2024
Depardieu, C., Lenz P., Marion, J., Nadeau S., Bégin C., Marchand W., Girardin M.P., Gessler A., Treydte K., Bousquet J., Savard, M.M. & Isabel N. 2024. Contrasting physiological strategies explain heterogeneous responses to severe drought conditions within local populations of a widespread conifer. Science of the Total Environment, 923: 171174 (14p.). (10.1016/j.scitotenv.2024.171174).
Hung, T.-H., Wu, E.T.Y., Zeltins, P., Jansons, A., Ullah, A., Erbilgin, N., Bohlmann, J., Bousquet, J., Birol, I., Clegg, S. & Mackay, JJ. 2024. Long-insert sequence capture detects high copy numbers in the defence beta-glucosidase gene βglu-1 with large variations in Picea glauca but not Picea abies. BMC Genomics, 25: 118 (16p.). (10.1186/s12864-024-09978-6).
Lo, T., Coombe L., Gagalova, K., Marr, A., Warren, R.L., Kirk, H., Pandoh, P., Zhao, Y., Moore, R.A., Mungall, A.J., Ritland, C., Pavy, N., Jones, S.M.J., Bohlmann, J., Bousquet, J., Birol, I. & Thomson, A. 2024. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response. G3 – Genes Genomes Genetics, 14: jkad247 (16p.) (10.1093/g3journal/jkad247).
Tumas, H., Ilska, J.J., Gérardi, S., Laroche, J., A’Hara, S., Boyle, B., Janes, M., McLean, P., Lopez, G., Lee, S.J., Cottrell, J., Gorjanc, G., Bousquet, J., Woolliams, J.A. & MacKay, J.J. 2024. High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers. G3 – Genes Genomes Genetics, 14: jkae020 (14p.). (10.1093/g3journal/jkae020).
Woudstra, Y., Tumas, H., van Gherlder, C., Hung, T.-H., Ilska, J.J., Gérardi, S., A’Hara, S., McLean, P., Cottrell, J., Bohlmann, J., Bousquet, J., Birol, I., Wooliams J.A. & Mackay, J.J. 2024. Conifers concentrate large numbers of NLR immune receptor genes on one chromosome. Genome Biology and Evolution, 16: evae113 (15p.). (10.1093/gbe/evae113).
2023
Nadeau, S., Beaulieu J., Gezan, S.A., Perron, M., Bousquet, J. & Lenz, P.R.N. 2023. Increasing genomic prediction accuracy for unphenotyped full-sib families by modeling additive and dominance effects
with large datasets in white spruce. Frontiers in Plant Science, 14: 1137834 (24p.) (10.3389/fpls.2023.1137834).
Soro, A., Lenz, P., Roussel, J.-R., Larochelle, F., Bousquet, J. & Achim, A. 2023. The phenotypic and genetic effects of drought-induced stress on apical growth, ring width, wood density and biomass in white spruce seedlings. New Forests, 54: 789-811 (10.1007/s11056-022-09939-5).
Soro, A., Lenz, P., Roussel, J.-R., Pothier, D., Bousquet, J. & Achim, A. 2023. The phenotypic and genetic effects of drought-induced stress on wood specific conductivity and anatomical properties in white spruce seedlings, and relationships with growth and wood density. Frontiers in Plant Science, 14: 1297314 (17p.) (10.3389/fpls.2023.1297314).
2022
Afshinfard, A., Jackman, S.D., Wong, J., Coombe, L., Chu, J., Nikolic, V., Dilek, G., Malkoç, Y., Warren, R.L. & Birol, I. 2022. Physlr: Next-Generation Physical Maps. DNA, 2: 116-130 (10.3390/dna2020009).
Beaulieu, J., Lenz, P. & Bousquet, J. 2022. Metadata analysis indicates biased estimation of genetic parameters and gains using pedigree information instead of genomic-based approaches in tree breeding. Scientific Reports, 12: 3933 (10p.) (10.1038/s41598-022-06681-y).
Benomar, L., Bousquet, J., Perron, M., Beaulieu, J. & Lamara, M. 2022. Tree maladaptation under mid-latitude early spring warming and late cold spells: implications for assisted migration. Frontiers in Plant Science, 13: 920852 (12p.) (10.3389/fpls.202).
