Comparative Genomics of 15 Tropical Fagaceae Species Using Shallow Illumina Sequencing and a Reference-Free Approach

We performed whole genome shotgun sequencing of fifteen Fagaceae species, focusing on the genus Lithocarpus but including taxa from the genera Castanopsis, Chrysolepis, and Trigonobalanus, on the Illumina DNA sequencing platform.  Given new measurements of genome size done as part of the study, depth of sequencing coverage typically ranges from 2 to 9x.   We employ a reference-free approach to compare the genomic data prior to assembly, using the composition and frequency of short nucleotide sequences (kmers) of 17-25 base pairs, particularly those shared among species.  This approach can effectively discover similarities and differences among the genomes and allows the localized assembly of de novo contigs centered on these informative regions.  These localized de novo contigs can identify informative SNPs for any subset of species, from individual taxa to the entire group.  Because of the assembly properties of the approach, the length of the de novo contigs increase with increased density of polymorphisms, both unique and shared and can thus pinpoint regions of sequence diversification and conservation, across any group of genomes included in the analysis.  We also examine contigs related to the chloroplast genome specifically and compare our results with the recently released Castanea plastid reference.  We discuss a number of findings made possible by this novel perspective on comparative genomics.