Strategies for Assembly and Comparison of Tree Genomes

We present methods and software developed by Gydle for the analysis of complex genomes using NGS data. These tools enable the study of genetically diverse organisms, the comparison of genomes with different evolution dynamics and the assembly and comparison of genome elements across populations and species including the high-throughput production of complete organelle genomes from total DNA.

Sequencing diploid, diverse organisms still represents a significant challenge for genome assembly and analysis. Indeed, most reference genomes of model organisms required manipulations to artificially reduce heterozygosity, utilizing both haploid segments (BACs or fosmids) and selection of inbred individuals. To demonstrate that the Gydle tools are shifting this paradigm, we selected a wild individual to sequence the major pulpwood plantation forest tree species Eucalyptus globulus Labill. (X46, Illumina HiSeq) and assemble a reference genome. We capture the high levels of local allelic divergence and can assemble allelic forms across large segments. We sequenced 42 further individuals representative of different populations in order to comprehensively track natural diversity and genome evolution in this species. We expand the investigation of simultaneous genome assembly and comparison, presenting results from 40 species representing symphyomyrts, monocalypts, eudesmids, corymbias and angophora, and spanning ~80 Mya of plant evolution. For very large genomes (e.g. conifers), we present methods to assemble the gene space directly from NGS sequencing of RNA and DNA. Advantages over capture-sequencing will be discussed, together with initial comparisons of gene space between species.

All these strategies have broad applications across other plant and animal genome studies.