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

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.

Figure 1

Map of the spruce genome and tandemly arrayed genes. The 12 spruce chromosomes were plotted with Circos [100]. From inside to outside: gene-rich regions in red; the 12 chromosomes with ticks representing the genes mapped along the spruce linkage groups, and with genetic distances in cM (Kosambi); distribution of the tandemly arrayed genes. The chromosome nomenclature and numbers of genes mapped are inside the circle. For the complete names of tandemly arrayed genes, see Additional file 4.

Figure 2

Molecular functions of the genes incorporated in the phylogenetic analyses. The pie chart includes the molecular functions assigned at level three of the Gene Ontology classification for the 527 sequences from the 157 gene families represented by two or more mapped genes in spruce and used in phylogenetic analyses.

Figure 3

Kernel density estimation for the spruce chromosomes. On each plot, the curve in bold is the kernel density function and the dotted curves represent the limits of the confidence interval. The horizontal line represents the expected density of the uniform gene distribution. The vertical dotted lines represent the boundaries of the gene-rich regions: chromosomal regions for which the lower limit of the confidence interval of the density function is above the uniform function.

Figure 4

A spruce/loblolly pine comparative map. The syntenic positions of the 161 homologous genes mapped on both spruce and loblolly pine genomes were plotted with Circos [100] and are indicated by colour-coded lines connecting the spruce (in colour) and the loblolly pine chromosomes (in grey). The chromosome numbers are indicated outside the circle.

Figure 5

Quercetin 3-O-methyltransferase gene family tree. Unrooted phylogenetic tree obtained from the strict consensus of 50%-bootstrap consensus neighbour-joining and parsimony trees and indicating two spruce gene duplications post-dating the gymnosperm-angiosperm split (no intervening Arabidopsis or rice sequence between spruce sequences) and one spruce gene duplication predating the gymnosperm-angiosperm split (with intervening Arabidopsis or rice sequences between spruce sequences). Sequences are from spruce (Pg), pine (Pt), Arabidopsis (AT) and rice (Os). GA: gymnosperm-angiosperm split, estimated at around 300 Mya [13].

Figure 6

Organization of the spruce gene space and duplications. Genome representation with spruce chromosomes (1 to 12) showing from outside to inside: the 12 chromosomes with ticks representing the genes mapped along the spruce linkage groups, and with genetic distances in cM (Kosambi); links between genes representing duplications within chromosomes and duplications followed by inter-chromosomal translocations. Links in grey illustrate ancient and links in red illustrate recent, referring to before or after the gymnosperm-angiosperm split, around 300 Mya [13].