Dissecting Genetic Mechanisms of Genome Divergence

Progress of sequencing technologies has generated a huge amount of genomic sequences, which provide a great opportunity to address fundamental questions about the genome itself. By investigating the Base Composition across SNPs (BCS) within species, we have discovered a conserved pattern, i.e., modern crops all have significantly higher [AT] value than their ancestors. This consistent pattern across multiple species implies BCS can well capture the overall genome divergence pattern assembled from millions of polymorphisms accumulated through evolution. We hypothesize that the genome divergence along history was not random and genetic component may contribute to the genome divergence. To test our hypothesis, 302 soybean genomes and 635 Arabidopsis genomes were analyzed. Motif enrichment analysis through searching genome region around the polymorphic sites reveals that both soybean and Arabidopsis SNPs are more likely arose from the solar UV signature motif. This indicates solar UV radiation is one of the major forces driving the genome divergence. Genome-wide scan results show that genes involved in UV damaged DNA repairing pathway are enriched nearby signals significantly associate with genome divergence. To further pinpoint the underlying genes of genome divergence, an appropriate set of Arabidopsis Near-Isogenic Lines (NILs) will be selected for functional assays. Research discoveries from this genetic mechanisms study will broadly enrich our understanding of genomics, genetics, and evolution.