Novel Tools and Resources for the Study of Highly Diverse Tree Genomes and their Application Across the Eucalyptus Clade

The Eucalyptus grandis (Brasuz1) genome sequence was a milestone in the acceleration of eucalyptus genomics. Here we report novel methods and tools for the analysis of highly diverse genomes, together with their applications across eucalypts.

We present Gydle software that enables the direct assembly of Illumina reads into finished-quality complete chloroplast genomes, providing unprecedented resolution and scalability for chloroplast studies. Using these tools, we produced 81 finished chloroplast genomes for 39 species spanning the eucalypt clade.

We then present other Gydle tools for diploid genome assembly and analysis, demonstrating their utility with the major temperate pulpwood plantation species Eucalyptus globulus as a case study. We sequenced the E. globulus X46 clone (Illumina paired reads, 58x coverage) and designed new methods and metrics to compare the E. globulus genome (535 Mbp) with that of E. grandis (635 Mbp), thus gaining insight into the drivers of genome evolution in eucalypts. We found that, contrary to the findings of other plant studies, transposable elements (TEs) only represent a minor fraction of the 90 Mbp genome difference, which is primarily composed of a large number of random sequences widely distributed across the genome. In discussing the analyses behind this comparison, we present solutions to challenges associated with wild genomes of high diversity, exemplified by X46 with up to 20% local allelic divergence and twice the SNP density of the F1-self Brasuz1.

We are now applying these methods to other angiosperm and coniferous tree species.