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Needle Retention in Christmas Trees: Balsam, Canaan, and Fraser fir

Needle Retention in Christmas Trees: Balsam, Canaan, and Fraser fir

Needle Retention in Christmas Trees: Balsam, Canaan, and Fraser fir

PLANT COMPUTATIONAL GENOMICS LAB – JILL WEGRZYN

PLANT COMPUTATIONAL GENOMICS LAB – JILL WEGRZYN

PLANT COMPUTATIONAL GENOMICS LAB – JILL WEGRZYN

Department of Ecology and Evolutionary Biology

Department of Ecology and Evolutionary Biology

Department of Ecology and Evolutionary Biology

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Publications
Pre-Prints
CartograPlant: Bridging genomic, phenotypic, and environmental data to advance plant resilience and eco-evolutionary insight.
Lind, B. M., Cobo-Simón, I., Myles, M., Barrett, G., Grau, E., Ramnath, R., Savitsky, V., & Wegrzyn, J. L. (2025)
EcoEvoRxiv, 2025.09.30.
Mink by mink: stitching together signatures of subspecies adaptation through a pangenome of threatened mustelids
Affini, A., Baranowski, H., Forbes, S., Foust, E. N., Hatley, K., Ni, E. L., McGuire, A., Paist, K., Rutter, M., Smith, R. N., Vargas, N., Akella, H., Castellano, K., Pauloski, N., Reid, N., O’Neill, R., King, T., Jockusch, E. L., Wegrzyn, J. L., & Hapeman, P. (2025)
bioRxiv, 2025.07.25.666817.
2025
Bryophytes hold a larger gene family space than vascular plants.
Dong, S., Wang, S., Li, L., Yu, J., Zhang, Y., Xue, J.-Y., Chen, H., Ma, J., Zeng, Y., Cai, Y., Huang, W., Zhou, X., Wu, J., Li, J., Yao, Y., Hu, R., Zhao, T., Villarreal, J.C.A., Dirick, L., Liu, L., Ignatov, M., Jin, M., Ruan, J., He, Y., Wang, H., Xu, B., Rozzi, R., Wegrzyn, J.L., Stevenson, D.W., Renzaglia, K.S., Chen, H., Zhang, L., Zhang, S., Mackenzie, R., Moreno, J.E., Melkonian, M., Wei, T., Gu, Y., Xu, X., Rensing, S.A., Huang, J., Long, M., Goffinet, B., Bowman, J.L., Van de Peer, Y., Liu, H., and Liu, Y. (2025)
Nature Genetics, 1–8.
Annotation of protein-coding genes in 49 diatom genomes from the Bacillariophyta clade.
Nenasheva, N., Pitzschel, C., Webster, C.N., Hart, A.J., Wegrzyn, J.L., Bengtsson, M.M., and Hoff, K.J. (2025)
Scientific Data, 12(1): 985.
A haplotype-resolved reference genome for Eucalyptus grandis.
Lötter, A., Bruna, T., Duong, T.A., Barry, K., Lipzen, A., Daum, C., Yoshinaga, Y., Grimwood, J., Jenkins, J.W., Talag, J., Borevitz, J., Lovell, J.T., Schmutz, J., Wegrzyn, J.L., and Myburg, A.A. (2025)
G3: Genes, Genomes, Genetics, 15(7): jkaf112.
Immediate premeiotic transcriptomic effects following nonchemically induced whole genome duplication in the moss Funaria hygrometrica.
Patel, N., Vuruputoor, V.S., Rahmatpour, N., Liu, Y., Szövényi, P., Goffinet, B., and Wegrzyn, J.L. (2025)
New Phytologist, 247(1).
Comparative analysis using a chromosome-scale genome assembly for Funaria hygrometrica suggests greater collinearity in mosses than in seed plants.
Kirbis, A., Rahmatpour, N., Dong, S., Yu, J., Waser, L., Huang, H., van Gessel, N., Waller, M., Reski, R., Lang, D., Rensing, S.A., Temsch, E.M., Wegrzyn, J.L., Goffinet, B., Liu, Y., and Szövényi, P. (2025)
Communications Biology, 8(1): 330.
Genome assembly of a living fossil, the Atlantic horseshoe crab Limulus polyphemus, reveals lineage-specific whole-genome duplications, transposable element-based centromeres, and a ZW sex chromosome system.