Gagalova, K.K., Warren, R.L., Coombe, L., Wong, J., Nip, K.M., Yuen, M.M.S., Whitehill, J.G.A., Celedon, J.M., Ritland, C., Taylor, G.A., Cheng, D., Plettner, P., Hammond, S.A., Mohamadi, H., Zhao, Y., Moore, R.A., Mungall, A.J., Boyle, B., Laroche, J., Cottrell, J., Mackay, J.J., Lamothe, M., Gérardi, S., Isabel, N., Pavy, N., Jones, S.J.M., Bohlmann, J., Bousquet, J. & Birol, I. 2022. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. The Plant Journal, 111: 1469-1485 (10.111/tpj.15889).
Gagalova, K.K., Whitehill, J.G.A., Culibrk, L., Lin, D., Lévesque-Tremblay, V., Keeling, C.I., Coombe, L., Yuen, M.M.S., Birol, I., Bohlmann, J. , Jones, S.J.M. 2022. The genome of the forest insect pest Pissodes strobi reveals genome expansion and evidence of a Wolbachia endosymbiont. G3 Genes Genomes Genetics, 12:jkac038 (10.1093/g3journal/jkac038 ).
Harikumar, A., D’Odorico, P., & Ensminger, I. 2022. Combining spectral, spatial-contextual, and structural information in multispectral UAV data for spruce crown delineation. Remote Sensing, 14: 244-263 (10.3390/rs14092044).
Laverdière, J.P., Lenz, P., Nadeau, S., Depardieu, C., Isabel, N., Perron, M., Beaulieu, J. & Bousquet, J. 2022. Breeding for adaptation to climate change: genomic selection for drought response in a white spruce multi-site polycross test. Evolutionary Applications, 15: 383-402
(10.1111/eva.13348).
Rashidi-Jouybari, I., Lenz, P., Beaulieu, J., Nadeau, S., Bousquet, J. & Achim, A. 2022. Muli-trait selection for improved solid wood physical and flexural properties in white spruce (Picea glauca). Forestry, 95: 492-503 (h10.1093/forestry/cpac006).
Soro, A., Lenz, P., Hassegawa, M., Roussel, J.-R., Bousquet, J. & Achim, A. 2022. Genetic influence on components of wood density in white spruce. Forestry, 75: 153-165 (10.1093/forestry/cpab044).
Wong, C.Y.S., Mercado, L.M., Arain, M.A. & Ensminger, I. 2022. Remotely sensed carotenoid dynamics improve modelling photosynthetic phenology in conifer and deciduous forests. Agriculture and Forest Meteorology, 321: 108977 (10.1016/j.agrformet.2022.108977 ).
2021
Bousquet, J., Gérardi, S., de Lafontaine, G., Jaramillo-Correa, J.P., Pavy, N., Prunier, J., Lenz, P. & Beaulieu, J. 2021. Spruce population genomics. In Population Genomics: Forest Trees. Ed. O.P. Rajora. Springer, 64p. (link.springer.com/chapter/10.1007/13836_2021_96#citeas).
Coombe, L., Li, J.X., Lo, T., Wong, J., Nikolic, V., Warren, R.L. & Birol, I. 2021. LongStitch: high-quality genome assembly correction and scaffolding using long reads. BMC Bioinformatics, 22: 534 (10.1186/s12859-021-04451-7).
Depardieu, C., Gérardi, S., Nadeau, S., Parent, G., Mackay, J., Lenz, P., Bousquet, J. & Isabel, N. 2021. Connecting tree-ring phenotypes, association genomics, and transcriptomics to decipher the genomic architecture of drought tolerance in a widespread conifer. Molecular Ecology, 30: 3898-3917 (10.1111/mec.15846). Cet article a été désigné pour la page de couverture du numéro du mois d’août 2021 du journal et à fait l’objet d’un article de perspective publié au pages 3893-3895 de ce même numéro.
