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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.

SUBMITTER: Neale DB

PROVIDER: S-EPMC4053751 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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

Neale David B DB Wegrzyn Jill L JL Stevens Kristian A KA Zimin Aleksey V AV Puiu Daniela D Crepeau Marc W MW Cardeno Charis C Koriabine Maxim M Holtz-Morris Ann E AE Liechty John D JD Martínez-García Pedro J PJ Vasquez-Gross Hans A HA Lin Brian Y BY Zieve Jacob J JJ Dougherty William M WM Fuentes-Soriano Sara S Wu Le-Shin LS Gilbert Don D Marçais Guillaume G Roberts Michael M Holt Carson C Yandell Mark M Davis John M JM Smith Katherine E KE Dean Jeffrey F D JF Lorenz W Walter WW Whetten Ross W RW Sederoff Ronald R Wheeler Nicholas N McGuire Patrick E PE Main Doreen D Loopstra Carol A CA Mockaitis Keithanne K deJong Pieter J PJ Yorke James A JA Salzberg Steven L SL Langley Charles H CH

Genome biology 20140304 3

<h4>Background</h4>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.<h4>Results</h4>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 pr ...[more]

PMID: 24647006

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Project description:BACKGROUND: Host-pathogen interactions that may lead to a competitive co-evolution of virulence and resistance mechanisms present an attractive system to study molecular evolution because strong, recent (or even current) selective pressure is expected at many genomic loci. However, it is unclear whether these selective forces would act to preserve existing diversity, promote novel diversity, or reduce linked neutral diversity during rapid fixation of advantageous alleles. In plants, the lack of adaptive immunity places a larger burden on genetic diversity to ensure survival of plant populations. This burden is even greater if the generation time of the plant is much longer than the generation time of the pathogen. METHODOLOGY/PRINCIPAL FINDINGS: Here, we present nucleotide polymorphism and substitution data for 41 candidate genes from the long-lived forest tree loblolly pine, selected primarily for their prospective influences on host-pathogen interactions. This dataset is analyzed together with 15 drought-tolerance and 13 wood-quality genes from previous studies. A wide range of neutrality tests were performed and tested against expectations from realistic demographic models. CONCLUSIONS/SIGNIFICANCE: Collectively, our analyses found that axr (auxin response factor), caf1 (chromatin assembly factor) and gatabp1 (gata binding protein 1) candidate genes carry patterns consistent with directional selection and erd3 (early response to drought 3) displays patterns suggestive of a selective sweep, both of which are consistent with the arm-race model of disease response evolution. Furthermore, we have identified patterns consistent with diversifying selection at erf1-like (ethylene responsive factor 1), ccoaoemt (caffeoyl-CoA-O-methyltransferase), cyp450-like (cytochrome p450-like) and pr4.3 (pathogen response 4.3), expected under the trench-warfare evolution model. Finally, a drought-tolerance candidate related to the plant cell wall, lp5, displayed patterns consistent with balancing selection. In conclusion, both arms-race and trench-warfare models seem compatible with patterns of polymorphism found in different disease-response candidate genes, indicating a mixed strategy of disease tolerance evolution for loblolly pine, a major tree crop in southeastern United States.

Dataset Information

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

Publications

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

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