Castellano, K.R., Neitzey, M.L., Starovoitov, A., Barrett, G.A., Reid, N.M., Vuruputoor, V.S., Webster, C.N., Storer, J.M., Pauloski, N.R., Ameral, N.J., McEvoy, S.L., McManus, M.C., Puritz, J.B., Wegrzyn, J.L., and O’Neill, R.J. (2025)
Molecular Biology and Evolution, 42(2): msaf021.
2024
Crossroads of assembling a moss genome: Navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana
Vuruputoor, V.S., Starovoitov, A., Cai, Y., Liu, Y., Rahmatpour, N., Hedderson, T.A., Wilding, N., Wegrzyn, J.L., and Goffinet, B. (2024)
G3: Genes, Genomes, Genetics, 14(7): jkae104.
Unveiling the genetic blueprint of a desert scorpion: A chromosome-level genome of Hadrurus arizonensis provides the first reference for Parvorder Iurida
Bryant, M.J., Coello, A.M., Glendening, A.M., Hilliman, S.A., Jara, C.F., Pring, S.S., Rodríguez Rivera, A., Santiago Membreño, J., Nigro, L., Pauloski, N., Graham, M.R., King, T., Jockusch, E.L., O’Neill, R.J., Wegrzyn, J.L., Santibáñez-López, C.E., and Webster, C.N. (2024)
Genome Biology and Evolution, 16(5): evae097.
A genome sequence for the threatened whitebark pine
Neale, D.B., Zimin, A.V., Meltzer, A., Bhattarai, A., Amee, M., Figueroa Corona, L., Allen, B.J., Puiu, D., Wright, J., De La Torre, A.R., McGuire, P.E., Timp, W., Salzberg, S.L., and Wegrzyn, J.L. (2024)
G3: Genes, Genomes, Genetics, 14(5): jkae061.
Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology
McEvoy, S.L., Grady, P.G.S., Pauloski, N., O’Neill, R.J., and Wegrzyn, J.L. (2024)
Evolutionary Applications, 17: e13669.
Conserving a threatened North American walnut: A chromosome-scale reference genome for butternut (Juglans cinerea)
Guzman-Torres, C.R., Trybulec, E., LeVasseur, H., Akella, H., Amee, M., Strickland, E., Pauloski, N., Williams, M., Romero-Severson, J., Hoban, S., Wegrzyn, J.L., and Woeste, K. (2024)
G3: Genes, Genomes, Genetics, 14(1): jkad189.
Chromosome-level genome assembly and annotation of a periodical cicada species: Magicicada septendecula
Bush, J., Webster, C., Wegrzyn, J., Simon, C., Wilcox, E., Khan, R., Weisz, D., Dudchenko, O., Lieberman Aiden, E., and Frandsen, P. (2024)
Genome Biology and Evolution, 16(1): evae001.
Urban living can rescue Darwin’s finches from the lethal effects of invasive vampire flies
Knutie, S.A., Webster, C.N., Vaziri, G.J., Albert, L., Harvey, J.A., LaRue, M., Verrett, T.B., Soldo, A., Koop, J.A.H., Chaves, J.A., and Wegrzyn, J.L. (2024)
Global Change Biology, 30(1): e17145.
2023
Association genetics of wood traits in European black poplar (Populus nigra L.)
Kaya, Z., Taşkıran, B., Uluğ, A., Güvendiren, A.D., Wegrzyn, J.L., and Neale, D.B. (2023)
Tree Genetics & Genomes, 19(4): 38.
Welcome to the big leaves: Best practices for improving genome annotation in non-model plant genomes
Vuruputoor, V.S., Monyak, D., Fetter, K.C., Webster, C., Bhattarai, A., Shrestha, B., Zaman, S., Bennett, J., McEvoy, S.L., Caballero, M., and Wegrzyn, J.L. (2023)
Applications in Plant Sciences, 11(4): e11533.
Characterizing biological responses to climate variability and extremes to improve biodiversity projections
Buckley, L.B., Carrington, E., Dillon, M.E., García-Robledo, C., Roberts, S.B., Wegrzyn, J.L., and Urban, M.C. (2023)
PLOS Climate, 2(6): e0000226.
Multispecies comparison of host responses to Fusarium circinatum challenge in tropical pines show consistency in resistance mechanisms
Visser, E.A., Kampmann, T.P., Wegrzyn, J.L., and Naidoo, S. (2023)
Plant, Cell & Environment, 46(5): 1705-1725.
