title: Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.
abstract: White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: René L
authors.initials: RL
authors.lastname: Warren
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Christopher I
authors.initials: CI
authors.lastname: Keeling
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Macaire Man Saint
authors.initials: MM
authors.lastname: Yuen
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Anthony
authors.initials: A
authors.lastname: Raymond
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Greg A
authors.initials: GA
authors.lastname: Taylor
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Vandervalk
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Hamid
authors.initials: H
authors.lastname: Mohamadi
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Daniel
authors.initials: D
authors.lastname: Paulino
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Readman
authors.initials: R
authors.lastname: Chiu
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Shaun D
authors.initials: SD
authors.lastname: Jackman
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Gordon
authors.initials: G
authors.lastname: Robertson
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Chen
authors.initials: C
authors.lastname: Yang
authors.affiliation: Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Brian
authors.initials: B
authors.lastname: Boyle
authors.affiliation: Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany.
authors.forename: Margarete
authors.initials: M
authors.lastname: Hoffmann
authors.affiliation: Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany.
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.affiliation: Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Nelson
authors.affiliation: Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Carol
authors.initials: C
authors.lastname: Ritland
authors.affiliation: Natural Resources Canada, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Isabel
authors.affiliation: British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada.
authors.forename: Barry
authors.initials: B
authors.lastname: Jaquish
authors.affiliation: British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada.
authors.forename: Alvin
authors.initials: A
authors.lastname: Yanchuk
authors.affiliation: Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Jean
authors.initials: J
authors.lastname: Bousquet
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.|Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.|School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.affiliation: Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada.|Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
authors.forename: John
authors.initials: J
authors.lastname: MacKay
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.|Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.|School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
authors.forename: Inanc
authors.initials: I
authors.lastname: Birol
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.|Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.|Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Joerg
authors.initials: J
authors.lastname: Bohlmann
mesh_terms: D019883:Alkyl and Aryl Transferases / Q000378:metabolism; D019295:Computational Biology; D003577:Cytochrome P-450 Enzyme System / Q000378:metabolism; D018745:Genome, Plant; D005810:Multigene Family; D010636:Phenols / Q000378:metabolism*; D028222:Picea / Q000235:genetics*; D013729:Terpenes / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D010636:Phenols; D013729:Terpenes; D003577:Cytochrome P-450 Enzyme System; D019883:Alkyl and Aryl Transferases; C108877:terpene synthase
keywords: ABySS; Bloom filter; conifer genomes; genome finishing; genome scaffolding; whole-genome shotgun assembly