueroa B, Gessler DD, Neale DB, Wegrzyn JL.

Mol Ecol Resour. 2013 May;13(3):528-37. doi: 10.1111/1755-0998.12067. Epub 2013 Feb 25.

PMID:
23433187
35.

Association genetics of chemical wood properties in black poplar (Populus nigra).

Guerra FP, Wegrzyn JL, Sykes R, Davis MF, Stanton BJ, Neale DB.

New Phytol. 2013 Jan;197(1):162-76. doi: 10.1111/nph.12003. Epub 2012 Nov 16.

36.

Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests.

Mosca E, Eckert AJ, Liechty JD, Wegrzyn JL, La Porta N, Vendramin GG, Neale DB.

Evol Appl. 2012 Nov;5(7):762-75. doi: 10.1111/j.1752-4571.2012.00256.x.

37.

The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps.

Mosca E, Eckert AJ, Di Pierro EA, Rocchini D, La Porta N, Belletti P, Neale DB.

Mol Ecol. 2012 Nov;21(22):5530-45. doi: 10.1111/mec.12043. Epub 2012 Oct 12.

PMID:
23058000
38.

Spatially variable natural selection and the divergence between parapatric subspecies of lodgepole pine (Pinus contorta, Pinaceae).

Eckert AJ, Shahi H, Datwyler SL, Neale DB.

Am J Bot. 2012 Aug;99(8):1323-34. doi: 10.3732/ajb.1200055. Epub 2012 Jul 26.

39.

Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome.

Eckert AJ, Wegrzyn JL, Cumbie WP, Goldfarb B, Huber DA, Tolstikov V, Fiehn O, Neale DB.

New Phytol. 2012 Mar;193(4):890-902. doi: 10.1111/j.1469-8137.2011.03976.x. Epub 2011 Nov 30.

40.

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine.

Chancerel E, Lepoittevin C, Le Provost G, Lin YC, Jaramillo-Correa JP, Eckert AJ, Wegrzyn JL, Zelenika D, Boland A, Frigerio JM, Chaumeil P, Garnier-Géré P, Boury C, Grivet D, González-Martínez SC, Rouzé P, Van de Peer Y, Neale DB, Cervera MT, Kremer A, Plomion C.

BMC Genomics. 2011 Jul 18;12:368. doi: 10.1186/1471-2164-12-368.

41.

DnaSAM: Software to perform neutrality testing for large datasets with complex null models.

Eckert AJ, Liechty JD, Tearse BR, Pande B, Neale DB.

Mol Ecol Resour. 2010 May;10(3):542-5. doi: 10.1111/j.1755-0998.2009.02768.x. Epub 2009 Oct 5.

PMID:
21565054
42.

Forest tree genomics: growing resources and applications.

Neale DB, Kremer A.

Nat Rev Genet. 2011 Feb;12(2):111-22. doi: 10.1038/nrg2931. Review.

PMID:
21245829
43.

Evolution of disease response genes in loblolly pine: insights from candidate genes.

Ersoz ES, Wright MH, González-Martínez SC, Langley CH, Neale DB.

PLoS One. 2010 Dec 6;5(12):e14234. doi: 10.1371/journal.pone.0014234.

44.

Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem.

Wegrzyn JL, Eckert AJ, Choi M, Lee JM, Stanton BJ, Sykes R, Davis MF, Tsai CJ, Neale DB.

New Phytol. 2010 Oct;188(2):515-32. doi: 10.1111/j.1469-8137.2010.03415.x. Epub 2010 Sep 10.

45.

Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae).

Eckert AJ, Bower AD, González-Martínez SC, Wegrzyn JL, Coop G, Neale DB.

Mol Ecol. 2010 Sep;19(17):3789-805. doi: 10.1111/j.1365-294X.2010.04698.x. Epub 2010 Aug 13.

PMID:
20723060
46.

Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.).

Quesada T, Gopal V, Cumbie WP, Eckert AJ, Wegrzyn JL, Neale DB, Goldfarb B, Huber DA, Casella G, Davis JM.

Genetics. 2010 Oct;186(2):677-86. doi: 10.1534/genetics.110.117549. Epub 2010 Jul 13.

47.

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences.

Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB.

BMC Genomics. 2010 Jul 7;11:420. doi: 10.1186/1471-2164-11-420.

48.

Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae).

Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J, González-Martínez SC, Neale DB.

Genetics. 2010 Jul;185(3):969-82. doi: 10.1534/genetics.110.115543. Epub 2010 May 3. Erratum in: Genetics. 2014 May;197(1):433.

49.

PineSAP--sequence alignment and SNP identification pipeline.

Wegrzyn JL, Lee JM, Liechty J, Neale DB.

Bioinformatics. 2009 Oct 1;25(19):2609-10. doi: 10.1093/bioinformatics/btp477. Epub 2009 Aug 10.

50.

Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas Fir (Pseudotsuga menziesii var. menziesii).

Eckert AJ, Wegrzyn JL, Pande B, Jermstad KD, Lee JM, Liechty JD, Tearse BR, Krutovsky KV, Neale DB.

Genetics. 2009 Sep;183(1):289-98. doi: 10.1534/genetics.109.103895. Epub 2009 Jul 13.

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