Depardieu, C., M. Girardin, S. Nadeau, S. Gérardi, P. Lenz, M. Lamothe, J. Bousquet & N. Isabel. 2021. L’amélioration de la résilience des forêts face aux épisodes climatiques extrêmes: savoir lire entre les cernes. Climatoscope 3 (Octobre): 64-69 (https://climatoscope.ca/wp-content/uploads/2021/10/Le_Climatoscope_Num3_2021_Depardieu.pdf)
D’Odorico,, P., Schönbeck, L., Vitali, V., Meusburger, K., Schaub, M., Ginzler, C., Zweifel, R., Marjorie, V., Velasco, E., Gisler, J., Gessier, A. & Ensminger, I. 2021. Drone‐based physiological index reveals long‐term acclimation and drought stress responses in trees. Plant, Cell & Environment, 44: 3552-3570 (10.1111/pce.14177).
Galeano, E., Bousquet, J. & Thomas, B.R. 2021. SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program. Scientific Reports, 11: 4990 (14p.) (10.1038/s41598-021-84566-2).
Girardin, M.P., Isabel, N., Guo, X.J., Lamothe, M., Duchesne, I. & Lenz, P. 2021. Annual aboveground carbon uptake enhancements from assisted gene flow in boreal black spruce forests are not long-lasting. Nature Communications, 12: 1169 (15p.) (10.1038/s41467-021-21222-3).
Harikumar, A., Suyi, W. & Ensminger, I. 2021. A band grouping based approach for phenotype-class mapping of tree genotypes using spectro-temporal information in hyperspectral time-series UAV data. IEEE International Geoscience and Remote Sensing Symposium IGARSS, (10.1109/IGARSS47720.2021.9555063).
Laoué, J., Depardieu, C., Gérardi, S., Lamothe, M., Bomal, C., Azaiez, A., Gros-Louis, M.C., Laroche, J., Boyle, B., Hammerbacher, A., Isabel N. & Bousquet, J. 2021. Combining QTL mapping and transcriptomics to decipher the genetic architecture of phenolic compounds metabolism in the conifer white spruce. Frontiers in Plant Science, 112: 793 (20p.) (10.3389/fpls.2021.675108).
Royer-Tardif, S., Boisvert-Marsh, L., Godbout, J., Isabel, N. & Aubin. I. 2021. Finding common ground: Toward comparable indicators of adaptive capacity of tree species to a changing climate. 2021. Ecology and evolution, 11: 13081-13100 (10.1002/ece3.8024).
Thiffault, N., Raymond, P., Lussier, J.-M., Aubin, I., Roy-Tardif, S., D’Amato, A., Doyon, F., Lafleur, B., Perron, M., Bousquet, J., Isabel, N., Carles, S., Lupien, P. & Malenfant, A. 2021. Sylviculture d’adaptation aux changements climatiques: des concepts à la réalité. The Forestry Chronicle, 97: 28-42 (10.5558/tfc2021-005).
Thiffault, N., Raymond, P., Lussier, J.-M., Aubin, I., Roy-Tardif, S., D’Amato, A., Doyon, F., Lafleur, B., Perron, M., Bousquet, J., Isabel, N., Carles, S., Lupien, P. & Malenfant, A. 2021. Sylviculture d’adaptation aux changements climatiques : des concepts à la réalité. The Forestry Chronicle, 97: 28-42 (10.5558/tfc2021-005 ).
Whitehill, J.G.A., Yuen, M.M.S. & Bohlmann, J. 2021. Constitutive and insect-induced transcriptomes of weevil-resistant and susceptible sitka spruce. Plant-Environment Interactions, 2:137-147
(10.1002/pei3.10053).
2020
Ahmed, S., Lemay, V., Yanchuk, A., Robinson, A., Marshall, P. & Bull, G. 2020. Meta-modelling to quantify yields of white spruce and hybrid spruce provenances in the canadian boreal forest. Evolutionary Applications, 13: 62-75 (10.3390/f11060609).
Beaulieu, J., Nadeau, S., Ding, C., Celedon, J.M., Azaiez, A., Ritland, C., Laverdière, J.-P., Deslauriers, M., Adams, G., Fullarton, M., Bohlmann, J., Lenz, P. & Bousquet, J. 2020. Genomic selection for resistance to spruce budworm in white spruce and relationships with growth and wood quality traits. Evolutionary Applications, 13: 2704-2722 (10.1111/eva.13076).
