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

Abstract

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. 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. 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.

DOI: 10.1186/gb-2014-15-3-r59

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@inproceedings{Neale2014DecodingTM, title={Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies}, author={David B. Neale and Jill L. Wegrzyn and Kristian Stevens and Aleksey V. Zimin and Daniela Puiu and Marc W. Crepeau and Charis M. Cardeno and Maxim Y. Koriabine and Ann E Holtz-Morris and John Liechty and Pedro Jos{\'e} Mart{\'i}nez-Garc{\'i}a and Hans A. Vasquez-Gross and Brian Y. Lin and Jacob J. Zieve and William M. Dougherty and Sara Fuentes-Soriano and Le-Shin Wu and Don G. Gilbert and Guillaume Marçais and Michael Roberts and Carson Holt and Mark Yandell and John M. Davis and Katherine Elizabeth Smith and Jeffrey F. D. Dean and W. Walter Lorenz and Ross W. Whetten and Ronald R. Sederoff and Nicholas C. Wheeler and Patrick E. Mcguire and Dorrie Main and Carol A. Loopstra and Keithanne Mockaitis and Pieter Dejong and James A. Yorke and Steven L Salzberg and Charles H. Langley}, booktitle={Genome Biology}, year={2014} }