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

Abstract

BackgroundSeed 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.ResultsTo 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.ConclusionsTaken 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.

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines

“…The discovery of genes that are involved in local adaptation to climate in both species could be expected given their relatively recent divergence (< 12 MYA) and the high degree of synteny among conserved orthologous genes in conifers (Pavy et al., 2012). One of those genes, a flavodoxin family protein (0_7001_01), was associated with the end of the frost‐free period (eFFP) and temperature‐related variables (DD5, TD) in both species.…”

Accuracy of genomic selection models in a large population of open-pollinated families in white spruce

“…The white spruce genome is B2100 cM (Pavy et al, 2012b); therefore, the full SNP data set analyzed in the present study represented 2660 gene loci with an average rate of 2.4 SNPs per locus that would result in average genome coverage of B1.27 marker locus per cM. Although it is true that LD appears to be low in white spruce genes in essentially unrelated trees from natural populations, many exceptions were found where LD was sizeable (Namroud et al, 2010;Pavy et al, 2012a).…”

The Norway spruce genome sequence and conifer genome evolution

“…Each chromosome has grown to a similar size-perhaps limited by physical constraints on, for instance, chromosomal replication-with genes separated by large regions of transposable-element-rich, highly polymorphic non-protein-coding regions with low recombination frequencies. The gradual increase in size, the lack of WGDs and a predominately out-crossing mating system have probably also buffered conifer genomes against chromosomal rearrangements (WGD reduces sensitivity to aneuploidy), thereby maintaining synteny over large phylogenetic distances 44 .…”