A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir)
Velasco, V.M., Ferreira, A., Zaman, S., Noordermeer, D., Ensminger, I., and Wegrzyn, J.L. (2023)
G3: Genes, Genomes, Genetics, 13(2): jkac304.
A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir)
Velasco, V.M., Ferreira, A., Zaman, S., Noordermeer, D., Ensminger, I., and Wegrzyn, J.L. (2023)
G3: Genes, Genomes, Genetics, 13(2): jkac304.
Contrasting transcriptomic patterns reveal a genomic basis for drought resilience in the relict fir Abies pinsapo Boiss
Cobo-Simón, I., Maloof, J., Li, R., Amini, H., Méndez-Cea, B., García-García, I., Gómez-Garrido, J., Esteve-Codina, A., Dabad, M., Alioto, T., Wegrzyn, J.L., Seco, J.I., Linares, J.C., and Gallego, F.J. (2023)
 Tree Physiology, 43(2): 315–334.
Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids
Lötter, L., Duong, T.A., Candotti, J., Mizrachi, E., Wegrzyn, J.L., Myburg, A.A. (2023)
GigaScience, 12: giad064.
2022
Changes in demography and geographic distribution in the weeping pinyon pine (Pinus pinceana) during the Pleistocene
Figueroa-Corona, L., Moreno-Letelier, A., Ortega-Del Vecchyo, D., Peláez, P., Gernandt, D. S., Eguiarte, L. E., Wegrzyn, J., & Piñero, D. (2022)
Ecology and Evolution, 12, e9369.
Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.)
Martínez-García, P.J., Mas-Gómez, J., Wegrzyn, J. and Botía, J.A. (2022)
Scientific Reports, 12(1): 1-10.
The Cycas genome and the early evolution of seed plants
Liu, Y., Wang, S., Li, L., Yang, T., Dong, S., Wei, T., Wu, S., Liu, Y., Gong, Y., Feng, X., Wegrzyn J.L., and Ma, J. (2022)
Nature Plants, 8: 1-13.
De novo assembly of a fruit transcriptome set identifies AmMYB10 as a key regulator of anthocyanin biosynthesis in Aronia melanocarpa
Mahoney, J.D., Wang, S., Iorio, L.A., Wegrzyn, J.L., Dorris, M., Martin, D., Bolling, B.W., Brand, M.H. and Wang, H. (2022)
BMC Plant Biology, 22(1): 1-16.
Strategies of tolerance reflected in two North American maple genomes
McEvoy, S.L., Sezen, U.U., Trouern‐Trend, A., McMahon, S.M., Schaberg, P.G., Yang, J., Wegrzyn, J.L. and Swenson, N.G. (2022)
The Plant Journal, 109(6): 1591-1613.
Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera
Webster, C., Figueroa‐Corona, L., Méndez‐González, I., Álvarez‐Soto, L., Neale, D., Jaramillo‐Correa, J., Wegrzyn, J.L, Vázquez‐Lobo, A. (2022)
Ecology and Evolution, 12(2): e8611.
NLR diversity and candidate fusiform rust resistance genes in loblolly pine
Ence, D., Smith, K.,Fan, S., Neves, L.G, Paul, R., Wegrzyn, J.L., Peter, G., Kirst, M., Brawner, J., Nelson, C., Davis, J. (2022)
G3: Genes|Genomes|Genetics, 12(2): jkab421.
A genome‐wide SNP genotyping resource for tropical pine tree species
Jackson, C., Christie, N., Reynolds, S.M., Marais, G.C., Tii‐kuzu, Y., Caballero, M., Kampman, T., Visser, E.A., Naidoo, S., Kain, D., Whetten, R.W., Isik, F., Wegrzyn, J.L., Hodge,G.R., Acosta, J.J., Myburg, A.A. (2022)
Molecular Ecology Resources, 22(2): 695-710.
Standards recommendations for the Earth BioGenome Project
Lawniczak, M.K., Durbin, R., Flicek, P., Lindblad-Toh, K., Wei, X., Archibald, J.M., Baker, W.J., Belov, K., Blaxter, M.L., Bonet, T.M., Childers, A.K., Coddington, J.A, Crandall, K.A., Crawford, A.J., Davey, R.P., Palma, F.D., Fang, Q., Haerty, W., Hall, N., … Wegrzyn, J.L. (2022)
Proceedings of the National Academy of Sciences, 72(4): 110-112.
