![]() Over 1.5 billion seedlings are planted annually, approximately 80% of which are genetically improved, driving its selection as the reference conifer genome. We chose to investigate the loblolly pine ( Pinus taeda L.) genome because of its well-developed scientific resources. Though today’s conifers may be considered relics of a once much-larger set of taxa that thrived throughout the age of the dinosaurs (250 to 65 millions of years ago), they remain the dominant life forms in many of the temperate and boreal ecosystems in the Northern Hemisphere and extend into subtropical regions and the Southern Hemisphere. Conifers will likely provide many genome-level insights on the origins of genetic diversity in higher plants. Gymnosperms, represented principally by a diverse and majestic array of conifer species (approximately 630 species, distributed across eight families and 70 genera ), are one of the oldest of the major plant clades, having arisen from ancestral seed plants some 300 million years ago. In 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.Īdvances in sequencing and assembly technologies have made it possible to obtain reference genome sequences for organisms once thought intractable, including the leviathan genomes (20 to 40 Gb) of 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. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. 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. 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. 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. ![]() We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination. The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. Genome Biology volume 15, Article number: R59 ( 2014) Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
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