Bernard, A. & Gélinas, N. 2020. Assessment of a public participation tool by experts: a case study of Québec, Canada. Natural Resources, 11: 283-307 (10.4236/nr.2020.117017).
Bernard, A., Gélinas, N. & Bélanger, L. 2020. Bilan de la gestion intégrée des ressources et du territoire au Québec. Forestry Chronicle, 96: 90-99 (10.5558/tfc2020-014).
Birol, I. & De La Torre, A.R. 2020. Sequencing and assembling the nuclear and organelle genomes of North American spruces. In The Spruce Genome. Eds. I. Porth & A.R. De La Torre. Springer Nature, 8p. (10.1007/978-3-030-21001-4_1).
Celedon, J., Whitehill, J., Madilo, L. & Bohlmann, J. 2020. Gymnosperm glandular trichomes: expanded dimensions of the conifer terpenoid defense system. Scientific Reports, 10: 12464 (9p.) (10.1038/s41598-020-69373-5).
Chamberland, V., Robichaud, F., Perron, M., Gélinas, N., Bousquet, J. & Beaulieu, J. 2020. Conventional versus genomic selection for white spruce improvement: a cost-benefit analysis for plantations on Québec public lands. Tree Genetics and Genomes, 16: 17 (16p.) (10.1007/s11295-019-1409-7).
Coombe, L., Nokolic, V., Chu, J., Birol, I. & Warren R.L. 2020. ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs. Bioinformatics, 26: 3885-3887 (10.1093/bioinformatics/btaa253).
Depardieu, C., Girardin, M.P., Nadeau, S., Lenz, P., Bousquet, J. & Isabel, N. 2020. Adaptive genetic variation to drought in a widely distributed conifer suggests a potential for increasing forest resilience in a drying climate. New Phytologist, 227: 427-439 (10.111/nph.16551).
D’Odorico, P., Besik, A., Wong, C.Y.S., Isabel, N. & Ensminger, I. 2020. High-throughput drone based remote sensing reliably tracks phenology in thousands of conifer seedlings. New Phytologist, 226: 1667-1681 (10.1111/nph.16488).
Hafezqorani, S., Yang, C., Lo, T., Nip, K.M., Warren, R.L. & Birol, I. 2020. Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data. GigaScience, 9(6): 1-7 (10.1093/gigascience/giaa061).
Hassegawa, M., Savard, M., Lenz, P.R.N., Duchateau, E., Gélinas, N., Bousquet, J. & Achim, A. 2020. White spruce wood quality for lumber products: priority traits and their enhancement through tree improvement. Forestry, 93: 16-37 (10.1093/forestry/cpz050).
Isabel, N., Holliday, J.A. & Aitken, S.N. 2020. Forest genomics: advancing climate adaptation, forest health, productivity, and conservation. Presentation of the Evolutionary Applications special issue of January 2020. Evolutionary Applications, 13: 3-10 (10.1111/eva.12902).
Jackman, S.D., Coombe, L., Warren, R.L., Kirk, H., Trinh, E., MacLeod, T., Pleasance, S., Pandoh, P., Zhao, Y., Coope, R.J., Bousquet, J., Bohlmann, J., Jones, S.J.M., Birol, I. 2020. Complete mitochondrial genome of a gymnosperm, Sitka spuce (Picea sitchensis), indicates a complex physical structure. Genome Biology and Evolution, 12: 1174-1179 (10.1093/gbe/evaa108).
Lenz, P.R.N., Nadeau, S., Azaiez, A., Gérardi, S., Deslauriers, M., Perron, M., Isabel, N., Beaulieu, J. & Bousquet, J. 2020. Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce. Heredity, 124: 562-578 (10.1038/s41437-019-0290-3).
Lenz, P.R.N., Nadeau, S., Mottet, M.-J., Perron, M., Isabel, I., Beaulieu, J. & Bousquet, J. 2020. Multi-trait genomic selection for weevil resistance, growth and wood quality traits in Norway spruce. Evolutionary Applications, 13: 76-94 (10.1111/eva.12823).
