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Development of nuclear microsatellite loci for Pinus albicaulis Engelm. (Pinaceae), a conifer of conservation concern.

Lea MV, Syring J, Jennings T, Cronn R, Bruederle LP, Neale JR, Tomback DF.

PLoS One. 2018 Oct 18;13(10):e0205423. doi: 10.1371/journal.pone.0205423. eCollection 2018.


eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications.

Coble AA, Flinders CA, Homyack JA, Penaluna BE, Cronn RC, Weitemier K.

Sci Total Environ. 2019 Feb 1;649:1157-1170. doi: 10.1016/j.scitotenv.2018.08.370. Epub 2018 Aug 28. Review.


Functional trait divergence and trait plasticity confer polyploid advantage in heterogeneous environments.

Wei N, Cronn R, Liston A, Ashman TL.

New Phytol. 2018 Oct 3. doi: 10.1111/nph.15508. [Epub ahead of print]


PacBio-Based Mitochondrial Genome Assembly of Leucaena trichandra (Leguminosae) and an Intrageneric Assessment of Mitochondrial RNA Editing.

Kovar L, Nageswara-Rao M, Ortega-Rodriguez S, Dugas DV, Straub S, Cronn R, Strickler SR, Hughes CE, Hanley KA, Rodriguez DN, Langhorst BW, Dimalanta ET, Bailey CD.

Genome Biol Evol. 2018 Sep 1;10(9):2501-2517. doi: 10.1093/gbe/evy179.


Evolution at the tips: Asclepias phylogenomics and new perspectives on leaf surfaces.

Fishbein M, Straub SCK, Boutte J, Hansen K, Cronn RC, Liston A.

Am J Bot. 2018 Mar;105(3):514-524. doi: 10.1002/ajb2.1062. Epub 2018 Apr 25.


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.


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.


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.


Source identification of western Oregon Douglas-fir wood cores using mass spectrometry and random forest classification.

Finch K, Espinoza E, Jones FA, Cronn R.

Appl Plant Sci. 2017 May 12;5(5). pii: apps.1600158. doi: 10.3732/apps.1600158. eCollection 2017 May.


A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny.

Pham KK, Hipp AL, Manos PS, Cronn RC.

Genome. 2017 Sep;60(9):720-732. doi: 10.1139/gen-2016-0191. Epub 2017 Apr 26.


Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus).

Schroeder H, Cronn R, Yanbaev Y, Jennings T, Mader M, Degen B, Kersten B.

PLoS One. 2016 Jun 28;11(6):e0158221. doi: 10.1371/journal.pone.0158221. eCollection 2016.


Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome.

Syring JV, Tennessen JA, Jennings TN, Wegrzyn J, Scelfo-Dalbey C, Cronn R.

Front Plant Sci. 2016 Apr 21;7:484. doi: 10.3389/fpls.2016.00484. eCollection 2016.


Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing.

Staton M, Best T, Khodwekar S, Owusu S, Xu T, Xu Y, Jennings T, Cronn R, Arumuganathan AK, Coggeshall M, Gailing O, Liang H, Romero-Severson J, Schlarbaum S, Carlson JE.

PLoS One. 2015 Dec 23;10(12):e0145031. doi: 10.1371/journal.pone.0145031. eCollection 2015.


Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae).

Schmickl R, Liston A, Zeisek V, Oberlander K, Weitemier K, Straub SC, Cronn RC, Dreyer LL, Suda J.

Mol Ecol Resour. 2016 Sep;16(5):1124-35. doi: 10.1111/1755-0998.12487. Epub 2015 Dec 15.


Fragaria: a genus with deep historical roots and ripe for evolutionary and ecological insights.

Liston A, Cronn R, Ashman TL.

Am J Bot. 2014 Oct;101(10):1686-99. doi: 10.3732/ajb.1400140. Epub 2014 Sep 17. Review.


Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics.

Weitemier K, Straub SC, Cronn RC, Fishbein M, Schmickl R, McDonnell A, Liston A.

Appl Plant Sci. 2014 Aug 29;2(9). pii: apps.1400042. doi: 10.3732/apps.1400042. eCollection 2014 Sep.


Microsatellite primers for the Pacific Northwest conifer Callitropsis nootkatensis (Cupressaceae).

Jennings TN, Knaus BJ, Alderman K, Hennon PE, D'Amore DV, Cronn R.

Appl Plant Sci. 2013 Sep 2;1(9). pii: apps.1300025. doi: 10.3732/apps.1300025. eCollection 2013 Sep.


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.


Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (apocynaceae).

Straub SC, Cronn RC, Edwards C, Fishbein M, Liston A.

Genome Biol Evol. 2013;5(10):1872-85. doi: 10.1093/gbe/evt140.


A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation.

Howe GT, Yu J, Knaus B, Cronn R, Kolpak S, Dolan P, Lorenz WW, Dean JF.

BMC Genomics. 2013 Feb 28;14:137. doi: 10.1186/1471-2164-14-137.


Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing.

Alexander A, Steel D, Slikas B, Hoekzema K, Carraher C, Parks M, Cronn R, Baker CS.

Genome Biol Evol. 2013;5(1):113-29. doi: 10.1093/gbe/evs126.


Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing.

Njuguna W, Liston A, Cronn R, Ashman TL, Bassil N.

Mol Phylogenet Evol. 2013 Jan;66(1):17-29. doi: 10.1016/j.ympev.2012.08.026. Epub 2012 Sep 14.


Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae).

Parks M, Cronn R, Liston A.

BMC Evol Biol. 2012 Jun 25;12:100. doi: 10.1186/1471-2148-12-100.


Targeted enrichment strategies for next-generation plant biology.

