David B Neale , 1 , Jill L Wegrzyn 1 , Kristian A Stevens 2 , Aleksey V Zimin 3 , Daniela Puiu 4 , Marc W Crepeau 2 , Charis Cardeno 2 , Maxim Koriabine 5 , Ann E Holtz-Morris 5 , John D Liechty 1 , Pedro J Martínez-García 1 , Hans A Vasquez-Gross 1 , Brian Y Lin 1 , Jacob J Zieve 1 , William M Dougherty 2 , Sara Fuentes-Soriano 6 , Le-Shin Wu 7 , Don Gilbert 6 , Guillaume Marçais 3 , Michael Roberts 3 , Carson Holt 8 , Mark Yandell 8 , John M Davis 9 , Katherine E Smith 10 , Jeffrey FD Dean 11 , W Walter Lorenz 11 , Ross W Whetten 12 , Ronald Sederoff 12 , Nicholas Wheeler 1 , Patrick E McGuire 1 , Doreen Main 13 , Carol A Loopstra 14 , Keithanne Mockaitis 6 , Pieter J deJong 5 , James A Yorke 3 , Steven L Salzberg 4 , Charles H Langley 2
4 March 2014
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.