Journal
Plant J
Authors
Kristina K Gagalova, René L Warren, Lauren Coombe, Johnathan Wong, Ka Ming Nip, Macaire Man Saint Yuen, Justin Ga Whitehill , Jose M Celedon, Carol Ritland, Greg A Taylor, Dean Cheng, Patrick Plettner, S Austin Hammond, Hamid Mohamadi, Yongjun Zhao, Richard A Moore, Andrew J Mungall, Brian Boyle, Jérôme Laroche, Joan Cottrell, John J Mackay, Manuel Lamothe, Sébastien Gérardi, Nathalie Isabel, Nathalie Pavy, Steven Jm Jones, Joerg Bohlmann, Jean Bousquet, Inanc Birol.

Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (P. sitchensis) together with improved and more contiguous genome assemblies for white spruce (P. glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of nonsynonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests.

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