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dc.contributor.authorNeale, David B
dc.contributor.authorWegrzyn, Jill L
dc.contributor.authorStevens, Kristian A
dc.contributor.authorZimin, Aleksey V
dc.contributor.authorPuiu, Daniela
dc.contributor.authorCrepeau, Marc W
dc.contributor.authorCardeno, Charis
dc.contributor.authorKoriabine, Maxim
dc.contributor.authorHoltz-Morris, Ann E
dc.contributor.authorLiechty, John D
dc.contributor.authorMartínez-García, Pedro J
dc.contributor.authorVasquez-Gross, Hans A
dc.contributor.authorLin, Brian Y
dc.contributor.authorZieve, Jacob J
dc.contributor.authorDougherty, William M
dc.contributor.authorFuentes-Soriano, Sara
dc.contributor.authorWu, Le-Shin
dc.contributor.authorGilbert, Don
dc.contributor.authorMarçais, Guillaume
dc.contributor.authorRoberts, Michael
dc.contributor.authorHolt, Carson
dc.contributor.authorYandell, Mark
dc.contributor.authorDavis, John M
dc.contributor.authorSmith, Katherine E
dc.contributor.authorDean, Jeffrey F
dc.contributor.authorLorenz, W W
dc.contributor.authorWhetten, Ross W
dc.contributor.authorSederoff, Ronald
dc.contributor.authorWheeler, Nicholas
dc.contributor.authorMcGuire, Patrick E
dc.contributor.authorMain, Doreen
dc.contributor.authorLoopstra, Carol A
dc.contributor.authorMockaitis, Keithanne
dc.contributor.authordeJong, Pieter J
dc.contributor.authorYorke, James A
dc.contributor.authorSalzberg, Steven L
dc.contributor.authorLangley, Charles H
dc.date.accessioned2015-09-24T16:40:39Z
dc.date.available2015-09-24T16:40:39Z
dc.date.issued2014-03-04
dc.identifier.citationGenome Biology. 2014 Mar 04;15(3):R59
dc.identifier.urihttp://dx.doi.org/10.1186/gb-2014-15-3-r59
dc.identifier.urihttp://hdl.handle.net/10724/32627
dc.description.abstractAbstract Background The 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. Results We 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. Conclusions 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.
dc.titleDecoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
dc.typeJournal Article
dc.date.updated2015-09-22T12:02:01Z
dc.language.rfc3066en
dc.rights.holderNeale et al.; licensee BioMed Central Ltd.


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