Lo, T., Coombe, L., Lin, D., Warren, R., Kirk, H., Pandoh, P., Zhao, Y., Moore, R., Mungall, A., Ritland, C., Bousquet, J., Jones, S., Bohlmann, J., Thomson, A. & Birol, I. 2020. Complete chloroplast genome sequence of a black spruce (Picea mariana) from Eastern Canada. Microbiology Resource Announcements, 8(23): e00381-19 (4p.) (10.1128/MRA.00877-20).
Marchand, W., Girardin, M.P., Hartmann, H., Depardieu, C., Isabel, N., Gauthier, S., Boucher, E. & Bergeron, Y. 2020. Strong overestimation of water-use efficiency responses to rising CO2 in tree-ring studies. Global Change Biology, 26: 4538-4558 (10.1111/gcb.15166).
Nip, K.M., Chiu, R., Yang, C., Chu, J., Mohamadi, H., Warren, R. & Birol, I. 2020. RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes. Genome Research, 30(8): 1191-1200 (10.1101/gr.260174.119).
Parent, G., Méndez-Espinoza, C., Giguère, I., Mageroy, M., Charest, M., Bauce, E., Bohlmann, J. & Mackay, J. 2020. Hydroxyacetophenone defenses in white spruce against spruce budworm. Evolutionary Applications, 13: 62-75 (10.1111/eva.12885).
Wong, C.Y.S, D’Odorico, P., Arain, M.A. & Ensminger, I. 2020. Tracking the phenology of photosynthesis using carotenoid-sensitive and near-infrared reflectance vegetation indices in a temperate evergreen and mixed deciduous forest. New Phytologist, 226: 1682-1695 (10.1111/eva.13076).
2019
Celedon, J. & Bohlmann, J. 2019. Oleoresin defenses in conifers: chemical diversity, terpene synthases, and limitations of oleoresin defense under climate change. New Phytologist, 224: 1444-1463 (10.1111/nph.15984).
Coursolle, C., Otis-Prud’homme, G., Lamothe, M. & Isabel, N. 2019. Measuring rapid A–Ci curves in boreal conifers: black spruce and balsam fir. Frontiers in Plant Science, 10: 1276 (9p.) (10.3389/fpls.2019.01276).
Jackman, S.D., Mozgacheva, T., Chen S., O’Huiginn, B., Bailey, L., Birol, I. & Jones, S.J.M. 2019. ORCA: A comprehensive bioinformatics container environment for education and research. Bioinformatics, 35(21): 4448-4450 (10.1093/bioinformatics/btz278).
Lin, D., Coombe, L., Jackman, S., Gagalova, K., Warren, R., Hammond, S., McDonald, H., Kirk, H., Pandoh, P., Zhao, Y., Moore, R., Mungall, A., Ritland, C., Doerksen, T., Jaquish, B., Bousquet, J., Jones, S., Bohlmann, J. & Birol, I. 2019. Complete chloroplast genome sequence of an Engelmann spruce (Picea engelmannii) genotype from western Canada. Microbiology Resource Announcements, 8(24): e00382-19 (3p.) (10.1128/MRA.00382-19).
Lin, D., Coombe, L., Jackman, S., Gagalova, K., Warren, R., Hammond, S., Kirk, H., Pandoh, P., Zhao. Y., Moore, R., Mungall, A., Ritland, C., Doerksen, T., Jaquish, B., Isabel, N., Bousquet, J., Jones, S., Bohlmann, J. & Birol, I. 2019. Complete chloroplast genome sequence of a white spruce (Picea glauca) genotype from eastern Canada. Microbiology Resource Announcements, 8(23): e00381-19 (4p.) (10.1128/MRA.00381-19).
Lochhead, K., Ghafghazi, S., LeMay, V. & Bull, G.Q. 2019. Examining the vulnerability of localized reforestation strategies to climate change at a macroscale. Journal of Environmental Management, 252: 109625 (14p.)(10.1016/j.jenvman.2019.109625).
Van Ghelder, C., Parent, G.J., Rigault, P., Prunier, J., Giguère, I., Caron, S., Stival Sena, J., Deslauriers, A., Bousquet, J., Esmenjaud, D. & Mackay, J. 2019. The large repertoire of conifer NLR conifer resistance genes includes drought responsive and highly diversified RNLs. Scientific Reports, 9: 11614 (13p.) (10.1038/s41598-019-47950-7).
