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.
At a glance
- 1993) & Paleobotany and the Evolution of Plants (Cambridge Univ. Press,
- Chloroplast and nuclear gene sequences indicate late Pennsylvanian time for the last common ancestor of extant seed plants. Proc. Natl Acad. Sci. USA 91, 5163–5167 (1994) et al.
- Hemisphere-scale differences in conifer evolutionary dynamics. Proc. Natl Acad. Sci. USA 109, 16217–16221 (2012) et al.
- Chromosome numbers and phylogeny in the gymnosperms. J. Arnold Arb. 17, 82–87 (1936)
- Evolution of genome size and complexity in Pinus. PLoS ONE 4, e4332 (2009) et al.
- The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 11, 420 (2010) et al.
- Evolution of genome size in conifers. Silvae Genet. 54, 126–137 (2005) &
- Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol. Biol. 12, 8 (2012) , , &
- The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms. BMC Evol. Biol. 10, 22 (2010) , &
- Nuclear DNA amounts in gymnosperms. Ann. Bot. (Lond.) 82, 3–15 (1998)
- The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490, 49–54 (2012) et al.
- GAM-NGS: genomic assemblies merger for next generation sequencing. BMC Bioinformatics 14, S6 (2013) , , , &
- Improved gap size estimation for scaffolding algorithms. Bioinformatics 28, 2215–2222 (2012) , , &
- Feature-by-feature–evaluating de novo sequence assembly. PLoS ONE 7, e31002 (2012) , &
- A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics 9, 484 (2008) et al.
- 36–49 (Blackwell, 2007) in Plant Mitochondria (ed. )
- Sequence composition and genome organization of maize. Proc. Natl Acad. Sci. USA 101, 14349–14354 (2004) et al.
- The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463–467 (2007) et al.
- Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7, 732–736 (2004) , , , &
- Inference of genome duplications from age distributions revisited. Mol. Biol. Evol. 30, 177–190 (2013) , &
- Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011) et al.
- Evolutionary aspects of functional and pseudogene members of the phytochrome gene family in Scots pine. J. Mol. Evol. 67, 222–232 (2008)
- Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine. PLoS ONE 6, e16214 (2011) et al.
- Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 22, 1646–1657 (2012) et al.
- The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775–1789 (2012) et al.
- Conifers have a unique small RNA silencing signature. RNA 14, 1508–1515 (2008) et al.
- Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res. 18, 571–584 (2008) et al.
- Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing. BMC Plant Biol. 12, 146 (2012) et al.
- Dynamic expression of small RNA populations in larch (Larix leptolepis). Planta 237, 89–101 (2013) et al.
- Epigenetic inheritance in plants. Nature 447, 418–424 (2007) &
- Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. (Lond.) 82, 37–44 (1998) &
- A unified classification system for eukaryotic transposable elements. Nature Rev. Genet. 8, 973–982 (2007) et al.
- Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12, 1075–1079 (2002) , &
- Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol. Biol. Evol. 20, 528–540 (2003) &
- Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11, 1769–1784 (1999) et al.
- Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution. Plant Physiol. 156, 1967–1977 (2011) et al.
- Analysis of conifer FLOWERING LOCUS T/TERMINAL FLOWER1-like genes provides evidence for dramatic biochemical evolution in the angiosperm FT lineage. New Phytol. 196, 1260–1273 (2012) , , , &
- A hitchhiker’s guide to the MADS world of plants. Genome Biol. 11, 214 (2010) &
- Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development 139, 3081–3098 (2012) et al.
- Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev. 19, 1855–1860 (2005) et al.
- Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16, 1262–1269 (2006) et al.
- Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res. 16, 1252–1261 (2006) , , , &
- Mechanisms of recent genome size variation in flowering plants. Ann. Bot. (Lond.) 95, 127–132 (2005) , &
- A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers. BMC Biol. 10, 84 (2012) et al.
- Do plants have a one way ticket to genomic obesity? Plant Cell 9, 1509–1514 (1997) &
- The flowering world: a tale of duplications. Trends Plant Sci. 14, 680–688 (2009) , , , &
- Presidential address. Transposable elements, epigenetics, and genome evolution. Science 338, 758–767 (2012)
- A mystery unveiled. Genome Biol. 12, 113 (2011)
- Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009) et al.
- Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl Acad. Sci. USA 101, 12404–12410 (2004) &
- Supplementary Information (12.4 MB)
This file contains Supplementary Sections 1-6, each of which contains Supplementary Text and Data, Supplementary Figures, Supplementary Tables and additional references. Please note that the following Supplementary Figures and Tables appear as separate files: Supplementary Figure 5.2 and Supplementary Tables 3.3, 3.4, 3.11, 3.12 and 3.14.
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- Supplementary Tables (18 KB)
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- Supplementary Tables (24 KB)
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- Supplementary Tables (14 KB)
This file contains Supplementary Table 3.11.
- Supplementary Tables (18 KB)
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- Supplementary Tables (16 KB)
This file contains Supplementary Table 3.14.