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Open Access Research article

A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers

Nathalie Pavy1*, Betty Pelgas12, Jérôme Laroche3, Philippe Rigault14, Nathalie Isabel12 and Jean Bousquet1

Author affiliations

1 Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada

2 Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 Rue du PEPS, CP 10380, Succ. Sainte-Foy, Québec, Québec G1V 4C7, Canada

3 Bioinformatics Platform, Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada

4 Gydle Inc., 1363 Avenue Maguire, Québec, Québec G1T 1Z2, Canada

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Citation and License

BMC Biology 2012, 10:84  doi:10.1186/1741-7007-10-84

Published: 26 October 2012

Abstract

Background

Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling.

Results

To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago.

Conclusions

Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants.

Keywords:
Angiosperm; duplication; evolution; gene families; genetic map; gymnosperm; phylogenomics; Picea; spruce; structural genomics