The genome of black spruce : genome annotation & analyses

Abiotic and biotic stresses associated with climate change have been identified as a dominant cause of forest tree mortality in boreal forests. Some tree populations may have the capacity for rapid adaptation or migration to keep pace with changing environmental conditions. One species of interest is black spruce (Picea mariana [Mill.] B.S.P.) as adaptive variation in relation to climate change has previously been reported for this transcontinental North American conifer. As exhibited in studies of other economically important forest trees, genomic resources play a critical role in advancing our understanding of the genomic basis of adaptive variation; however, such resources are lacking for black spruce, with the few available being predominantly transcriptome-related. This thesis describes the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. To showcase the value of this new genomic resource, phylogenetic and comparative genomics analyses were performed. Phylogenetic trees were estimated from the nuclear and organelle genome sequences of P. mariana and five other spruces. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and three other taxa found in western North America, followed by the European P. abies. In contrast, mixed topologies with weaker statistical support were obtained in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these two genomes. Clustering of protein-coding sequences from the six Picea taxa and two Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups indicate gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.

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