Warren, R.L., Coombe, L., Mohamadi, H., Zhang, J., Jaquish, B., Isabel, N., Jones, S.J.M., Bousquet, J., Bohlmann, J. & Birol, I. 2019. ntEdit: scalable genome sequence polishing. Bioinformatics, 35(21): 4430-4432 (10.1093/bioinformatics/btz400).
Whitehill, J.G.A. & Bohlmann, J. 2019. A molecular and genomic reference system for conifer defense against insects. Plant, Cell, & Environment, 42: 2844-2859 (10.1111/pce.13571).
Whitehill, J.G.A., Yuen, M.M.S., Henderson, H., Madilao, L., Kshatriya, K., Bryan, J., Jaquish, B. & Bohlmann, J. 2019. Functions of stone cells and oleoresin terpenes in the conifer defense syndrome. New Phytologist, 221: 1503-1517 (10.1111/nph.15477).
Wong, C., D’Odorico, P., Bhathena, Y., Arain, A. & Ensminger, I. 2019. Carotenoid based vegetation indices for accurate monitoring of the phenology of photosynthesis at the leaf-scale in deciduous and evergreen trees. Remote Sensing of Environment, 233: 111407 (14p.) (10.1016/j.rse.2019.111407).
2018
Azaiez, A., Pavy, N., Gérardi, S., Laroche, J., Boyle, B., Gagnon, F., Mottet, M.-J., Beaulieu, J. & Bousquet, J. 2018. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics 19: 942 (13p.) (10.1186/s12864-018-5247-z).
Celedon, J.M. & Bohlmann, J. 2018. An extended model of heartwood secondary metabolism informed by functional genomics. Tree Physiology 38: 311-319 (10.1093/treephys/tpx070).
Coombe, L., Zhang, J., Vandervalk, B.P., Chu, J., Jackman, S.D., Birol, I. & Warren, R.L. 2018. ARKS: chromosome-scale scaffolding of human genome drafts with linked reads. BMC Bioinformatics 19: 234 (10p.) (10.1186/s12859-018-2243-x).
Housset, J.M., Nadeau, S., Isabel, N., Depardieu, C., Duchesne, I., Lenz, P. & Girardin, M.P. 2018. Tree rings provide a new class of phenotypes for genetic associations that foster insights into adaptation of conifers to climate change. New Phytologist 216: 630-645 (10.1111/nph.14968).
Jackman, S.D., Coombe, L., Chu, J., Warren, R.L., Vandervalk, B.P., Yeo, S., Xue, Z., Mohamadi, H., Bohlmann, J., Jones, S.J.M. & Birol, I. 2018. Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinformatics 19: 393 (10.1186/s12859-018-2425-6).
Khan, H., Mohamadi, H., Vandervalk, B.P., Warren, R.L., Chu, J. & Birol, I. 2018. ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. Bioinformatics 34: 1697-1704 (10.1093/bioinformatics/btx839).
Lamara, M., Parent, G.J., Giguère, I., Beaulieu, J., Bousquet, J. & MacKay, J. 2018. Association genetics of acetophenone defence against spruce budworm in mature white spruce. BMC Plant Biology 18: 231 (15p.) (10.1186/s12870-018-1434-y).
Lochhead, K., LeMay, V., Bull, G., Schwab, O. & Halperin, J. 2018. Multivariate estimation for accurate and logically-consistent forest attributes maps at macroscales. Canadian Journal of Forest Research 48: 345–359 (10.1139/cjfr-2017-0221).
Méndez-Espinoza, C., Parent, G.J., Lenz, P., Rainville, A., Tremblay, L., Adams, G., McCartney, A., Bauce, E. & MacKay, J. 2018. Genetic control and evolutionary potential of a constitutive resistance mechanism against the spruce budworm (Choristoneura fumiferana) in white spruce (Picea glauca). Heredity 121: 142–154 (10.1038/s41437-018-0061-6).
Parent, G.J., Giguère, I., Mageroy, M., Bohlmann, J. & MacKay, J.J. 2018. Evolution of the biosynthesis of two hydroxyacetophenones in plants. Plant, Cell & Environment 41: 620-629 (10.1111/pce.13134).
