Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

Abstract

BackgroundThe size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.ResultsWe develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome.ConclusionsIn addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.

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.…”

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). …”

A genome for gnetophytes and early evolution of seed plants

“…Consequently, several possible hypotheses have been put forward that place gnetophytes as sister to (1) Pinaceae ('Gnepine' hypothesis); (2) cupressophytes ('Gnecup' hypothesis); (3) all conifers ('Gnetifer' hypothesis); (4) all other gymnosperms; or (5) all seed plants 9 . Currently, the emerging consensus, based on both older and more recent studies, and recently released data from the 1KP initiative (see https://sites.google.com/a/ualberta.ca/onekp/, and Wickett et al 8 ), indicates that gnetophytes are sister to, or within, the conifers.So far, the availability of whole genome sequences for gymnosperms has been limited to conifers (specifically to Pinaceae) [10][11][12][13] and G. biloba 14 , with no whole genome assemblies available for the two remaining major seed plant lineages-cycads and gnetophytes. This deficiency, together with the conflicting phylogenetic evidence for relationships among these groups, is impeding our understanding of genome evolution across all seed plants.…”

“…Further, the majority of individual repeat types (repeat clusters in RepeatExplorer) were shown to be species specific (containing Illumina reads from just one species, data not shown). The species-specific nature of the repeat profiles probably reflects the long estimated divergence times between species (for example, the two Gnetum species are likely to have diverged between approximately 25 Ma and 75 Ma) 17,18 .Previously, it was reported from conifers and G. biloba that LTRRTs have accumulated steadily over the last approximately 25 Ma, especially between 16 and 24 Ma, a process contributing to their large genome sizes 11,12,14 . This interpretation is consistent with the data here (Supplementary Table 10), which show that most LTR-RTs in conifers are intact (solo LTR/intact LTR ratio ranged from 0.16:1 to 0.72:1, Supplementary Table 10).…”