Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

Abstract

These authors contributed equally to this work. SUMMARYWhite 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.

A genome for gnetophytes and early evolution of seed plants

“…gymnosperms showed large-scale specific expansions of pfam domains in genes associated with defence and secondary metabolism, as previously suggested (Supplementary Table 16) 10,11 . The clustering of G. montanum with non-seed plants in the heatmap (Fig.…”

“…So far, the availability of whole genome sequences for gymnosperms has been limited to conifers (specifically to Pinaceae) [10][11][12][13] and G. biloba 14 , with no whole genome assemblies available for the two remaining major seed plant lineages-cycads and gnetophytes. This deficiency, together with the conflicting phylogenetic evidence for relationships among these groups, is impeding our understanding of genome evolution across all seed plants.…”

“…Consequently, several possible hypotheses have been put forward that place gnetophytes as sister to (1) Pinaceae ('Gnepine' hypothesis); (2) cupressophytes ('Gnecup' hypothesis); (3) all conifers ('Gnetifer' hypothesis); (4) all other gymnosperms; or (5) all seed plants 9 . Currently, the emerging consensus, based on both older and more recent studies, and recently released data from the 1KP initiative (see https://sites.google.com/a/ualberta.ca/onekp/, and Wickett et al 8 ), indicates that gnetophytes are sister to, or within, the conifers.So far, the availability of whole genome sequences for gymnosperms has been limited to conifers (specifically to Pinaceae) [10][11][12][13] and G. biloba 14 , with no whole genome assemblies available for the two remaining major seed plant lineages-cycads and gnetophytes. This deficiency, together with the conflicting phylogenetic evidence for relationships among these groups, is impeding our understanding of genome evolution across all seed plants.…”

A Conifer UDP-Sugar Dependent Glycosyltransferase Contributes to Acetophenone Metabolism and Defense against Insects

“…UGTs involved in these processes have been characterized in several angiosperms, but very few UGTs involved in the glycosylation of small molecules have been described in gymnosperms. The recent development of genome and transcriptome assemblies for white spruce (Birol et al, 2013;Warren et al, 2015) made it possible to define large gene families, such as UGTs, in the extremely large space of an ;20-Gb conifer genome. However, functional annotation of UGTs remains a major challenge.…”

“…Research on UGTs in gymnosperms has been limited due to the lack of genetic and genomic resources and the difficulty in recombinant expression of the encoded proteins. Recent advances in the development of genome and transcriptome resources for white spruce, a conifer, have enabled our ability to better explore this gene family in the background of a large gymnosperm genome (Birol et al, 2013;Warren et al, 2015).…”