Stival Senna, J., Giguère, I., Rigault, P., Bousquet, J. & Mackay, J.J. 2018. Expansion of the dehydrin gene family in conifers is associated with considerable structural diversity and drought-responsive expression. Tree Physiology 38: 442-456 (10.1093/treephys/tpx125).
Tsai, C.J., Harding, S. & Cooke, J. 2018. Branching out: a new era of investigating physiological processes in forest trees using genomic tools. Tree Physiology 38: 303–310 (10.1093/treephys/tpy026).
Warren, R.L. 2018. Visualizing genome synteny with xmatchview. Journal of Open Source Software, 3: 497-500 (10.21105/joss.00497).
Yeo, S., Coombe, L., Warren, R.L., Chu, J. & Birol, I. 2018. ARCS: scaffolding genome drafts with linked reads. Bioinformatics 34: 725-731 (10.1093/bioinformatics/btx675).
2017
Celedon, J.M., Yuen, M.M.S., Chiang, A., Henderson, H., Reid, K.E. & Bohlmann, J. 2017. Cell-type and tissue specific transcriptomes of the white spruce (Picea glauca) bark unmask fine-scale spatial patterns of constitutive and induced conifer defense. The Plant Journal 92: 710-726 (10.1111/tpj.13673).
Ghafghazi, S., Lochhead, K., Mathey, A., Forsell, N., Leduc, S., Mabee, W. & Bull, G.Q. 2017. Estimating mill residue surplus in Canada: A spatial forest fibre cascade modelling approach. Forest Products Journal 67: 205-218 (10.13073/FPJ-D-16-00031).
Godbout, J., Tremblay, L., Levasseur, C., Lavigne, P., Rainville, A., MacKay, J., Bousquet, J. & Isabel, N. 2017. Development of a traceability system based on a SNP array for large-scale production of high-value white spruce (Picea glauca). Frontiers in Plant Science 8: 1264 (13p.) (10.3389/fpls.2017.01264).
Kucuk, E., Chu, J., Vandervalk, B.P., Hammon, A., Warren, R.L. & Birol, I. 2017. Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinformatics 33: 1782-1788 (10.1093/bioinformatics/btx405).
Lenz, P., Beaulieu, J., Clement, S., Mansfield, S., Desponts, M. & Bousquet, J. 2017. Factors affecting the accuracy of genomic selection for growth and wood quality traits in an advanced-breeding population of black spruce (Picea mariana). BMC Genomics 18: 335 (17p.) (10.1186/s12864-017-3715-5).
Mageroy, M.H., Jancsik, S., Yuen, M.M.S., Fischer, M., Withers, S.G., Paetz, C., Schneider, B. & Bohlmann, J. 2017. A conifer UDP-sugar dependent glycosyltransferase contributes to acetophenone metabolism and defense against insects. Plant Physiology 175: 641-651 (10.1104/pp.17.00611).
Mageroy, M.H, Lachance, D., Jancsik, S., Parent, G., Séguin, A., MacKay, J. & Bohlmann, J. 2017. In vivo function of Pgßglu-1 in the release of acetophenones in white spruce. PeerJ 5: e3535 (11p.) (10.7717/peerj.3535).
Mohamadi, H., Khan, H. & Birol, I. 2017. ntCard: a streaming algorithm for cardinality estimation in genomics data. Bioinformatics, 33: 1324-1330 (10.1093/bioinformatics/btw832).
Pavy, N., Lamothe, M., Pelgas, B., Gagnon, F., Birol, I., Bohlmann, J., Mackay, J., Isabel, N. & Bousquet, J. 2017. A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. The Plant Journal 90: 189-203 (10.1111/tpj.13478).
Prunier, J., Caron, S., Lamothe, M., Blais, S., Bousquet, J., Isabel, N. & Mackay, J. 2017. Gene copy number variations and adaptive evolution: the genomic architecture of gene CNVs revealed by genetic mapping and their adaptive role in a non domesticated species, white spruce. Molecular Ecology 26: 5989-6001 (10.1111/mec.14337).