Green plant genomes: What we know in an era of rapidly expanding opportunities
Kress, W.J., Soltis, D.E., Kersey, P.J., Wegrzyn, J.L., Leebens-Mack, J.H., Gostel, M.R., Liu, X. and Soltis, P.S. (2022)
Proceedings of the National Academy of Sciences, 119(4): e2115640118.
Assembled and Annotated 26.5 Gbp Coast Redwood Genome: A Resource for Estimating Evolutionary Adaptive Potential and Investigating Hexaploid Origin
Neale, D.B., Zimin, A.V., Zaman, S., Scott, A.D., Shrestha, B., Workman, R.E., Puiu, D., Allen, B.J., Moore, Z.J., Sekhwal, M.K., De La Torre, A.R., McGuire, P.E., Burns, E., Timp, W., Wegrzyn, J.L., and Salzberg, S.L. (2022)
G3: Genes|Genomes|Genetics, 12(1): jkab380.
2021
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases
Staton, M., Cannon, E., Sanderson, L., Wegrzyn, J.L., Anderson, T., Buehler, S., Cobo-Simón, I., Faaberg, K., Grau, E., Guignon, V., Gunoskey, J., Inderski, B., Jung, S., Lager, K., Main, D., Poelchau, M., Ramnath, R., Richter, P., West, J., Ficklin, S. (2021)
Briefings in Bioinformatics, bbab238: 17.
How to Publish at Pandemic Speed
Urban, M.C., Merow, C., Wegrzyn, J.L., Maitner, B.S. and Corcoran, D. (2021)
BioScience, 71(10): 1001-1003.
Gene Frequency Shift in Relict Abies pinsapo Forests Associated with Drought-Induced Mortality: Preliminary Evidence of Local-Scale Divergent Selection
Cobo-Simón, I., Méndez-Cea, B., Seco, J.I., Wegrzyn, J., Linares, J.C. and Gallego, F.J. (2021)
Forests, 12(9): 1220.
Transcriptome of weeping pinyon pine, Pinus pinceana, shows differences across heterogeneous habitats
Figueroa-Corona, L., Delgado Valerio, P., Wegrzyn, J.L., Piñero, D. (2021)
Trees, 35: 1351-1365.
Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome
Caballero, M., Lauer, E., Bennett, J., Zaman, S., McEvoy, S., Acosta, J., Jackson, C., Townsend, L., Eckert, A., Whetten, R. W., Loopstra C., Holliday J., Mandal, M., Wegrzyn, J. L., Isik, F. (2021)
Applications in Plant Sciences, 9(6): e11439.
Extensive variation in drought-induced gene expression changes between loblolly pine genotypes
Li, J., West, J. B., Hart, A., Wegrzyn, J. L., Smith, M. A., Domec, J., Loopstra, C. A., Casola, C. (2021)
Frontiers in Genetics, 12:659.
A reference genome sequence for Giant Sequoia
Scott, A., Zimin, A., Puiu, D., Workman, R., Britton, M., Zaman, S., Caballero, M., Read, A., Bogdanove, A., Burns, E., Wegrzyn J.L., Timp, W., Salzberg, S. and Neale, D. (2020)
G3; Genes|Genomes|Genetics, 10(11): 3907-3919.
High gene space divergence contrasts with frozen vegetative architecture in the moss family Funariaceae
Rahmatpour, N., Perera, N. V., Singh, V., Wegrzyn, J.L. L., & Goffinet, B. (2021)
Molecular Phylogenetics and Evolution, 154:106965.
2020
Comparative genomics of six Juglans species reveals disease‐associated gene family contractions
Trouern‐Trend, A.J.G, Falk, T.T, Zaman, S.G, Caballero, M.U, Neale, D.B., Langley, C.H., Dandekar, A.M., Stevens, K.A. and Wegrzyn, J.L. (2020)
The Plant Journal, 102(2): 410-423.
EnTAP: Bringing faster and smarter functional annotation to non‐model eukaryotic transcriptomes
Hart, A. J.G, Ginzburg, S.U, Xu, M. (Sam)U, Fisher, C. R.G, Rahmatpour, N.G, Mitton, J. B., Paul, R.P, and Wegrzyn, J. L. (2020)
Molecular Ecology Resources, 20: 591-604.
Co-option of wing-patterning genes underlies the evolution of the treehopper helmet
Fisher, C.R.G, Wegrzyn, J.L. and Jockusch, E.L. (2020)
Nature Ecology & Evolution, 4: 250-260.
