Abstracts (first author)
Sympatric speciation in two wild rice species: insights from genome-wide SNPs and expression patterns
The genetic basis of speciation and adaptation is a fundamental question in evolutionary biology and remains largely unknown. Two wild rice species (Oryza nivara and O. rufipogon) are sympatric but distinct morphologically and ecologically. Thus they are typically incipient species and provide a unique opportunity to study ecological speciation at the genome scale. Here we investigate genome-wide variation responsible for speciation between the two species using next-generation sequencing technology. First, we obtained 5.3 million SNPs based on the re-sequencing data with an average 2-10x coverage for 11 individuals from each of the two species. We located and characterized 126 genomic regions or islands that are significantly differentiated between the two species. These speciation islands located across all 12 rice chromosomes, encompassed 30.5 M (7.98%) of the genome and contained 2308 predicted genes. These candidate speciation genes involve mainly transcription factors, regulation of gene expression, flower development, pollination, and reproduction. Second, we used RNA-seq to measure gene expression in three different tissues of the two species. We obtained 15390, 18938, and 19311 expressed genes for flag leaves, booting panicle, and flowering panicle, respectively. Of them, 3.1-5.4% of expressed genes have divergent expression (DE) between the two species, with the number of under-expressed genes being slightly more than that of over-expressed genes in O. nivara for all three tissues. The GO annotations indicated that the DE genes involved the pollination, reproduction, growth and development, response to stress, secondary metabolic process, etc. These results demonstrate that both coding sequence variation and regulatory changes contribute to adaptive differentiation of species. This study provides new insights into the genetic mechanisms underlying the differentiation and adaption of two wild rice species and plant speciation in general.