Rossi, S. & Isabel, N. 2017. The timing of bud break in warming conditions: variation among seven sympatric conifers. International Journal of Biometeorology 61: 1983-1991 (doi.10.1007/s00484-017-1391-4).
Yang, C., Chu, J., Warren, R.L. & Birol, I. 2017. NanoSim: nanopore sequence read simulator based on statistical characterization. GigaScience, 6: 1-6 (10.1093/gigascience/gix010).
Yeo, S., Coombe, L., Warren, R.L., Chu, J. & Birol, I. 2017. ARCS: scaffolding genome drafts with linked reads. Bioinformatics, 43: 725 (10.1093/bioinformatics/btx675).
2016
Aubin, I., Munson, A.D., Cardou, G., Burton, P.J., Isabel, N., Pedlar, J.H., Paquette, A., Taylor, A.R., Delagrange, S., Kebli, H., Messier, C., Shipley, B., Valladares, F., Kattge, J., Boisvert-Marsh, L. & McKenney, D. 2016. Traits to stay, traits to move: a review of functional traits to assess sensitivity and adaptive capacity of temperate and boreal trees to climate change. Environmental Reviews, 24: 164-186 (10.1139/er-2015-0072).
Coombe, L., Warren, R.L., Yang, C., Vandervalk, B.P., Mayo, M., Moore, R.A., Pleasance, S., Coope, R.J., Bohlmann, J., Holt, R.A., Jones, S.J.M. & Birol, I. 2016. Assembly of the complete Sitka spruce chloroplast genome using 10X Genomics’ GemCode sequencing data. PLoS ONE 11(9): e0163059 (13p.) (10.1371/journal.pone.0163059).
Geisler, K., Jensen, N.B., Yuen, M.M.S., Madilao, L. & Bohlmann, J. 2016. Modularity of conifer diterpene resin acid biosynthesis: P450 enzymes of different CYP720B clades use alternative substrates and converge on the same products. Plant Physiology 171: 152-164 (10.1104/pp.16.00180).
Jackman, S.D., Warren, R.L., Gibb, E.A., Vandervalk, B.P., Mohamadi, H., Chu, J., Raymond, A., Pleasance, S., Coope, R., Wildung, M.R., Ritland, C.E., Bousquet, J., Jones, S.J., Bohlmann, J. & Birol, I. 2016. Organellar genomes of white spruce (Picea glauca): Assembly and annotation. Genome Biology and Evolution 8: 29-41 (10.1093/gbe/evv244).
Lamara, M., Raherison, E., Lenz, P., Beaulieu, J., Bousquet, J. & Mackay, J. 2016. Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce. New Phytologist 210: 240-255 (10.1111/nph.13762).
Lochhead, K., Ghafghazi, S., Havlik, P., Forsell, N., Obersteiner, M., Bull, G. & Mabee, W. 2016. Price trends and volatility scenarios for designing forest sector transformation. Energy Economics 57: 184-191 (ENEECO-D-13-00353R1).
Park, Y.-S., Beaulieu, J. & Bousquet, J. 2016. Multi-varietal forestry integrating genomic selection and somatic embryogenesis. In Park, Y.-S., Bonga, J. & Moon, H.-K. (eds). Vegetative Propagation of Forest Trees. National Institute of Forest Science, Seoul, South Korea. Pp. 302-322.
Pavy, N., Gagnon, F., Deschênes, A., Boyle, B., Beaulieu, J. & Bousquet, J. 2016. Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from boreal black spruce (Picea mariana). Molecular Ecology Resources 16: 588-598 (0.1111/1755-0998.12468).
Whitehill, J.G.A., Henderson, H., Schuetz, M., Skyba, O., Yuen, M.M.S., King, J., Samuels, A.L., Mansfield, S.D. & Bohlmann, J. 2016. Histology and cell wall biochemistry of stone cells in the physical defense of conifers against insects. Plant, Cell & Environment 39: 1646-1661 (10.1111/pce.12654).
Whitehill, J.G.A., Henderson, H., Strong, W., Jaquish, B. & Bohlmann, J. 2016. Functions of Sitka spruce stone cells as a physical defense against white pine weevil. Plant, Cell & Environment 39: 2545-2556 (10.1111/pce.12810).