Tripal and Galaxy: Supporting reproducible scientific workflows for community biological databases
Spoor, S., Wytko, C., Soto, B., Chen, M., Almsaeed, A., Condon, B., Herndon, N., Hough, H., Jung, S., Staton, M., Wegrzyn, J., Main, D., Feltus, F. A., & Ficklin, S. P. (2020)
Database, baaa032.
2019
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees
Wegrzyn, J.L., Falk, T., Grau, E, Buehler, S., Ramnath, R., Herndon, N. (2019)
Evolutionary Applications, 13: 228– 241.
Dual RNA-Seq analysis of the pine-Fusarium circinatum interaction in resistant (Pinus tecunumanii) and susceptible (Pinus patula) hosts
Visser, E. A., Wegrzyn, J. L., Steenkamp, E. T., Myburg, A. A., and Naidoo, S. (2019)
Microorganisms, 7(9): 315.
Cyberinfrastructure to improve forest health and productivity: The role of tree databases in connecting genomes, phenomes, and the environment
Wegrzyn, J.L., Staton, M.A., Street, N.R., Main, D., Grau, E., Herndon, N., Buehler, S., Falk, T., Zaman, S., Ramnath, R., Richter, P., Sun, L., Condon, B., Almsaeed, A., Chen, M., Mannapperuma, C., Jung, S. and Ficklin, S. (2019)
Frontiers in Plant Science, 10:813.
gFACs: Filtering, analysis, and conversion to unify genome annotations across alignment and gene prediction frameworks
Caballero, M.U and Wegrzyn, J.L. (2019)
Genomics, Proteomics, and Bioinformatics, 17(3): 305-310.
Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps
Buble, K., Jung, S., Humann, J. L., Yu, J., Cheng, C. H., Lee, T., Ficklin, S. P., Hough, H., Condon, B., Staton, M. E., Wegrzyn, J. L., and Main, D. (2019)
Database, baz100.
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases
Spoor, S., Cheng, C. H., Sanderson, L. A., Condon, B., Almsaeed, A., Chen, M., Bretaudeau, A., Rasche, H., Jung, S., Main, D., Bett, K., Staton, M., Wegrzyn, J. L., Feltus, F. A., and Ficklin, S. P. (2019)
Database, baz077.
2018
15 years of GDR: New data and functionality in the Genome Database for Rosaceae
Jung, S., Lee, T., Cheng, C.-H., Buble, K., Zheng, P., Yu, J., Humann, J., Ficklin, S. P., Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Evans, K., Peace, C., Olmstead, M., DeVetter, L. W., McFerson, J., Coe, M., Wegrzyn, J. L., Staton, M. E., Abbott, A. G., & Main, D. (2018)
Nucleic Acids Research, 47(D1): D1137–D1145.
Growing and cultivating the forest genomics database, TreeGenes
Falk, T., Herndon, N., Grau, E., Buehler, S., Richter, P., Zaman, S., Baker, E.M., Ramnath, R., Ficklin, S., Staton, M., Feltus, F.A., Jung, S., Main, D., and Wegrzyn, J. L. (2018)
Database, 2018: bay084-bay084.
Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation)
Visser, E. A., Wegrzyn, J. L., Myburg, A. A., & Naidoo, S. (2018)
BMC Genomics, 19(1): 632.
JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process
Wang, L., Jiang, Z., Huang, D., Wegrzyn, J.L., et al. (2018)
BMC Genomics, 19, 183.
Forward genetic analysis defines candidate genes for fusiform rust resistance in loblolly pine and avirulence in Cronartium quercuum f. sp fusiforme
Ence, D., Smith, K. M., Kirst, M., Yandell, M., Wegrzyn J.L., Nelson, C. D., & Davis, J. (2018)
Phytopathology, 108(10): 171-172.
Comparative transcriptomics among four white pine species
Baker, E. A.G., Wegrzyn, J. L., Sezen, U. U., Falk, T., Maloney, P. E., Vogler, D. R., Delfino-Mix, A., Jensen, C., Mitton, J., Wright, J., Knaus, B., Rai, H., Cronn, R., Gonzalez-Ibeas, D., Vasquez-Gross, H. A., Famula, R. A., Liu, J., Kueppers, L. M., & Neale, D. B. (2018)
G3: Genes, Genomes, Genetics, g3. 200257.2018.
