2020

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, In press.

Bernard, A. & Gélinas, N. 2020. Assessment of a public participation tool by experts: a case study of Québec, Canada. Natural Resources, 11: 283-306 (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, In press.

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).

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).

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, In press.

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).

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).

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).

Lenz, P.R.N., Nadeau, S., Mottet, M-J., Perron, M., Isabel, N., Beaulieu, J., Bousquet, J., 2019. Multi-trait genomic selection for weevil resistance, growth, and wood quality in Norway spruce. Evolutionary Applications. 2019; 00 (10.1111/eva.12823).

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 (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 (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, 2: 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).

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).

Jackman, S.D., Vandervalk, B.P., Mohamadi, H., Chu, J., Yeo, S., Hammond, S.A., Jahesh, G., Khan, H., Coombe, L., Warren, R.L. & Birol, I. 2017. ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Genome Res. 27:768 (10.1101/gr.214346.116).

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).

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).

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

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: 1-13 (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).