Cronn R, Knaus BJ, Liston A, Maughan PJ, Parks M, Syring JV, Udall J.

Am J Bot. 2012 Feb;99(2):291-311. doi: 10.3732/ajb.1100356. Epub 2012 Feb 6.


Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.

Straub SC, Parks M, Weitemier K, Fishbein M, Cronn RC, Liston A.

Am J Bot. 2012 Feb;99(2):349-64. doi: 10.3732/ajb.1100335. Epub 2011 Dec 14.


Microsatellite primers for the Pacific Northwest endemic conifer Chamaecyparis lawsoniana (Cupressaceae).

Jennings TN, Knaus BJ, Kolpak S, Cronn R.

Am J Bot. 2011 Nov;98(11):e323-5. doi: 10.3732/ajb.1100317. Epub 2011 Oct 19.


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.


Newly developed primers for complete ycf1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility.

Parks M, Liston A, Cronn R.

Am J Bot. 2011 Jul;98(7):e185-8. doi: 10.3732/ajb.1100088. Epub 2011 Jun 17.


Multiplexed microsatellite recovery using massively parallel sequencing.

Jennings TN, Knaus BJ, Mullins TD, Haig SM, Cronn RC.

Mol Ecol Resour. 2011 Nov;11(6):1060-7. doi: 10.1111/j.1755-0998.2011.03033.x. Epub 2011 Jun 16.


Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera.

Zapiola ML, Cronn RC, Mallory-Smith CA.

Mol Ecol Resour. 2010 Jul;10(4):738-40. doi: 10.1111/j.1755-0998.2009.02828.x. Epub 2010 Jan 20.


Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.

Straub SC, Fishbein M, Livshultz T, Foster Z, Parks M, Weitemier K, Cronn RC, Liston A.

BMC Genomics. 2011 May 4;12:211. doi: 10.1186/1471-2164-12-211.


Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore.

Knaus BJ, Cronn R, Liston A, Pilgrim K, Schwartz MK.

BMC Ecol. 2011 Apr 20;11:10. doi: 10.1186/1472-6785-11-10.


Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine.

Magbanua ZV, Ozkan S, Bartlett BD, Chouvarine P, Saski CA, Liston A, Cronn RC, Nelson CD, Peterson DG.

PLoS One. 2011 Jan 21;6(1):e16214. doi: 10.1371/journal.pone.0016214.


Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines.

Whittall JB, Syring J, Parks M, Buenrostro J, Dick C, Liston A, Cronn R.

Mol Ecol. 2010 Mar;19 Suppl 1:100-14. doi: 10.1111/j.1365-294X.2009.04474.x.


Tangled trios?: Characterizing a hybrid zone in Castilleja (Orobanchaceae).

Hersch-Green EI, Cronn R.

Am J Bot. 2009 Aug;96(8):1519-31. doi: 10.3732/ajb.0800357. Epub 2009 Jul 6.


Reticulate evolution and incomplete lineage sorting among the ponderosa pines.

Willyard A, Cronn R, Liston A.

Mol Phylogenet Evol. 2009 Aug;52(2):498-511. doi: 10.1016/j.ympev.2009.02.011. Epub 2009 Feb 26.


Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology.

Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T.

Nucleic Acids Res. 2008 Nov;36(19):e122. doi: 10.1093/nar/gkn502. Epub 2008 Aug 27.


Interspecific phylogenetic analysis enhances intraspecific phylogeographical inference: a case study in Pinus lambertiana.

Liston A, Parker-Defeniks M, Syring JV, Willyard A, Cronn R.

Mol Ecol. 2007 Sep;16(18):3926-37.


Widespread genealogical nonmonophyly in species of Pinus subgenus Strobus.

Syring J, Farrell K, Businsk√Ĺ R, Cronn R, Liston A.

Syst Biol. 2007 Apr;56(2):163-81.


Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for pinus.

Willyard A, Syring J, Gernandt DS, Liston A, Cronn R.

Mol Biol Evol. 2007 Jan;24(1):90-101. Epub 2006 Sep 22. Erratum in: Mol Biol Evol. 2007 Feb;24(2):620. Ann, Willyard [corrected to Willyard, Ann].


Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci.

Syring J, Willyard A, Cronn R, Liston A.

Am J Bot. 2005 Dec;92(12):2086-100. doi: 10.3732/ajb.92.12.2086.


Cryptic repeated genomic recombination during speciation in Gossypium gossypioides.

Cronn R, Small RL, Haselkorn T, Wendel JF.

Evolution. 2003 Nov;57(11):2475-89.


Rate variation among nuclear genes and the age of polyploidy in Gossypium.

Senchina DS, Alvarez I, Cronn RC, Liu B, Rong J, Noyes RD, Paterson AH, Wing RA, Wilkins TA, Wendel JF.

Mol Biol Evol. 2003 Apr;20(4):633-43. Epub 2003 Apr 2.


Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing.

Adams KL, Cronn R, Percifield R, Wendel JF.

Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4649-54. Epub 2003 Mar 28.


Evolution and expression of MYB genes in diploid and polyploid cotton.

Cedroni ML, Cronn RC, Adams KL, Wilkins TA, Wendel JF.

Plant Mol Biol. 2003 Feb;51(3):313-25.


PCR-mediated recombination in amplification products derived from polyploid cotton.

Cronn R, Cedroni M, Haselkorn T, Grover C, Wendel JF.

Theor Appl Genet. 2002 Feb;104(2-3):482-489.


Length and sequence heterogeneity in 5S rDNA of Populus deltoides.

Negi MS, Rajagopal J, Chauhan N, Cronn R, Lakshmikumaran M.

Genome. 2002 Dec;45(6):1181-8.


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