Linking phenotype, genotype and environment to unravel genetic components underlying cold hardiness in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii)
Vangestel, C., Eckert, A. J., Wegrzyn, J. L., St Clair, J. B., & Neale, D. B. (2018)
Tree Genetics & Genomes, 14(1):10.
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., Andorf, C., Arnaud, E., Berardini, T.Z., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C.G., Farmer, A., Ficklin, S.P., Grant, D., Grau, E., Herndon, N., Hu, Z., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C., Munoz-Torres, M.C., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L., Sen, T.Z., Staton, M., Subramaniam, S., Tello-Ruiz, M.K., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J.L., Williams, J., Woodhouse, M., Yu, J., and Main, D. (2018)
Database, bay088.
2017
Finding loci associated with partial resistance to white pine blister rust in sugar pine (Pinus lambertiana Dougl.)
Vázquez-Lobo, A., De La Torre, A. R., Martínez-García, P. J., Vangestel, C., Wegrzyn, J. L., Ćalić, I., Burton, D., Davis, D., Kinloch, B., Vogler, D., & Neale, D. B. (2017)
Tree Genetics & Genomes, 13, 108.
The Douglas-Fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae
Neale, D. B., McGuire, P. E., Wheeler, N. C., Stevens, K. A., Crepeau, M. W., Cardeno, C., … & Wegrzyn, J. L. (2017)
G3: Genes|Genomes|Genetics, 7(9), 3157-3167.
Transcription through the eye of a needle: Daily and annual cyclic gene expression variation in Douglas-Fir needles
Cronn, R., Dolan, P. C., Jogdeo, S., Wegrzyn, J. L., Neale, D. B., Clair, J. S., & Denver, D. R. (2017)
BMC Genomics, 18(1), 558.
Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA
Lind, B. M., Friedline, C. J., Wegrzyn, J. L., Maloney, P. E., Vogler, D. R., Neale, D. B., & Eckert, A. J. (2017)
Molecular Ecology, 26(12), 3168-3185.
ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications
Sablok, G., Chen, T.-W., Lee, C.-C., Yang, C., Gan, R.-C., Wegrzyn, J. L., … & Tang, P. (2017)
DNA Research, dsw044.
Expression profiling in Pinus radiata infected with Fusarium circinatum
Carrasco, A., Wegrzyn, J. L., Durán, R., Fernández, M., Donoso, A., Rodriguez, V., … & Valenzuela, S. (2017)
Tree Genetics & Genomes, 13(2), 46.
Drought stress in Pinus taeda L. induces coordinated transcript accumulation of genes involved in the homogentisate pathway
Frelin, O., Dervinis, C., Wegrzyn, J. L., Davis, J. M., & Hanson, A. D. (2017)
Tree Genetics & Genomes, 13(1), 27.
Transcriptomic imprints of adaptation to fresh water: Parallel evolution of osmoregulatory gene expression in the Alewife
Velotta, J. P., Wegrzyn, J. L., Ginzburg, S., Kang, L., Czesny, S., O’Neill, R. J., … & Schultz, E. T. (2017)
Molecular Ecology, 26(3), 831–848.
TreeGenes and CartograTree: Enabling visualization and analysis in forest tree genomics
Grau, E. S., Demurjian, S. A., Vasquez-Gross, H. A., Gessler, D. G., Neale, D. B., & Wegrzyn, J. L. (2017)
In R. A. Sniezko, G. Man, V. Hipkins, K. Woeste, D. Gwaze, J. T. Kliejunas, & B. A. McTeague (Eds.), Gene conservation of tree species—banking on the future (p. 117). U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station.
New extension software modules to enhance searching and display of transcriptome data in Tripal databases
Chen, M., Henry, N., Almsaeed, A., Zhou, X., Wegrzyn, J. L., Ficklin, S., & Staton, M. (2017)
Database. bax052.
Transcriptome Analysis Reveals Differential Gene Expression and a Possible Role of Gibberellins in a Shade-Tolerant Mutant of Perennial Ryegrass
Li, W., Katin-Grazzini, L., Gu, X., Wang, X., El-tanbouly, R., Yer, H., Thammina, C., Inguagiato, J., Guillard, K., McAvoy, R., Wegrzyn, J. L., Gu, T., & Li, Y. (2017)
Frontiers in Plant Science. 8: 868.
An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing
Zimin, A. V., Stevens, K. A., Crepeau, M. W., Puiu, D., Wegrzyn, J. L., Yorke, J. A., … Salzberg, S. L. (2017)
GigaScience. 6(1): 1–4.