The Norway spruce genome sequence and conifer genome evolution

Abstract

Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the .100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (.10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

“…Silver birch, B. pendula, is a pioneer species in boreal forests of Eurasia. Flowering of the species can be artificially accelerated 4 , giving it an advantage over other tree species with published genome sequences (such as poplar 5 , spruce 6 , and pine 7 ) for the optimization of fiber and biomass production.…”

On plant defense signaling networks and early land plant evolution

“…Conifers have undergone a dramatic expansion of their suite of NBS-LRR genes: while 69 putative NBS-LRR genes are predicted for P. patens and 16 for the lycophyte Selaginella moellendorffii, P. abies and Pinus taeda have been predicted to possess 562 and 677 putative NBS-LRR genes, respectively [88,89]. It is noteworthy that gymnosperms tend to have large genomes (often more than 10 Gbp in size [90]), which could suggest that the expansion of NBS-LRRs in plants is related to genome size of the respective plant. Yet, the large genomes of gymnosperms appear to be the result of an expansion of intron size because of repeated insertion of transposable elements and the total number of genes is in fact similar to that observed in A. thaliana [90].…”

“…It is noteworthy that gymnosperms tend to have large genomes (often more than 10 Gbp in size [90]), which could suggest that the expansion of NBS-LRRs in plants is related to genome size of the respective plant. Yet, the large genomes of gymnosperms appear to be the result of an expansion of intron size because of repeated insertion of transposable elements and the total number of genes is in fact similar to that observed in A. thaliana [90]. Additionally, numbers of NBS-LRRs reported in Zhang et al [88] seem to not necessarily be related to genome size.…”

Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce

“…However, the variation in quantitative traits explained by individual SNP markers is generally low and rarely exceeds 5% (Dillon et al ., 2010; Guerra et al ., 2013), consistent with multigenic control (Evans et al ., 2014) and the relatively shallow genomic sampling in most studies to date (< 1% and 10% of estimated gene coding loci per genome) (Nystedt et al ., 2013; Neale et al ., 2014). …”